[{"hash":"2070845965524886206","title":"Genome maintenance and signaling regulators","description":"This cluster shows strong enrichment for core DNA processes (mitotic cell cycle, DNA replication, DNA-templated transcription, DNA repair) alongside signaling and movement-related terms (focal adhesion regulation, chemotaxis, Wnt signaling, axon extension, T cell receptor signaling). This suggests proteins that couple genome maintenance with regulation of signaling pathways and cell motility/adherence, coordinating proliferation with responses to external cues.","confidence":"Medium","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000278","count":24},{"id":"GO:0006260","count":24},{"id":"GO:0006351","count":22},{"id":"GO:0006281","count":22},{"id":"GO:0051893","count":22}]},{"hash":"2209154911370847496","title":"Unknown","description":"The top GO terms span plant cell wall biosynthesis (glucuronoxylan, arabinan, plant-type secondary cell wall), plant defense signaling (salicylic acid), and vertebrate development (BMP signaling, endoderm development, embryonic pectoral fin morphogenesis), plus miscellaneous metabolic and proteoglycan biosynthesis terms. This cross-kingdom mix offers no single coherent theme or shared pathway to tie the proteins together, so the cluster is best labeled Unknown with no confidence.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0046835","count":6},{"id":"GO:0009636","count":4},{"id":"GO:0035118","count":4},{"id":"GO:0010417","count":4},{"id":"GO:0009863","count":4}]},{"hash":"916764233297643327","title":"Redox Detoxification and Glutathione Metabolism","description":"The cluster is enriched for redox and detox pathways: cellular oxidant detoxification, redox homeostasis, glutathione metabolic and derivative biosynthesis, and xenobiotic/toxin catabolic processes. Nucleotide-excision repair and cell cycle regulation also appear, suggesting a broader stress response link. The dominant signal is oxidative stress management and detoxification with glutathione involvement, complemented by repair and growth control.","confidence":"High","size":29,"edges":351,"triangles":2434,"max_degree":28,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":14},{"id":"GO:0055114","count":13},{"id":"GO:0045454","count":11},{"id":"GO:0006289","count":9},{"id":"GO:0009407","count":8}]},{"hash":"2087608420389172772","title":"Unknown","description":"The top GO terms span mitotic cell cycle, apoptosis regulation, neuronal signaling and plasticity (LTP, EPSP, axonogenesis, visual perception), and even a plant-specific abscisic acid pathway, indicating no single cohesive function ties the cluster together. This diversity suggests the proteins are either multifunctional or the annotations are not coherent for a single cluster label. ","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":18},{"id":"GO:0043065","count":16},{"id":"GO:0060291","count":16},{"id":"GO:0060079","count":16},{"id":"GO:0007409","count":16}]},{"hash":"1505486656416885686","title":"Immune signaling and angiogenesis","description":"This cluster is dominated by immune-related signaling terms (T cell receptor signaling, IL-1\u2013mediated signaling) alongside angiogenesis and endothelial cell migration terms, suggesting a theme of inflammatory signaling coupled with vascular development. While there are DNA-templated transcription and DNA replication/repair terms also present, the strongest collective signal ties immune activation to angiogenic processes, with some cross-talk indicated by Wnt pathway regulation. ","confidence":"Medium","size":29,"edges":34,"triangles":6,"max_degree":28,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050852","count":4},{"id":"GO:0001525","count":4},{"id":"GO:0070498","count":4},{"id":"GO:0001402","count":4},{"id":"GO:0060716","count":4}]},{"hash":"574736078627866312","title":"Broad Biosynthesis and Metabolic Processes","description":"The top GO terms show a clear emphasis on biosynthetic and metabolic activities (cobalamin, biotin, antibiotic, and methionine biosynthesis; tRNA methylation) plus ancillary processes like cellulose catabolism and cellular growth, with some oxidation-reduction and detoxification terms. This suggests the cluster represents diverse metabolic biosynthesis tasks rather than a single tightly defined pathway. Edge information is absent, so the label is based on functional themes rather than network structure.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":5},{"id":"GO:0017000","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0098869","count":4},{"id":"GO:0042135","count":4}]},{"hash":"295705585883616562","title":"Transcription Regulation and ER Protein Folding","description":"This cluster centers on DNA-templated transcription and regulation of transcription by RNA polymerase II, implying a core of transcriptional regulators. The additional terms point to endoplasmic reticulum\u2013associated protein folding and redox/homeostasis processes (including prolyl hydroxylation and oxidant detoxification), suggesting a broader connection to ER stress responses that can influence transcriptional control. Given the mixed but coherent themes\u2014nuclear transcription regulation with supporting ER/redox context\u2014the label seems appropriate with Medium confidence.","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:0034975","count":2},{"id":"GO:0018401","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0043388","count":2}]},{"hash":"175010762324832700","title":"Lipid biosynthesis and remodeling","description":"The cluster shows strong enrichment for lipid-related biosynthetic processes, including triglyceride biosynthesis, CDP-diacylglycerol biosynthesis, ether lipid biosynthesis, phosphatidylcholine acyl-chain remodeling, and platelet activating factor biosynthesis, suggesting a cohesive theme around lipid metabolism and membrane lipid remodeling. Some terms like translation and certain developmental processes are present but appear less central to the main signal. Therefore, a lipid metabolism-focused label is most representative. ","confidence":"Medium","size":29,"edges":108,"triangles":203,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0019432","count":8},{"id":"GO:0016024","count":5},{"id":"GO:0002071","count":5},{"id":"GO:0021587","count":5}]},{"hash":"1588253997211173662","title":"Ribosome biogenesis and rRNA maturation","description":"The strongest signals are maturation of SSU- and LSU-rRNA and large subunit preribosome assembly, i.e., ribosome biogenesis. Additional terms on RNA processing (nonsense-mediated decay and spliceosome-regulated splicing) align with RNA maturation pathways supporting ribosome production; development terms are less central.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000463","count":4},{"id":"GO:0042254","count":3},{"id":"GO:1902626","count":3},{"id":"GO:0000184","count":3},{"id":"GO:0031047","count":3}]},{"hash":"2177174093259590121","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":405,"triangles":3627,"max_degree":28,"top_function":null,"top_go_terms":[{"id":"GO:0006458","count":2},{"id":"GO:0032543","count":2},{"id":"GO:0018339","count":1},{"id":"GO:0006782","count":1},{"id":"GO:0009102","count":1}]},{"hash":"1713676956937995243","title":"Mitochondrial respiration and vitamin biosynthesis","description":"The cluster shows strong signals for mitochondrial energy metabolism, including NADH to ubiquinone electron transport and complex II assembly, along with biosynthetic pathways for vitamins such as cobalamin and biotin, and even chlorophyll biosynthesis in plastids. These converge on a metabolic core centered on energy production and essential cofactor synthesis, with additional RNA/protein modification terms suggesting multifunctional roles. Therefore, this label captures the predominant theme of the cluster.","confidence":"Medium","size":29,"edges":361,"triangles":2607,"max_degree":28,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":3},{"id":"GO:0007049","count":2},{"id":"GO:0034553","count":2},{"id":"GO:0006120","count":2},{"id":"GO:0019919","count":2}]},{"hash":"1301506063848385410","title":"Iron-Sulfur Cluster Assembly and Homeostasis","description":"The terms cluster around iron-sulfur (Fe-S) cluster biosynthesis and iron homeostasis, including Fe-S cluster assembly, maturation, and intracellular iron regulation, suggesting the proteins coordinate Fe-S cluster biosynthesis and maintenance. Some connected functions (DNA recombination, translation) may reflect Fe-S\u2013dependent enzymes involved in these processes; a few terms (nitrogen fixation, ncRNA-mediated gene silencing) are less directly tied and may reflect broader annotations.","confidence":"Medium","size":29,"edges":380,"triangles":3211,"max_degree":28,"top_function":null,"top_go_terms":[{"id":"GO:0006310","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0009399","count":1},{"id":"GO:0006879","count":1}]},{"hash":"2203391266149444783","title":"Glycosylation and epithelial polarity in development","description":"The cluster shows strong signals for glycan biosynthesis and glycoprotein modification (poly-N-acetyllactosamine biosynthesis, arabinogalactan protein metabolism, Lewis a epitope biosynthesis, mucilage biosynthesis) together with processes maintaining epithelial polarity and cell adhesion (follicle epithelium polarity, follicle cell adhesion). This points to a common theme where cell-surface glycans regulate cell\u2013cell interactions and tissue organization during development, spanning across different organ systems and species.","confidence":"Medium","size":29,"edges":39,"triangles":3,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0080147","count":8},{"id":"GO:0030311","count":7},{"id":"GO:0007299","count":7},{"id":"GO:0010493","count":7},{"id":"GO:0075015","count":7}]},{"hash":"1568863490809846326","title":"Ubiquitin-Proteasome ERAD Proteostasis","description":"The cluster is dominated by GO terms for ubiquitin-dependent degradation, notably ER-associated degradation (ERAD) and SCF-proteasomal pathways, plus related protein processing. While there are also cell-cycle and DNA replication signals, the strongest theme across terms is regulated protein turnover and quality control via the ubiquitin-proteasome/ERAD system, with possible neuronal and contextual associations (substantia nigra development, ethanol response).","confidence":"Medium","size":29,"edges":4,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030433","count":6},{"id":"GO:0021762","count":6},{"id":"GO:0016540","count":4},{"id":"GO:0031146","count":4},{"id":"GO:0000278","count":4}]},{"hash":"2007066205050887853","title":"Hypoxia-regulated transcription and vascular development","description":"The cluster centers on amino acid peptidyl hydroxylation terms (aspartic, asparagine, histidine), suggesting enzymes that mediate post-translational hydroxylation. Coupled with GO terms for transcription (DNA-templated transcription) and vascular development (positive regulation of vasculogenesis) and notes of Notch signaling regulation, the data point to a theme where oxygen-sensing\u2013driven transcriptional control intersects with vascular differentiation. Some terms are obsolete, but the overarching connection appears to be hypoxia-related transcriptional regulation influencing vascular development. Confidence: Medium","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042264","count":14},{"id":"GO:0045663","count":13},{"id":"GO:0042265","count":13},{"id":"GO:2001214","count":13},{"id":"GO:0006351","count":13}]},{"hash":"1250619470137506470","title":"Developmental calcium signaling proteins","description":"This cluster shows a mix of developmental processes (multicellular organism development, skin development, spinal cord development) and calcium signaling regulation (release of calcium from the sarcoplasmic reticulum, negative regulation of ryanodine receptor activity), suggesting proteins involved in development with modulatory calcium signaling. Other terms like ribosomal biogenesis and cell division indicate broader cellular roles, but the two themes above are the most representative. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0042542","count":2},{"id":"GO:0014808","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0060315","count":2}]},{"hash":"42158852729489242","title":"DNA Replication and Recombination","description":"The terms point to nuclear DNA metabolism with emphasis on recombination, replication, and DNA damage response (meiotic gene conversion, DNA recombination, DNA replication, SOS response). Additional signals of transcriptional regulation by RNA Pol II and ncRNA-mediated gene silencing suggest coordinated genome regulation, with a peripheral note of ribosomal RNA maturation. This combination supports a cohesive label focused on genome maintenance and related transcription control.","confidence":"High","size":29,"edges":6,"triangles":1,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006311","count":6},{"id":"GO:0006310","count":6},{"id":"GO:0045944","count":6},{"id":"GO:0006260","count":6},{"id":"GO:0000462","count":5}]},{"hash":"269696509712791737","title":"Regulated neuronal signaling and axonogenesis","description":"The top GO terms converge on modulation of signaling pathways (protein kinase activity, dephosphorylation, ubiquitination, calcineurin-NFAT signaling) together with processes tied to neuronal development (axonogenesis) and memory. This suggests a core theme of regulated neuronal signaling influencing axon growth and synaptic function, with a minor touch of non-neuronal development terms due to broad GO annotations.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":3},{"id":"GO:0007409","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0008360","count":2},{"id":"GO:0006470","count":2}]},{"hash":"1195746853371431430","title":"Plant Cell Wall Biosynthesis and Root Hair Development","description":"The top GO terms are dominated by plant-specific processes such as cell wall organization and rhamnogalacturonan II biosynthesis, which tie to pectin synthesis in the plant cell wall, along with root hair cell development. Additional terms for keratan sulfate/heparan proteoglycan biosynthesis and flavonoid/xenobiotic metabolism align with broader plant metabolism. The collective signal points to a cluster centered on plant cell wall construction and root hair growth, with some outlier terms. ","confidence":"High","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":5},{"id":"GO:0010306","count":4},{"id":"GO:0080147","count":4},{"id":"GO:0018146","count":3},{"id":"GO:0007114","count":2}]},{"hash":"2174822678438531768","title":"Transcriptional regulation and cell-cycle control","description":"These proteins cluster around transcriptional control (DNA-templated transcription; transcription from RNA Pol II promoter) and chromosome/mitotic processes (cell cycle; spindle assembly; subtelomeric heterochromatin formation). The presence of endodermal differentiation and protein complex assembly terms suggests involvement in transcriptional regulation and chromatin dynamics that support cell division and developmental programs. Overall, the module appears to coordinate gene expression with chromosome organization during division and development, hence the label.","confidence":"Medium","size":29,"edges":15,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0035948","count":2},{"id":"GO:0070208","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0035987","count":2}]},{"hash":"929064357190422244","title":"Developmental Regulation and Differentiation","description":"The GO terms cluster around development and cell fate decisions across tissues (neuronal, cardiac, lung, oocyte) along with regulatory processes (apoptosis, Wnt signaling, GTPase signaling, migration, and chromatid cohesion), suggesting a shared theme of developmental signaling and lineage specification.","confidence":"Medium","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0043065","count":10},{"id":"GO:0090090","count":10},{"id":"GO:0008285","count":10},{"id":"GO:0016477","count":10},{"id":"GO:0070602","count":10}]},{"hash":"77564167149555930","title":"Developmental signaling and differentiation","description":"Top terms suggest a coordinated developmental program: Wnt and Hippo signaling regulate growth and fate decisions; keratinocyte differentiation and embryonic cranial skeleton morphogenesis indicate broad tissue development; apoptosis and cell-cycle-related terms (DNA replication, transcription) reflect proliferation and fate selection; Rho signaling and synapse localization point to morphogenesis and neural aspects. Overall, the cluster centers on development, growth control, and differentiation decision processes.","confidence":"Medium","size":29,"edges":7,"triangles":0,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006915","count":13},{"id":"GO:0090263","count":11},{"id":"GO:0030216","count":11},{"id":"GO:0035329","count":11},{"id":"GO:0060044","count":11}]},{"hash":"381859531420597824","title":"Neural development and transcriptional regulation","description":"This cluster is enriched for neural-related processes (positive regulation of axon extension, cell morphogenesis, visual learning) and for regulation of DNA-templated transcription, pointing to a cohesive theme of neuronal development coupled with gene expression control. While there are also DNA replication and cell cycle terms, they do not outweigh the neural-development signal. ","confidence":"Medium","size":29,"edges":4,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":5},{"id":"GO:0048240","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0006695","count":4},{"id":"GO:0008542","count":4}]},{"hash":"726851254851317537","title":"Spliceosome and RNA Processing","description":"The cluster is dominated by RNA splicing and mRNA processing terms (spliceosomal snRNP and tri-snRNP assembly, RNA splicing, mRNA processing) and nucleolus organization, suggesting core involvement in RNA maturation and spliceosome assembly. A few development-related terms appear but likely reflect broader annotations. Overall, the shared theme is pre-mRNA splicing and related RNA processing machinery.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002181","count":2},{"id":"GO:0045572","count":1},{"id":"GO:0035214","count":1},{"id":"GO:0007000","count":1},{"id":"GO:0040022","count":1}]},{"hash":"1418027838463176075","title":"Ubiquitin-Proteasome Degradation Pathway","description":"Dominant enrichment for ubiquitin-dependent proteolysis terms (ubiquitination, K48 linkage, SCF-dependent degradation) implies a cohesive cluster of proteins functioning in tagging substrates for destruction by the proteasome. While a few outliers pertain to peroxisome import or histone turnover, the prevailing theme is ubiquitin-mediated protein degradation.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042787","count":10},{"id":"GO:0051865","count":10},{"id":"GO:0070936","count":10},{"id":"GO:0030433","count":9},{"id":"GO:0085020","count":9}]},{"hash":"1735965056453478489","title":"RNA processing and translation regulation","description":"This cluster is enriched in RNA-related processes: maturation of LSU-rRNA, rRNA pseudouridine synthesis, and negative regulation of mRNA splicing, along with positive regulation of selenocysteine incorporation, pointing to roles in ribosome biogenesis, RNA modification, and translation control. Other terms touching development and stress (multicellular/br ain development, autophagy, oxidative response) may reflect broader cellular contexts, but the strongest shared signal lies in RNA processing and translation regulation.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0006914","count":2},{"id":"GO:0070301","count":2},{"id":"GO:0060313","count":2},{"id":"GO:0007420","count":2}]},{"hash":"825585507381663966","title":"Protein and RNA modification pathways","description":"The cluster shows strong enrichment for protein post-translational modifications (peptidyl-arginine hydroxylation/methylation, N-terminal methylation) and a tRNA wobble uridine modification, suggesting a common theme of macromolecule modification; biosynthesis terms (biotin, cobalamin, chlorophyll) provide metabolic context but do not redefine the core modification-focused theme.","confidence":"Medium","size":29,"edges":22,"triangles":3,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":3},{"id":"GO:0030961","count":3},{"id":"GO:0035690","count":3},{"id":"GO:0002098","count":2},{"id":"GO:0019919","count":2}]},{"hash":"892686262489583797","title":"Photosynthesis Light Harvesting and Light Response","description":"The top GO terms cluster around photosynthesis and light-driven processes (nonphotochemical quenching; light harvesting in photosystem I and II; responses to blue, red, and far-red light; responses to light intensity). This points to components of the photosynthetic apparatus and its light-regulated functions, so the label captures the shared theme of light harvesting and light-responsive regulation. Confidence: High","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0010196","count":5},{"id":"GO:0009768","count":5},{"id":"GO:0009637","count":5},{"id":"GO:0010218","count":5},{"id":"GO:0071486","count":5}]},{"hash":"985378962722230176","title":"Unknown","description":"The top terms are scattered across diverse, and often obsolete, processes (angiogenesis, heme/inositol/sorbitol metabolism, transcription regulation) with no evident shared function and no interactions, so a cohesive functional label cannot be inferred.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0001525","count":2},{"id":"GO:0042167","count":1},{"id":"GO:0019878","count":1},{"id":"GO:0000122","count":1}]},{"hash":"405942364831328969","title":"Fungal biofilm formation and cell wall polysaccharide catabolism","description":"Top GO terms point to fungal single-species biofilm formation on host or substrate and remodeling/metabolism of fungal cell wall components (beta-glucan, mannan) with concurrent catabolism of polysaccharides like xylan and cellulose; lipid metabolism terms appear but do not override the main theme. This suggests a coherent cluster of fungi engaging in biofilm formation with cell wall carbohydrate metabolism.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044407","count":4},{"id":"GO:0045493","count":4},{"id":"GO:1904462","count":4},{"id":"GO:0070879","count":4},{"id":"GO:0030245","count":4}]},{"hash":"64622534692022434","title":"Unknown","description":"The listed GO terms cover very different biological areas: responses to cold or herbicide, mitochondrial electron transport, various differentiation programs (megakaryocytes, primitive erythrocytes, sperm capacitation), thiamine biosynthesis, and aging. With no clear shared function or pathway, and several terms marked obsolete, there is no consistent theme that unites the proteins. Therefore, the cluster is best described as Unknown.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009409","count":6},{"id":"GO:0006120","count":6},{"id":"GO:0045654","count":6},{"id":"GO:0009635","count":6},{"id":"GO:0009228","count":6}]},{"hash":"1279919259294024798","title":"DNA Repair and Ribosome Biogenesis","description":"The cluster\u2019s top GO terms are dominated by SOS response (DNA damage response) and ribosome biogenesis, including ribosomal subunit export, and homologous recombination repair, which together suggest a module coordinating genomic maintenance with protein synthesis under stress. Additional transport and cytochrome assembly terms indicate broader metabolic adaptation, but the strongest signal centers on DNA repair and ribosome-related processes.","confidence":"Medium","size":28,"edges":93,"triangles":123,"max_degree":12,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0009432","count":10},{"id":"GO:0042254","count":10},{"id":"GO:0000056","count":8},{"id":"GO:0000724","count":7},{"id":"GO:0001407","count":7}]},{"hash":"1845947997241724626","title":"Central Carbon Metabolism and Stress Response","description":"The top GO terms cluster around core energy metabolism (glycolysis, fructose metabolism, carbohydrate phosphorylation, PPP regulation) and include autophagy and xenobiotic response, suggesting a theme of metabolic flux combined with cellular stress responses; the presence of a biosynthetic term (cobalamin biosynthesis) supports a broader metabolic capability rather than a single pathway. Confidence: Medium","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0046835","count":6},{"id":"GO:0009236","count":4},{"id":"GO:0006000","count":4},{"id":"GO:0007585","count":4},{"id":"GO:0006096","count":4}]},{"hash":"2001827587415867726","title":"DNA Replication, Repair, and Cell-Cycle Machinery","description":"This cluster centers on nuclear processes: DNA replication, DNA repair, mitotic cell cycle, and DNA-templated transcription, indicating a core set of proteins involved in genome maintenance and cell division. Embryonic development signaling and immune or metabolic pathways appear as secondary associations, suggesting multifunctionality rather than a distinct separate pathway. The label captures the dominant theme of genome maintenance with cell-cycle progression.","confidence":"Medium","size":28,"edges":102,"triangles":137,"max_degree":20,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":27},{"id":"GO:0048701","count":24},{"id":"GO:0006281","count":24},{"id":"GO:0000278","count":23},{"id":"GO:0006351","count":23}]},{"hash":"1221264525234577448","title":"Unknown","description":"The Top GO terms span a wide range of unrelated processes (cell adhesion signaling, NF-kappaB signaling, plant hormone biosynthesis, immunoglobulin class switching, neuronal structure, spindle checkpoint signaling, transcription elongation control, ion channel regulation, chromatin silencing, and mating-type regulation). They do not converge on a single coherent function or pathway for the protein cluster, suggesting no common theme beyond general regulatory roles across systems. ","confidence":"","size":28,"edges":154,"triangles":261,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0033624","count":7},{"id":"GO:0007249","count":7},{"id":"GO:0009688","count":7},{"id":"GO:0045190","count":7},{"id":"GO:0021693","count":7}]},{"hash":"828771168437312755","title":"ER-Golgi Vesicle Trafficking","description":"The top GO terms are dominated by ER-to-Golgi transport, COPII-coated vesicle budding, and retrograde Golgi-ER transport, indicating the secretory pathway as the cluster\u2019s core function; brain development and cell-cycle terms appear as secondary associations but do not override the vesicle trafficking signal.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":10},{"id":"GO:0007420","count":9},{"id":"GO:0051301","count":9},{"id":"GO:0006890","count":9},{"id":"GO:0008283","count":9}]},{"hash":"193091911181541707","title":"Ribosome Biogenesis & Translation","description":"The top GO terms concentrate on protein synthesis and ribosome assembly (translation; mitochondrial ribosome assembly; ribosomal subunit export; tRNA methylation), indicating a core theme of ribosome biogenesis and function. Additional mitochondrial metabolic processes (ubiquinone/biotin biosynthesis) and stress responses ( xenobiotic, hyperosmotic) appear as related but secondary aspects, suggesting this cluster centers on ribosome-related processes with mitochondrial metabolism and stress adaptation as context.","confidence":"High","size":28,"edges":57,"triangles":9,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0061668","count":4},{"id":"GO:0046677","count":3},{"id":"GO:0006067","count":3},{"id":"GO:0009102","count":2}]},{"hash":"541079824892898751","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006281","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0015074","count":2},{"id":"GO:0031119","count":2},{"id":"GO:0000455","count":2}]},{"hash":"1616077138995264805","title":"Redox and xenobiotic stress response","description":"The top GO terms cluster around redox balance and responses to chemical stress: cell redox homeostasis, oxidation-reduction process, and responses to selenium, aluminum, ethanol, corticosteroid (stress hormone), and xenobiotic stimuli. Although a couple terms are obsolete, the dominant signal points to cellular defense against oxidative stress and chemical challenge, with a touch of metabolic and detoxification processes (e.g., thiamine biosynthesis). This suggests a coherent theme of redox regulation and xenobiotic/metabolic stress response.","confidence":"High","size":28,"edges":6,"triangles":0,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":16},{"id":"GO:0009228","count":15},{"id":"GO:0043046","count":14},{"id":"GO:0045454","count":14},{"id":"GO:0010269","count":14}]},{"hash":"148041487856065365","title":"Hydroxylation-Linked Transcription and Vasculogenesis","description":"The top GO terms point to peptidyl hydroxylation (aspartic, asparagine, histidine) as a core activity, paired with transcription-related processes (DNA-templated transcription) and developmental regulation (positive regulation of myoblast differentiation, vasculogenesis) as well as modulation of Notch signaling. This pattern suggests a cluster of proteins involved in post-translational hydroxylation that also influence gene expression and vascular/differentiation pathways. Some terms are obsolete, but the recurrent themes support a cohesive theme around hydroxylation-linked regulation of transcription and vascular development.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042264","count":8},{"id":"GO:0055114","count":7},{"id":"GO:0042265","count":7},{"id":"GO:0045663","count":7},{"id":"GO:0006351","count":7}]},{"hash":"1189681662033737668","title":"RNA metabolism and translation regulation","description":"This cluster includes GO terms spanning RNA processing, transcription regulation, mRNA maturation, and translation control (including translation, regulation of translation, and IRES-dependent translation), plus rRNA maturation and stress-related responses. The common thread is involvement in RNA metabolism and the control of gene expression at both transcriptional and translational levels, with some link to amino acid starvation and ribosome function. Confidence: Medium","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":2},{"id":"GO:0075522","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0000462","count":1},{"id":"GO:0006417","count":1}]},{"hash":"731350689134751679","title":"Sphingolipid and fatty acid metabolism","description":"Top GO terms point to lipid biosynthesis pathways, notably sphingolipid metabolism (mannosyl-inositol phosphorylceramide metabolic process; sphingosine biosynthetic process) and fatty acid/sterol metabolism (fatty acid biosynthetic process; 4-alpha-methyl-delta7-sterol oxidation). The inclusion of CNS myelin maintenance and sebaceous gland differentiation suggests lipid-rich tissue contexts, reinforcing a theme of lipid biosynthesis and lipid homeostasis across neural and skin functions. Despite no network edges, the shared lipid-centric terms support labeling the cluster as lipid metabolism-related.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006675","count":5},{"id":"GO:0001949","count":5},{"id":"GO:0032286","count":5},{"id":"GO:0070542","count":4},{"id":"GO:0046512","count":3}]},{"hash":"224884443439596076","title":"TGF-beta/SMAD signaling regulation via dephosphorylation","description":"This cluster's GO terms concentrate on dephosphorylation events (protein dephosphorylation, peptidyl-threonine dephosphorylation) and modulation of TGF-beta signaling (negative regulation of TGF-beta receptor signaling, SMAD-related assembly, cellular response to TGF-beta stimulus). The ER-to-Golgi vesicle transport term suggests a link to trafficking that can affect signaling as well. Although a few terms appear unrelated (e.g., xenobiotic response, photosystem terms), the dominant theme is regulation of TGF-beta/SMAD signaling through dephosphorylation.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0035690","count":3},{"id":"GO:0006470","count":3},{"id":"GO:0030512","count":3},{"id":"GO:0042347","count":3}]},{"hash":"71044392184172884","title":"ER Stress Proteostasis via Ubiquitin-Dependent Degradation","description":"The top GO terms converge on protein quality control in the endoplasmic reticulum, including unfolded protein response, ER-associated ubiquitin-dependent degradation, and K11-linked ubiquitination, signaling a proteostasis-focused cluster. Peripheral terms related to metabolism and cell cycle appear less cohesive with this main theme, but do not override the dominant proteostasis signal.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0006986","count":8},{"id":"GO:0051348","count":8},{"id":"GO:0070979","count":8},{"id":"GO:0009938","count":8},{"id":"GO:0090526","count":8}]},{"hash":"2167821334121950592","title":"Transmembrane Transport and Neurotransmitter Loading","description":"The cluster shows a strong representation of diverse transmembrane transport GO terms (sodium, potassium, nitrate, galactose, xenobiotic, and phosphate ion transport) plus a neuron-specific term for neurotransmitter loading into synaptic vesicles, suggesting a core function in membrane transport with vesicle trafficking/neuronal packaging roles. The presence of a GO term related to GTPase activity regulation also aligns with vesicle transport control, reinforcing a transport/trafficking theme.","confidence":"Medium","size":28,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0098700","count":3},{"id":"GO:0035435","count":3},{"id":"GO:0006855","count":3},{"id":"GO:0015706","count":3}]},{"hash":"2094055928934362150","title":"Neuronal GPCR signaling and vesicle priming","description":"The top GO terms cluster around G protein-coupled receptor signaling, GPCR internalization, and synaptic vesicle priming, with sensory perception of sound and membrane-related processes (sterol biosynthesis) hinting at neuronal signaling contexts. Together, these suggest a functional module centered on neuronal GPCR signaling and vesicle cycling.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":3},{"id":"GO:0007605","count":3},{"id":"GO:0030845","count":3},{"id":"GO:0051262","count":3},{"id":"GO:0007205","count":3}]},{"hash":"2023480546742442104","title":"Innate antiviral dsRNA/interferon response","description":"The cluster\u2019s top GO terms are dominated by cellular responses to exogenous dsRNA and to type I interferon, which are classic features of innate antiviral signaling. While there are additional terms related to unfolded protein response and RNA processing, these are less central to the main pattern. Overall, the dominant theme is antiviral defense driven by dsRNA sensing and interferon pathways.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071360","count":4},{"id":"GO:0046661","count":4},{"id":"GO:0006463","count":4},{"id":"GO:0071357","count":4},{"id":"GO:0030850","count":4}]},{"hash":"1508478458757378409","title":"Cytoskeleton remodeling and vesicle trafficking","description":"The top terms point to actin cytoskeleton dynamics (Arp2/3-mediated nucleation) and ER-to-Golgi vesicle transport, with supporting signals from ubiquitination and general cellular regulation (translation initiation, chromatin modification). This suggests a theme around intracellular organization, movement, and remodeling rather than a single isolated function. Neural tube closure and pigmentation hints reflect developmental and regulatory contexts of these processes but don\u2019t override the central cytoskeletal/trafficking signal, so the name captures the core cluster function.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001843","count":3},{"id":"GO:0001731","count":2},{"id":"GO:2000601","count":2},{"id":"GO:0051567","count":2},{"id":"GO:2001162","count":2}]},{"hash":"1006839136475657026","title":"Mitochondrial Metabolite Transport","description":"This cluster is characterized by GO terms tied to transport of various metabolites into or across the mitochondrial membranes (e.g., alpha-ketoglutarate, citrate, glycine, ornithine, pyrimidine nucleotides) and related mitochondrial processes such as the malate-aspartate shuttle and ATP transmembrane transport, along with a response to superoxide. The common thread is mitochondria-centered metabolite transport and maintenance, supporting a cohesive mitochondrial function cluster.","confidence":"High","size":28,"edges":155,"triangles":451,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":23},{"id":"GO:1990544","count":22},{"id":"GO:0000303","count":22},{"id":"GO:1990519","count":22},{"id":"GO:0015742","count":22}]},{"hash":"1772241666853150217","title":"Unknown","description":"The top GO terms span core gene expression (DNA-templated transcription, transcription elongation regulation, translation, DNA replication), signaling regulation (negative regulation of protein kinase activity), and organism- or context-specific processes (heart development, isotype switching, proanthocyanidin biosynthesis, L-valine catabolic process). With no dominant shared function across the 28 proteins, and an empty edge/triangle structure suggesting no tight interaction, there is no reliable unifying label.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0034244","count":3},{"id":"GO:0006469","count":3}]},{"hash":"881930640656967999","title":"Gram-negative cell envelope biosynthesis","description":"Top GO terms point to synthesis of outer envelope components (lipid A, LPS, slime layer polysaccharides) and regulation of cell shape, plus antibiotic response, indicating a cohesive program of Gram-negative envelope biogenesis; the photosynthesis term appears as an outlier but does not override the envelope-related theme.","confidence":"High","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0009245","count":3},{"id":"GO:0015979","count":3},{"id":"GO:0000902","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0008360","count":2}]},{"hash":"122519753835171054","title":"Spliceosome and Translation Initiation Components","description":"The cluster shows enrichment for RNA processing (splicing via spliceosome, mRNA splicing) and translation (cytoplasmic translation, formation of translation preinitiation complex). While there are a few signaling terms (EGF and GM-CSF responses), the dominant theme is RNA maturation and initiation of translation, pointing to proteins involved in post-transcriptional regulation.","confidence":"Medium","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002181","count":2},{"id":"GO:0071364","count":2},{"id":"GO:0001782","count":2},{"id":"GO:0045657","count":2},{"id":"GO:0006378","count":2}]},{"hash":"332022747806807667","title":"Developmental signaling and cytoskeletal remodeling","description":"The cluster shows enrichment in developmental processes (mitotic cell cycle, multicellular organism development, skin development) and signaling regulation (positive regulation of GTPase activity, protein autophosphorylation, serine/threonine kinase activity), along with cytoskeletal remodeling hints (Arp2/3-mediated actin nucleation). The combination suggests proteins that coordinate development with signaling and cytoskeletal dynamics.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":11},{"id":"GO:0000278","count":9},{"id":"GO:0007275","count":9},{"id":"GO:0043588","count":9},{"id":"GO:0051028","count":9}]},{"hash":"12479510178124180","title":"Growth, Stress, and Secretory Signaling","description":"The cluster shows growth-related processes (ribosome biogenesis, DNA replication), ER stress response (unfolded protein response), metabolic signaling (insulin receptor signaling), and secretory machinery (dense core granule exocytosis, synaptic vesicle priming, GPCR internalization), plus immune signaling (IL-18 pathway, B cell homeostasis). This combination suggests a theme around cellular growth with interconnected stress and secretory/immune signaling.","confidence":"Medium","size":28,"edges":10,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0006986","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0032094","count":2},{"id":"GO:0035655","count":2}]},{"hash":"1697124815261019686","title":"Viral replication and host interaction","description":"The GO terms cluster around viral life-cycle steps (virion assembly, ESCRT-mediated budding, proviral latency, DNA integration) with some supporting host-process terms, suggesting a cohesive theme of virus replication and virus\u2013host interactions.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":1},{"id":"GO:0042985","count":1},{"id":"GO:0040016","count":1},{"id":"GO:0032929","count":1},{"id":"GO:0000398","count":1}]},{"hash":"851289832891754115","title":"Unknown","description":"The Top Terms show a mix of antibiotic biosynthesis, tRNA wybutosine modification, methylation, chromatin organization, metabolism, and cell-cycle regulation, with no single dominant process. Because there is no cohesive functional theme linking the terms, a specific representative label cannot be assigned beyond Unknown.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":2},{"id":"GO:0060316","count":2},{"id":"GO:0006481","count":1},{"id":"GO:1901106","count":1},{"id":"GO:0010906","count":1}]},{"hash":"1973448052389825369","title":"Neuronal Synaptic Transmission and Plasticity","description":"This cluster is dominated by GO terms related to neuronal communication: neurotransmitter secretion, glutamatergic synaptic transmission, regulation of synaptic vesicle exocytosis, calcium-triggered signaling, and long-term potentiation, all pointing to synaptic signaling and activity-dependent plasticity. Additional terms like PI-mediated signaling and GTPase regulation support signaling control at synapses, while a plant-specific term appears incidental. Overall, the label captures the core neuronal synaptic function of the proteins.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0043087","count":5},{"id":"GO:0043065","count":4},{"id":"GO:0048015","count":4},{"id":"GO:0060291","count":4},{"id":"GO:2000300","count":4}]},{"hash":"1553563271464594963","title":"Neural development and signaling","description":"The terms cluster around brain-related signaling and transcriptional control: FGFR signaling in cortex development, insulin receptor pathways, axon regeneration, trans-synaptic signaling, and DNA-templated transcription dominate, with some cytokine regulation reflecting neuroimmune interactions. This supports labeling as Neural development and signaling. ","confidence":"High","size":27,"edges":192,"triangles":526,"max_degree":22,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":26},{"id":"GO:0046827","count":26},{"id":"GO:0002741","count":25},{"id":"GO:0035607","count":25},{"id":"GO:0008286","count":25}]},{"hash":"1739761050649367748","title":"Rho GTPase\u2013mediated dendritic spine morphogenesis","description":"This cluster centers on Rho GTPase signaling and JNK cascade regulation, with terms for dendritic spine morphogenesis and synapse organization, suggesting a neuron-focused module governing cytoskeletal remodeling and synapse development. Proteolysis and protein localization terms may reflect synaptic protein turnover and trafficking, but the dominant themes point to Rho/JNK-driven spine formation and synaptic maintenance.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0046328","count":6},{"id":"GO:0006508","count":5},{"id":"GO:0050808","count":4},{"id":"GO:2000009","count":4},{"id":"GO:0035023","count":4}]},{"hash":"788633572307738624","title":"Environmental Stress and Xenobiotic Response","description":"The top GO terms are dominated by responses to chemical and microbial stimuli (xenobiotic stimulus, lipopolysaccharide, ethanol, selenium ion) and redox-related processes, suggesting the proteins function mainly in environmental stress responses. A few outlier terms (e.g., capsule biosynthesis, spliceosome-related splicing, megakaryocyte differentiation) appear but do not override the overall theme of environmental response.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":11},{"id":"GO:0045654","count":11},{"id":"GO:0043046","count":11},{"id":"GO:0045227","count":11},{"id":"GO:0042493","count":10}]},{"hash":"2192256105073859378","title":"Biosynthesis and RNA Modification Cluster","description":"The Top Terms show enrichment for diverse biosynthetic processes (antibiotic, biotin, polyamines, phosphatidylcholine, cobalamin) alongside RNA/protein methylation and RNA modification (rRNA modification, guanine-N7 methylation, tRNA wobble uridine modification, peptidyl-arginine methylation). This points to a theme of metabolic biosynthesis coupled with RNA/protein modification activities, suggesting a cluster of enzymes involved in biosynthetic pathways and post-transcriptional/post-translational modifications. Overall, a coherent though broad linkage to biosynthesis and methylation-based modifications; confidence Medium.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":6},{"id":"GO:0009102","count":5},{"id":"GO:0000154","count":4},{"id":"GO:0036265","count":4},{"id":"GO:0006596","count":4}]},{"hash":"1106304138183390944","title":"Bacterial Sensing and Ion Homeostasis","description":"This cluster combines environmental sensing (aerotaxis; cellular responses to cAMP and cGMP) with ion balance/transport (Mg2+ homeostasis; sodium import), pointing to bacterial signaling linked to ion regulation. Some metabolic/modification terms appear peripheral to the core theme.","confidence":"Medium","size":27,"edges":27,"triangles":0,"max_degree":25,"top_function":null,"top_go_terms":[{"id":"GO:0010961","count":2},{"id":"GO:0009454","count":2},{"id":"GO:0010754","count":2},{"id":"GO:0071320","count":2},{"id":"GO:0071321","count":2}]},{"hash":"1177331845249970863","title":"Cyclic Nucleotide Signaling Regulation","description":"The cluster\u2019s top GO terms center on regulation and response of cyclic nucleotide signaling (cAMP and cGMP), including negative regulation of guanylyl cyclase signaling and positive regulation of adenylate cyclase activity, plus related cellular responses and some transport/sensory processes. This coherence suggests proteins that modulate cyclic nucleotide\u2013driven signaling pathways and downstream effects, making the label Cyclic Nucleotide Signaling Regulation appropriate.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0010754","count":11},{"id":"GO:0071320","count":11},{"id":"GO:0071321","count":11},{"id":"GO:0098719","count":11},{"id":"GO:0009454","count":11}]},{"hash":"499235689264712961","title":"Sensory perception and ion transport","description":"The cluster is dominated by GO terms for sensory modalities (pain, touch, cold) and for ion transport across membranes (Na+, K+, Ca2+) with associated membrane hyperpolarization, pointing to neuronal sensory signaling and regulation of membrane potential. Development is present but appears less central to the cluster\u2019s core function. ","confidence":"High","size":27,"edges":8,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":19},{"id":"GO:0019233","count":19},{"id":"GO:0098719","count":19},{"id":"GO:0060081","count":18},{"id":"GO:0097623","count":18}]},{"hash":"1722232224441372918","title":"Developmental Regulation and Signaling","description":"This cluster centers on developmental processes (heart development, Schwann cell development, multicellular organism development) and transcriptional/kinase regulation (DNA-templated transcription, regulation of GTPase activity, serine/threonine kinase activity, autophosphorylation) with some apoptotic regulation. The combination suggests genes coordinating development through regulatory signaling and transcriptional control, with proliferative context from the mitotic cell cycle. Confidence reflects a coherent developmental signaling theme, but the broad scope keeps it from being more specific.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":12},{"id":"GO:0007275","count":11},{"id":"GO:0006351","count":9},{"id":"GO:0043547","count":9},{"id":"GO:0071902","count":9}]},{"hash":"2113444115139641422","title":"Transcriptional Regulation and Metabolism","description":"The cluster shows enrichment for DNA-templated transcription and negative regulation of translation, plus core metabolic processes (ATP synthesis/electron transport, ferredoxin and xanthine catabolism) and ion transport. This suggests a set of proteins coordinating gene expression with cellular energy metabolism, with additional context in developmental signals (endothelial differentiation, VEGF signaling, lactation) that may reflect tissue-specific regulatory needs. Overall, it points to a broad theme of transcriptional control linked to metabolism rather than a single narrow function.","confidence":"Medium","size":27,"edges":52,"triangles":34,"max_degree":25,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0010124","count":4},{"id":"GO:0017148","count":3},{"id":"GO:0006124","count":3},{"id":"GO:0045602","count":3}]},{"hash":"1976452118176323098","title":"Plant root hair development and cell wall biosynthesis","description":"Top GO terms cluster around plant-specific processes of cell wall organization and root hair development (e.g., GO:0071555, GO:0010306, GO:0080147), suggesting the proteins act together in cell wall construction/remodeling and root hair formation. Other terms are more general or noisy (e.g., mRNA stability, redox homeostasis, peptide hormone response), but the dominant theme is plant cell wall dynamics linked to root hair growth.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":4},{"id":"GO:0010306","count":3},{"id":"GO:0080147","count":3},{"id":"GO:2001153","count":2},{"id":"GO:1900087","count":2}]},{"hash":"108278782205877856","title":"Cardiovascular and mesodermal development","description":"The top GO terms cluster around heart development, mesoderm formation, hemopoiesis, vascular VEGF signaling, and broader multicellular development, suggesting a core role in cardiovascular lineage specification and vascular signaling. Additional terms like insulin signaling, sodium transport, and DNA-templated transcription imply broader regulatory context, possibly reflecting pleiotropy in development and metabolism. Overall, the proteins appear linked to cardiac/vascular development and mesoderm-derived lineages.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007507","count":4},{"id":"GO:0008286","count":3},{"id":"GO:0010765","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0007275","count":3}]},{"hash":"2157925048454814703","title":"Nutrient Transport and Metabolic Processes","description":"The cluster centers on transmembrane transport and nutrient metabolism, with GO terms for nitrate transmembrane transport, nitrate assimilation, galactose transmembrane transport, fucose metabolic process, and phosphate ion transmembrane transport dominating. These suggest proteins involved in uptake and processing of nutrients. Some terms like cell migration, protein folding, and mismatch repair are present but appear less central, likely representing background or pleiotropic functions. Overall, the theme is transport and metabolism of nutrients.","confidence":"Medium","size":27,"edges":24,"triangles":7,"max_degree":11,"top_function":"protein folding","top_go_terms":[{"id":"GO:0016477","count":3},{"id":"GO:0009651","count":3},{"id":"GO:0006457","count":3},{"id":"GO:0006298","count":3},{"id":"GO:0042128","count":3}]},{"hash":"160470131602271903","title":"Heat-induced protein folding and quality control","description":"The cluster is dominated by terms tied to heat response, unfolded protein response, and proteostasis\u2014specifically chaperone-assisted refolding and nuclear ubiquitin-proteasome quality control\u2014indicating a cohesive theme of maintaining protein integrity under stress. Some additional terms touch on membrane targeting and development, but the core signal is proteostasis under thermal stress.","confidence":"High","size":27,"edges":49,"triangles":24,"max_degree":18,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009408","count":15},{"id":"GO:0006469","count":15},{"id":"GO:0006986","count":14},{"id":"GO:0071630","count":14},{"id":"GO:0070389","count":14}]},{"hash":"1994214428132648874","title":"Ubiquitin-like Modifications and Autophagy","description":"The top GO terms are dominated by ubiquitin-like modification processes (sumoylation, deubiquitination, ufmylation) and autophagy-related processes (macroautophagy, nucleophagy). This suggests the cluster centers on protein post-translational modification via ubiquitin-like modifiers and related degradation pathways, with some auxiliary roles in cell-cycle regulation. ","confidence":"High","size":27,"edges":63,"triangles":98,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":6},{"id":"GO:0016579","count":5},{"id":"GO:0002143","count":4},{"id":"GO:0018192","count":4},{"id":"GO:0051726","count":4}]},{"hash":"1124003332510849721","title":"Cellular stress response and nutrient sensing","description":"These proteins cluster around cellular stress and nutrient-signaling pathways: amino acid starvation/GNC2 signaling, regulation of responses to amino acid deprivation, UV-C and pH stress, DNA damage checkpoint signaling, and hypoxia/HIF-1alpha signaling. While a few terms touch on other processes, the dominant theme is cellular responses to environmental and nutritional stress, justifying a concise label focused on stress and nutrient sensing.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060765","count":1},{"id":"GO:0031953","count":1},{"id":"GO:0097201","count":1},{"id":"GO:0060733","count":1},{"id":"GO:0071232","count":1}]},{"hash":"128168117643061860","title":"Spliceosome-driven mRNA processing","description":"Top GO terms center on spliceosome-mediated mRNA processing and regulation. Several entries describe mRNA splicing (cis and alternative) via the spliceosome, small-subunit processome assembly, and mRNA modification, pointing to core RNA processing machinery. Additional terms about mRNA stability under stress and regulatory ncRNA-mediated gene silencing suggest broader RNA metabolism and regulation. Together these indicate a cluster of proteins involved in RNA splicing/processing and initiation of translation.","confidence":"High","size":27,"edges":3,"triangles":0,"max_degree":2,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":12},{"id":"GO:0048026","count":12},{"id":"GO:0010610","count":12},{"id":"GO:1901407","count":12},{"id":"GO:0006378","count":11}]},{"hash":"2196616968146429651","title":"Ribosome Biogenesis and RNA Modification","description":"Enrichment of cytoplasmic translation and multiple pseudouridine synthesis activities (snRNA, mRNA, tRNA) alongside ribosomal large subunit export from the nucleus indicates a core theme of ribosome biogenesis and RNA modification. While terms for cell division and cellular fusion appear, the dominant signal is RNA processing and ribosome assembly, suggesting proteins in this cluster collaborate on building and preparing ribosomes for translation.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0002181","count":3},{"id":"GO:0031120","count":2},{"id":"GO:1990481","count":2},{"id":"GO:0031119","count":2},{"id":"GO:0000055","count":2}]},{"hash":"652624089045888559","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006970","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0000086","count":2},{"id":"GO:0045792","count":2},{"id":"GO:0000389","count":1}]},{"hash":"37573077088805439","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":2},{"id":"GO:0039702","count":2},{"id":"GO:0048709","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0060576","count":1}]},{"hash":"1618049941709806170","title":"Telomere maintenance and chromatin remodeling","description":"The cluster shows a clear emphasis on chromatin remodeling and DNA-binding/ helicase regulation, paired with telomere-specific processes such as shelterin complex assembly, telomeric loop formation, and regulation of localization to telomeres, plus G-quadruplex DNA formation. While an ethylene-response term appears, the dominant signal is telomere maintenance coupled with chromatin dynamics.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":3},{"id":"GO:0051096","count":2},{"id":"GO:0043388","count":2},{"id":"GO:0014718","count":2},{"id":"GO:0033234","count":2}]},{"hash":"1237295753399716187","title":"Membrane Transporters and Vesicular Loading","description":"The top GO terms cluster around transmembrane transport activities (phosphate, xenobiotic, nitrate, 4-hydroxyphenylacetate transport) and neurotransmitter loading into synaptic vesicles, pointing to proteins mainly involved in moving substances across membranes and into vesicles. Cardiac development/contraction terms are present but likely reflect tissue-specific expression rather than core function of the cluster. Overall, the shared theme is membrane transport, especially vesicular transport.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0060048","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0016477","count":3}]},{"hash":"373109356090707527","title":"DNA repair and genome maintenance","description":"This cluster is dominated by GO terms tied to DNA damage response, repair, replication, and chromatid cohesion (e.g., leading strand elongation, mismatch repair, error-free translesion synthesis, and maintenance of trinucleotide repeats), indicating a functional module of DNA repair and genome stability factors. A couple of terms appear incidental (response to L-glutamate, response to dexamethasone) but do not override the DNA repair signal.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006272","count":1},{"id":"GO:0042769","count":1},{"id":"GO:1902394","count":1},{"id":"GO:1902065","count":1},{"id":"GO:0000710","count":1}]},{"hash":"782905480399001462","title":"Unknown","description":"The top terms span transcriptional regulation and cAMP signaling in some contexts, but also include aerotaxis, heart rate regulation, and immune/drug response terms across different organisms, showing no single cohesive function. With no edges linking the proteins into a common pathway, a specific, representative label cannot be confidently assigned.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0009454","count":2},{"id":"GO:0045762","count":2},{"id":"GO:0002027","count":2},{"id":"GO:0045013","count":2}]},{"hash":"771435273033565469","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":179,"triangles":630,"max_degree":24,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":25},{"id":"GO:0042068","count":23},{"id":"GO:0002098","count":23},{"id":"GO:1905608","count":23},{"id":"GO:1905869","count":23}]},{"hash":"1714821481612964761","title":"Nuclear signaling and transcription regulation","description":"This cluster is enriched in terms tied to transport into the nucleus (NLS-bearing import), regulation of protein phosphorylation/dephosphorylation, and activation of transcription by RNA polymerase II, including calcium-NFAT signaling. Together these point to a core theme of signaling pathways that modulate gene expression in the nucleus, despite some outlier terms related to development or memory. ","confidence":"Medium","size":26,"edges":199,"triangles":782,"max_degree":25,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006607","count":5},{"id":"GO:0006469","count":5},{"id":"GO:0045944","count":5},{"id":"GO:0008360","count":4},{"id":"GO:0006470","count":4}]},{"hash":"1271214823505615594","title":"Embryogenesis and cell-cycle control","description":"The terms are dominated by core cell-cycle processes (mitotic cell cycle, centrosome cycle, DNA replication) but also include developmental and signaling pathways (embryonic cranial skeleton morphogenesis, keratinocyte differentiation, visual perception, Wnt and Rho signaling). This suggests proteins involved in coordinating development with cell proliferation and signaling, rather than a single narrow function.","confidence":"Medium","size":26,"edges":45,"triangles":21,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000278","count":22},{"id":"GO:0007266","count":22},{"id":"GO:0090263","count":22},{"id":"GO:0048701","count":22},{"id":"GO:0046827","count":22}]},{"hash":"861273805317067418","title":"DNA replication and genome maintenance","description":"The top GO terms cluster around DNA replication, unwinding, and repair (DNA replication, SOS response, DNA unwinding), plus transcription regulation and mRNA surveillance. This pattern suggests a functional module focused on genome integrity and DNA metabolism, with ancillary transcriptional control.","confidence":"Medium","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000184","count":15},{"id":"GO:0090305","count":10},{"id":"GO:0032508","count":10},{"id":"GO:0009432","count":9},{"id":"GO:0006268","count":9}]},{"hash":"68893491505581438","title":"Centrosome cycle and DNA replication","description":"This cluster is enriched for GO terms related to mitotic centrosome separation, centrosome cycle, DNA replication, and nuclear DNA-templated transcription, pointing to a core function in cell cycle progression and centrosome dynamics during development. Developmental morphogenesis terms (placenta, cranial skeleton, dendrite morphogenesis) likely reflect contexts where these cell cycle processes are active, while the potassium ion transport term appears less connected. ","confidence":"Medium","size":26,"edges":48,"triangles":25,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007100","count":10},{"id":"GO:0048701","count":10},{"id":"GO:0006813","count":10},{"id":"GO:0007098","count":9},{"id":"GO:0048813","count":9}]},{"hash":"1618495523267366142","title":"Amino acid biosynthesis and metabolism","description":"This cluster is dominated by amino acid metabolic processes (pyruvate-to-alanine, threonine, tryptophan biosynthesis, and cysteine/kynurenine pathways) and related catabolic steps, plus a DNA-templated transcription term that suggests regulatory roles. Notably, there are outliers related to signaling (Notch pathway) and morphine response, which may reflect broader regulatory associations or annotation cross-talk rather than core metabolic function. Overall, the common theme is amino acid metabolism with supportive transcriptional/signaling links.","confidence":"Medium","size":26,"edges":301,"triangles":2131,"max_degree":25,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042866","count":8},{"id":"GO:0017000","count":8},{"id":"GO:0043278","count":7},{"id":"GO:0006351","count":6},{"id":"GO:0097053","count":6}]},{"hash":"1339889927842138173","title":"Plant telomere maintenance and chromatin remodeling","description":"The top terms cluster around telomere biology (telomeric loop formation, shelterin complex assembly, protein localization to telomeres) and chromatin remodeling, with supporting links to G-quadruplex DNA formation. Plant hormone responses (ethylene, ABA, cytokinin) likely reflect a plant context for these telomere/chromatin processes, supporting a cohesive theme of telomere maintenance and chromatin dynamics in plants.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009236","count":7},{"id":"GO:0042135","count":7},{"id":"GO:0043044","count":6},{"id":"GO:0009736","count":6},{"id":"GO:1904850","count":5}]},{"hash":"299300766532067404","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":13,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000453","count":5},{"id":"GO:0002938","count":5},{"id":"GO:0046835","count":4},{"id":"GO:0001302","count":3},{"id":"GO:0006769","count":3}]},{"hash":"57046578723338705","title":"Metabolism and Differentiation Regulation","description":"The cluster's top GO terms include central metabolic processes (thiamine biosynthesis, tetrahydrofolate metabolism, mitochondrial electron transport) alongside differentiation-related terms (megakaryocyte and erythrocyte differentiation) and gamete-associated processes, suggesting a broad theme of energy/metabolic pathways with regulatory roles in cellular differentiation. However, the mix is quite diverse, so the label reflects a general metabolism-and-differentiation theme rather than a narrow function.","confidence":"Medium","size":26,"edges":12,"triangles":3,"max_degree":6,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009228","count":11},{"id":"GO:0046653","count":11},{"id":"GO:0009409","count":10},{"id":"GO:0006120","count":10},{"id":"GO:0045654","count":10}]},{"hash":"1732545782807919996","title":"Membrane Ion Transporters","description":"This cluster is dominated by GO terms for membrane ion transport (potassium and sodium transmembrane transport, and calcium import across the plasma membrane), suggesting the proteins are mainly involved in moving ions across membranes. The other terms (root hair development, cerebellar granule neuron differentiation, Notch signaling, and plant cell wall glycosylation) are less frequent and may reflect broader multifunctionality or annotation noise, but do not override the central theme of ion transport.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":3},{"id":"GO:0080147","count":3},{"id":"GO:0035725","count":2},{"id":"GO:0006004","count":2},{"id":"GO:0098703","count":2}]},{"hash":"2264171160135270666","title":"Unknown","description":"The GO terms point to proteostasis (protein peptidyl-prolyl isomerization and response to unfolded protein) but also include unrelated themes such as dsRNA response and photoreceptor outer segment localization, with several terms marked obsolete, making it hard to identify a single cohesive function for the cluster.","confidence":"","size":26,"edges":36,"triangles":9,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0019878","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0000413","count":5},{"id":"GO:0071360","count":5},{"id":"GO:0006986","count":5}]},{"hash":"768851371700033077","title":"Steroid signaling in male reproductive development","description":"This cluster is driven by terms like steroid hormone receptor complex assembly, male sex differentiation, and prostate gland development, which together point to a theme of steroid signaling guiding male reproductive development. Additional terms related to innate immune responses and dsRNA suggest some multifunctional roles or incidental associations, but the strongest signal centers on steroid signaling and male reproductive biology.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0006463","count":10},{"id":"GO:0046661","count":10},{"id":"GO:0030850","count":10},{"id":"GO:0071357","count":9},{"id":"GO:0051301","count":8}]},{"hash":"1067175540333315454","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":87,"triangles":137,"max_degree":17,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":8},{"id":"GO:0048026","count":7},{"id":"GO:0000398","count":6},{"id":"GO:0071031","count":5},{"id":"GO:0000381","count":5}]},{"hash":"1149076631787117118","title":"Secretory Vesicle Trafficking and Signaling","description":"This cluster centers on vesicle-mediated processes and receptor trafficking, with GO terms such as dense core granule exocytosis, synaptic vesicle priming, and GPCR internalization, plus signaling pathways like insulin receptor signaling and IL-18-mediated signaling, suggesting a cohesive theme of secretory vesicle dynamics and signal transduction across immune, endocrine, and neural contexts. Some additional terms (sterol biosynthesis, transcription regulation) hint at broader membrane biology and gene regulation, but the dominant pattern is vesicle trafficking and signaling. ","confidence":"Medium","size":26,"edges":91,"triangles":102,"max_degree":19,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0016126","count":8},{"id":"GO:0000122","count":7},{"id":"GO:0060303","count":6},{"id":"GO:0032094","count":6},{"id":"GO:0035655","count":6}]},{"hash":"2162556854639699392","title":"Heat and Oxidative Stress Response","description":"This cluster is dominated by GO terms tied to stress responses\u2014especially heat, hydrogen peroxide, ROS, and UV-related responses\u2014as well as regulation of ROS and aging-related processes, indicating a shared role in protecting cells from oxidative and thermal stress; tissue-specific terms like lens morphogenesis or estradiol response appear ancillary. ","confidence":"High","size":26,"edges":325,"triangles":2600,"max_degree":25,"top_function":null,"top_go_terms":[{"id":"GO:0030308","count":15},{"id":"GO:1900034","count":15},{"id":"GO:0042542","count":15},{"id":"GO:1905907","count":15},{"id":"GO:0007568","count":15}]},{"hash":"2262955026196899477","title":"Unknown","description":"The cluster\u2019s top GO terms span stress responses (response to cold, response to herbicide), energy metabolism (mitochondrial electron transport, thiamine biosynthetic process), and various hematopoietic/gametogenesis-related processes (megakaryocyte differentiation, erythrocyte differentiation, sperm capacitation), with no clear unifying function. There are no edges or direct interactions (Edges: 0; Triangles: 0; Max Degree: 0), and several terms are obsolete, suggesting noise rather than a coherent biological module. Therefore, no single representative label can be confidently assigned.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009409","count":13},{"id":"GO:0006120","count":12},{"id":"GO:0045654","count":12},{"id":"GO:0009635","count":12},{"id":"GO:0009228","count":12}]},{"hash":"1654946938844771978","title":"Unknown","description":"The top terms span stress responses, hormone and signaling pathways, renal water balance, anti-apoptotic regulation, and diverse carbohydrate catabolism. This wide mix lacks a single coherent biological theme, so a unified label is not evident.","confidence":"","size":26,"edges":324,"triangles":2576,"max_degree":25,"top_function":null,"top_go_terms":[{"id":"GO:0097238","count":25},{"id":"GO:0042448","count":25},{"id":"GO:0003091","count":25},{"id":"GO:0042415","count":25},{"id":"GO:0046427","count":25}]},{"hash":"2069716489980761766","title":"Steroid and retinoid hormone biosynthesis","description":"The cluster is dominated by GO terms for steroid biosynthesis (testosterone, glucocorticoids) and retinoid metabolism (retinol, retinal, retinoic acid), with supporting lipid biosynthesis terms. This suggests a cohesive module focused on lipid-derived signaling molecules, despite a peripheral \u201cresponse to antibiotic\u201d term.","confidence":"High","size":26,"edges":132,"triangles":272,"max_degree":19,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0046677","count":26},{"id":"GO:0042761","count":25},{"id":"GO:0006355","count":25},{"id":"GO:0055114","count":25},{"id":"GO:0042574","count":25}]},{"hash":"1851190636952085079","title":"Unknown","description":"The top terms show a mix of DNA repair and telomere maintenance, cell cycle regulation, neurotransmitter signaling, and immune/inflammatory responses, with no single dominant function linking the proteins. Because the terms span very different biological themes and there are no shared, cohesive GO terms driving the cluster, there isn't a clear unifying process to name. Therefore I label this as Unknown.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990414","count":2},{"id":"GO:0061820","count":2},{"id":"GO:0032092","count":2},{"id":"GO:0051770","count":2},{"id":"GO:0045842","count":2}]},{"hash":"711081592969990173","title":"Epigenetic Regulation and Metabolism","description":"The top GO terms include chromatin-related activities (nucleosome assembly, chromatin remodeling) and histone-related processes alongside biosynthetic and catabolic metabolism (biotin and antibiotic biosynthesis, polysaccharide catabolic processes), suggesting a cluster of proteins involved in both chromatin dynamics and core metabolic pathways.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0019391","count":3},{"id":"GO:0006334","count":3},{"id":"GO:0016049","count":3}]},{"hash":"1014135597539500850","title":"Ubiquitin-Mediated Transcription and Signaling Regulation","description":"The top GO terms cluster around ubiquitin-related processes (ERAD pathway, autoubiquitination, K63-linked ubiquitination) and downstream effects on transcription and signaling (negative regulation of RNA Pol II transcription, NF-kappaB signaling). This points to a unifying theme of ubiquitin-driven modulation of gene expression and signaling pathways, despite a few outliers that may reflect broader multifunctionality. ","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":5},{"id":"GO:0051865","count":5},{"id":"GO:0000122","count":4},{"id":"GO:0070534","count":4},{"id":"GO:0033280","count":4}]},{"hash":"485798552063191452","title":"Epigenetic Regulation of Transcription","description":"Most of the top GO terms point to transcriptional regulation by RNA polymerase II and to chromatin-level control (histone modification, heterochromatin assembly, DNA methylation, and epigenetic silencing), with vernalization-related chromatin changes strongly suggesting plant epigenetic regulation of gene expression as a unifying theme. A few terms about heart development or hormone secretion appear as outliers.","confidence":"Medium","size":26,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006368","count":2},{"id":"GO:0010048","count":2},{"id":"GO:0033697","count":1},{"id":"GO:0036091","count":1},{"id":"GO:0071894","count":1}]},{"hash":"391757083265536267","title":"Heart Development and SA Node Regulation","description":"The cluster shows strong representation for heart development and regulation of SA node cell action potentials, pointing to cardiac development and pacemaker electrophysiology. While other terms (neural crest, calcium signaling) align with broader developmental processes, the clearest theme centers on cardiac formation and electrical conduction, supported by multiple counts for heart-related GO terms.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0098907","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0072075","count":2}]},{"hash":"2165919918957018539","title":"Organogenesis and developmental signaling","description":"This cluster shows strong representation of developmental and morphogenetic processes across tissues: organogenesis (lung, oviduct, ventricular heart, dorsal root ganglion), regulation of signaling (negative Wnt), control of cell proliferation and apoptosis, and cell migration. The proton transmembrane transport term may reflect membrane transporters active during development. Overall, the common theme is developmental signaling driving organ formation and tissue patterning.","confidence":"Medium","size":26,"edges":220,"triangles":953,"max_degree":25,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0015991","count":16},{"id":"GO:0043065","count":16},{"id":"GO:0090090","count":16},{"id":"GO:0008285","count":16},{"id":"GO:0016477","count":16}]},{"hash":"1086878358820055343","title":"Calcium signaling and synaptic regulation","description":"GO terms show a clear pattern of calcium flux (import and release) and synaptic modulation (receptor localization, synaptic plasticity), with vasopressin secretion tying into neuroendocrine signaling. While ubiquitination and other terms appear, the dominant theme is calcium-dependent signaling at neural synapses, justifying this label.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":8},{"id":"GO:0071260","count":7},{"id":"GO:0098703","count":7},{"id":"GO:0009409","count":7},{"id":"GO:0051209","count":7}]},{"hash":"435819617328027250","title":"Nuclear transport and transcription regulation","description":"This cluster shows strong representation of nuclear import (NLS-bearing and ribosomal protein import), mRNA transport, and DNA-templated transcription, suggesting a nucleus-centered gene expression/program regulation theme. Additional terms like TORC1 signaling, GTPase regulation, and cell division point to regulation of growth and cell-cycle\u2013related processes connected to nuclear functions.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043547","count":12},{"id":"GO:0006607","count":10},{"id":"GO:0051028","count":9},{"id":"GO:0006351","count":8},{"id":"GO:0051301","count":8}]},{"hash":"442137489281124944","title":"RNA processing and translation initiation","description":"This cluster is dominated by GO terms related to mRNA processing (splicing, polyadenylation, mRNA stability) and translation initiation/reinitiation, indicating a core theme of RNA maturation and control of protein synthesis. A few terms point to ER\u2013Golgi trafficking (COPII), which may reflect associated cellular processes in secretory pathway contexts, but the dominant signal remains RNA processing and translation control.","confidence":"Medium","size":26,"edges":291,"triangles":1937,"max_degree":25,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0048208","count":3},{"id":"GO:0000381","count":3}]},{"hash":"1679044378558276642","title":"Diverse membrane solute transporters","description":"The GO terms are dominated by transmembrane transport of a variety of substrates (nitrate, galactose, arabinose, sodium, phosphate, fucose, 4-hydroxyphenylacetate, etc.) and a vesicle-associated neurotransmitter loading term, indicating a cluster of membrane transport proteins with broad substrate specificity, including vesicular transport. This cohesive theme justifies naming the cluster as diverse membrane transporters.","confidence":"High","size":26,"edges":20,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":11},{"id":"GO:0015757","count":11},{"id":"GO:0098700","count":11},{"id":"GO:0015706","count":11},{"id":"GO:0006004","count":11}]},{"hash":"1482045362376731899","title":"Vascular development and smooth muscle migration","description":"The top GO terms include hepatocyte growth factor receptor signaling, smooth muscle cell migration, and coronary artery morphogenesis, all pointing to vascular development and remodeling. Additional terms about regulation of smooth muscle migration, blood-brain barrier maintenance, and related cellular processes further support a vascular/smooth muscle\u2013focused theme rather than unrelated pathways. This combination suggests a coherent cluster centered on vascular development and smooth muscle dynamics.","confidence":"High","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048012","count":3},{"id":"GO:0014909","count":3},{"id":"GO:0060982","count":3},{"id":"GO:0014910","count":3},{"id":"GO:0036335","count":2}]},{"hash":"1392658806875365153","title":"Ubiquinone and lipid metabolism regulation","description":"Top GO terms center on regulation of ubiquinone biosynthesis and regulation of tocopherol cyclase activity, both linked to mitochondrial/lipid metabolism, along with general lipid homeostasis. Although a Purkinje cell layer morphogenesis term appears, the dominant shared function across the cluster is regulation of lipid-soluble vitamin and lipid biosynthesis pathways, suggesting the cluster represents proteins involved in mitochondrial lipid metabolism and coenzyme Q/tocopherol regulation rather than neural development.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0010795","count":10},{"id":"GO:1902171","count":10},{"id":"GO:0021692","count":10},{"id":"GO:0055088","count":10},{"id":"GO:1901006","count":10}]},{"hash":"2152300621765158008","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0019243","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006749","count":2},{"id":"GO:0042594","count":2}]},{"hash":"1239701829072836015","title":"Steroid signaling and innate immune response","description":"Most top GO terms point to male reproductive development and steroid signaling (prostate gland development, male sex differentiation, steroid hormone receptor complex assembly). A subset also maps to innate immunity (cellular response to type I interferon, cellular response to exogenous dsRNA) and stress responses (unfolded protein). The convergence suggests a cluster of proteins involved in hormonal signaling with immune-related functions, hence the chosen label.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0030850","count":6},{"id":"GO:0046661","count":6},{"id":"GO:0006463","count":6},{"id":"GO:0071357","count":6},{"id":"GO:0051301","count":6}]},{"hash":"1744873253785846270","title":"Nuclear RNA processing and decay","description":"The top terms cluster around nuclear RNA processing and decay pathways, including rRNA and histone mRNA catabolism, nuclear mRNA surveillance, nonsense-mediated decay, and transcription termination coupled to poly(A). This suggests a cohesive role in RNA quality control and turnover within the nucleus.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071035","count":1},{"id":"GO:0071044","count":1},{"id":"GO:0030846","count":1},{"id":"GO:0000184","count":1},{"id":"GO:0070370","count":1}]},{"hash":"1442974814225545717","title":"Glucose-limited fungal morphogenesis and invasion","description":"The top GO terms point to invasive and pseudohyphal growth driven by glucose limitation, a classic fungal morphogenesis program under nutrient stress. Coupled with regulation of GTPase activity for signaling and components of nuclear transport and vesicle trafficking (nuclear import, nuclear pore assembly, endosome-to-melanosome transport), this cluster seems to coordinate growth morphology with intracellular transport during nutrient limitation. Confidence: Medium","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0000902","count":3},{"id":"GO:0007124","count":3},{"id":"GO:0001403","count":3},{"id":"GO:0060188","count":2}]},{"hash":"1988825103100303392","title":"Unknown","description":"The top GO terms span viral processes, plant cytokinin signaling, interferon response, stress responses, redox processes, and cell cycle steps, showing a heterogeneous mix without a single coherent biological theme. This makes a reliable, concise label difficult to assign.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":4},{"id":"GO:0009736","count":4},{"id":"GO:0006470","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0006970","count":3}]},{"hash":"1584150406300127141","title":"Germ cell chromatin remodeling and transcription regulation","description":"The terms cluster around nuclear gene regulation and germ cell development: transcription initiation, chromatin remodeling, histone modification, mRNA processing, and translation initiation, with explicit germ cell processes like oocyte maturation and spermatid differentiation. This suggests a module coordinating chromatin state and gene expression during gametogenesis, despite a few unrelated signaling terms.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035413","count":1},{"id":"GO:0048096","count":1},{"id":"GO:1901315","count":1},{"id":"GO:2000780","count":1},{"id":"GO:0050847","count":1}]},{"hash":"1457630518979030535","title":"Neuronal calcium signaling and synaptic plasticity","description":"Predominant GO terms point to neuronal calcium signaling and synaptic plasticity (calcium import and release, receptor localization at synapse, vasopressin secretion); a few terms reflect general mechanical stress or obsolete annotations, but the core theme is calcium-mediated neuronal signaling.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":3},{"id":"GO:0098703","count":3},{"id":"GO:0009409","count":3},{"id":"GO:0051209","count":3},{"id":"GO:1900383","count":3}]},{"hash":"1605362155508127887","title":"Cardiac Electrophysiology and Calcium Handling","description":"Most terms point to cardiac excitability and Ca2+ handling (action potentials in AV/atria/ventricle, potassium channel regulation, Ca2+ import and SR Ca2+ release). A couple of terms about touch and optic nerve structure appear as annotation noise but do not override the central cardiac theme.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0086045","count":3},{"id":"GO:0098911","count":3},{"id":"GO:0050976","count":3},{"id":"GO:0021633","count":3},{"id":"GO:0098703","count":3}]},{"hash":"1774640057907668182","title":"Unknown","description":"The top GO terms are highly diverse, covering lipid catabolism, signaling pathways, plant and animal development, and general cellular organization. There isn\u2019t a clear, single biological theme tying these 26 proteins together, suggesting the cluster is heterogeneous rather than a cohesive functional module.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009097","count":4},{"id":"GO:0006660","count":4},{"id":"GO:0019433","count":4},{"id":"GO:0052651","count":4},{"id":"GO:2000124","count":4}]},{"hash":"1753438680423717109","title":"Ubiquitin-Dependent Protein Degradation & Regulation","description":"This cluster is dominated by GO terms for ubiquitination and proteolysis (e.g., ubiquitin-dependent protein catabolic process, polyubiquitination, K48- and K6-linked ubiquitination, autoubiquitination), with additional terms for histone catabolic and general protein ubiquitination, indicating a common theme of protein turnover and regulation via ubiquitin tagging. Some links to TNF signaling and vitamin D response appear, but the core signal is ubiquitin-mediated degradation and control of protein levels.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":9},{"id":"GO:0036205","count":7},{"id":"GO:0085020","count":7},{"id":"GO:0051865","count":7},{"id":"GO:1903265","count":7}]},{"hash":"1165750647487794222","title":"Lipid and carbohydrate metabolism cluster","description":"Top terms show enrichment for lipid catabolic processes (fatty acid metabolism, triglyceride and diacylglycerol catabolism) and a carbohydrate catabolic process (cellulose). Additional signals include protein depalmitoylation and regulation of endocannabinoid signaling, along with various biosynthetic processes. Taken together, the cluster appears to function broadly in metabolism, especially lipid metabolism, with some carbohydrate metabolism and protein lipid-modifying activities.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":5},{"id":"GO:0042997","count":5},{"id":"GO:0006631","count":5},{"id":"GO:0002084","count":5},{"id":"GO:0042136","count":4}]},{"hash":"510167222302523460","title":"Metabolic Biosynthesis and Catabolism","description":"The top GO terms point to multiple biosynthetic pathways (GMP, fatty acids, serine, hydrogen sulfide) and catabolic processes (serine and homocysteine), plus carbohydrate metabolism and gluconeogenesis regulation, indicating a broad metabolic cluster centered on synthesis and breakdown of metabolites rather than a single pathway. Protein homotetramerization may reflect enzyme assembly in these processes.","confidence":"Medium","size":25,"edges":298,"triangles":2254,"max_degree":24,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0006177","count":11},{"id":"GO:0006633","count":11},{"id":"GO:0006535","count":11},{"id":"GO:0055114","count":11},{"id":"GO:0006565","count":11}]},{"hash":"1244902476127565268","title":"Unknown","description":"The top terms are highly heterogeneous, including photosynthesis-related terms (photosynthesis, nonphotochemical quenching), xenobiotic/organic compound catabolism (carbazole and toluene catabolic processes), defense response to bacteria, and basic processes like proton transport and ubiquitination, plus several obsolete GO terms. This lack of a single cohesive function makes a clear, specific label inappropriate.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0010196","count":4},{"id":"GO:0046381","count":4},{"id":"GO:0046232","count":4},{"id":"GO:0015979","count":4}]},{"hash":"1348890991482233177","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032543","count":1},{"id":"GO:0051084","count":1},{"id":"GO:0033617","count":1},{"id":"GO:0022417","count":1},{"id":"GO:0045041","count":1}]},{"hash":"1794336652137169552","title":"Neural development and axonogenesis signaling","description":"This cluster is dominated by GO terms for nervous system development, brain development, and positive regulation of axonogenesis, with Hedgehog (Smoothened) signaling and PI3K/AKT and Rho-related pathways, pointing to neural differentiation and axon growth; calcium-independent cell-matrix adhesion supports neural pathfinding. Some immune-related terms appear, which may reflect shared signaling components rather than actual immune functions, but the core theme remains neural development and axonogenesis.","confidence":"High","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":5},{"id":"GO:0007420","count":4},{"id":"GO:0035987","count":4},{"id":"GO:0007161","count":4},{"id":"GO:0035023","count":4}]},{"hash":"2268944307507685933","title":"Ribosome biogenesis and translation","description":"This cluster is dominated by GO terms for translation and ribosome biogenesis (translation, ribosome biogenesis, ribosomal large subunit biogenesis) with additional transcription-related terms, suggesting a core theme around protein synthesis and ribosome assembly, with a few peripheral terms that may reflect broader gene expression or cell envelope-related processes. ","confidence":"High","size":25,"edges":252,"triangles":1598,"max_degree":23,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0046677","count":5},{"id":"GO:0006412","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0000902","count":3},{"id":"GO:0006353","count":3}]},{"hash":"1979083137107773131","title":"Unknown","description":"The cluster's top GO terms span translation (including translational fidelity), antibiotic response, and a mix of metabolic processes (fatty acid oxidation and methyl-branched fatty acids), along with ectoine biosynthesis/catabolism and even verruculogen biosynthesis. This wide spread indicates no single cohesive biological function ties all members together, suggesting a heterogeneous collection rather than a functionally coherent cluster.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0001561","count":2},{"id":"GO:0042400","count":2}]},{"hash":"536148714150942935","title":"Unknown","description":"The terms in this cluster span immune chemotaxis, fungal/plant metabolism (pinoresinol/lariciresinol, ergosterol, GDP-mannose), transcriptional repression, cytolysis, and polysaccharide biosynthesis, including obsolete annotations. This mixes disparate biological themes and likely reflects annotation noise rather than a single cohesive function, so a specific representative label cannot be assigned.","confidence":"","size":25,"edges":9,"triangles":0,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035754","count":6},{"id":"GO:0055114","count":4},{"id":"GO:0001081","count":3},{"id":"GO:1902125","count":3},{"id":"GO:0045226","count":3}]},{"hash":"983030942641564937","title":"Metabolism and Inflammatory Signaling","description":"The cluster\u2019s top terms show central metabolism (glycolysis, L-valine and L-alanine catabolic processes, NADPH regeneration) alongside immune signaling pathways (TNF-mediated signaling, NF-kappaB activation) and T cell homeostasis, suggesting a link between metabolic state and inflammatory regulation. Ubiquitin-related processes (ERAD and histone ubiquitination) indicate broader protein quality control and gene regulation in stress responses, but the cohesive theme appears to be metabolism intertwined with immune signaling rather than a single narrow function.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0006574","count":2},{"id":"GO:0043029","count":2},{"id":"GO:0043123","count":2}]},{"hash":"1947731239145522663","title":"Proteostasis and stress-response proteins","description":"This cluster shows enrichment for protein quality control and folding under stress, including unfolded protein response, ubiquitin-proteasome\u2013mediated quality control, chaperone-assisted refolding, negative regulation of protein kinase activity, and heat response. While some terms touch on trafficking and development, the dominant signal is maintenance of protein homeostasis under stress.","confidence":"High","size":25,"edges":35,"triangles":1,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006469","count":6},{"id":"GO:0006986","count":5},{"id":"GO:0071630","count":5},{"id":"GO:0070389","count":5},{"id":"GO:0031204","count":5}]},{"hash":"1024954478954182164","title":"Ubiquitin-Proteasome Regulation of Circadian and Cell Cycle","description":"Top GO terms indicate a strong focus on ubiquitin-dependent proteolysis (including SCF complexes and protein polyubiquitination) and regulation of circadian rhythm and cell cycle entry, suggesting the cluster centers on proteostasis-controlled timing and progression of the cell cycle. Stress-response terms to metals further reflect ubiquitin-mediated quality control and apoptosis signaling under toxic conditions. ","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":13},{"id":"GO:0031146","count":11},{"id":"GO:0042752","count":11},{"id":"GO:0000083","count":9},{"id":"GO:0000209","count":8}]},{"hash":"846905668814465418","title":"Nuclear Transport and Ribosome Biogenesis","description":"The top GO terms are dominated by nuclear import/export and ribosome handling (nuclear pore complex assembly, ribosomal protein import into the nucleus, ribosomal large subunit export from the nucleus, NLS-bearing protein import), with a note on regulatory desumoylation. This suggests a cohesive theme around nuclear transport and ribosome biogenesis, with a few ancillary processes.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060188","count":3},{"id":"GO:0006610","count":3},{"id":"GO:0000060","count":3},{"id":"GO:0051292","count":3},{"id":"GO:0043547","count":3}]},{"hash":"1475587530658004901","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000480","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0035767","count":2},{"id":"GO:0051301","count":1},{"id":"GO:0090266","count":1}]},{"hash":"66622053332201000","title":"Unknown","description":"The top GO terms are highly diverse (ubiquitin recycling, proteolysis regulation, mitochondrial respiration, insulin signaling, protein oligomerization, PQQ biosynthesis, pheromone maturation, viral and symbiont entry processes), with no single dominant function connecting the 25 proteins. This suggests no cohesive cluster theme, so the label Unknown is appropriate.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010992","count":2},{"id":"GO:0045861","count":2},{"id":"GO:0006122","count":2},{"id":"GO:0008286","count":2},{"id":"GO:0051291","count":2}]},{"hash":"1169795230770849831","title":"NF-kB\u2013regulated immune signaling and antigen processing","description":"These proteins cluster around immune signaling and antigen presentation: terms point to regulation of canonical and non-canonical NF-kappaB pathways, IL-1 production, defense against viruses, and dendritic cell antigen processing/presentation, with proteasomal degradation supporting antigen processing. Some broader terms (cornea development, defecation rhythm) may reflect pleiotropic annotations rather than core function; however, the dominant theme is NF-kB\u2013driven immune signaling and antigen presentation.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043124","count":3},{"id":"GO:0042345","count":2},{"id":"GO:0051770","count":2},{"id":"GO:0050701","count":2},{"id":"GO:0002606","count":2}]},{"hash":"61490138140500598","title":"Unknown","description":"The top GO terms point to diverse cellular processes (mitotic cell cycle, negative regulation of kinase activity, mRNA transport, hypoxia response, GTPase signaling, heart tissue morphogenesis, vacuole fusion, cell shape regulation, protein dephosphorylation, and apoptotic regulation). There is no single coherent molecular function or pathway that unites these terms, suggesting the proteins participate in multiple distinct processes rather than a single well-defined module. A concise, specific label is not evident.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":6},{"id":"GO:0006469","count":5},{"id":"GO:0051028","count":5},{"id":"GO:0071456","count":5},{"id":"GO:0043547","count":5}]},{"hash":"432674766388199831","title":"Neural signaling, trafficking, and splicing regulation","description":"The cluster shows strong signals for neuronal processes: Golgi-to-plasma membrane trafficking, receptor internalization, neuronal action potential regulation, and long-term synaptic depression, along with alternative mRNA splicing by the spliceosome. These together point to neural signaling and membrane trafficking with gene expression regulation. Some terms related to cellular/host-virus responses appear but are minor compared to the neural-focused terms.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006893","count":2},{"id":"GO:2000766","count":1},{"id":"GO:0002092","count":1},{"id":"GO:0048755","count":1},{"id":"GO:0000381","count":1}]},{"hash":"1029291894271128822","title":"Cardiac development and calcium signaling","description":"Based on GO terms like left ventricular cardiac muscle tissue morphogenesis, atrial muscle cell action potential regulation, outflow tract morphogenesis, and regulation of ryanodine-sensitive calcium-release channel activity, the cluster shows a clear focus on cardiac muscle development and calcium handling. The inclusion of calcium release from the sarcoplasmic reticulum further reinforces a role in cardiac calcium signaling, though there are also broader development terms such as bone ossification and skin development. Overall, the strongest signal is for heart development coupled with calcium dynamics.","confidence":"Medium","size":24,"edges":113,"triangles":264,"max_degree":18,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0014808","count":14},{"id":"GO:0097050","count":13},{"id":"GO:0043931","count":13},{"id":"GO:0007275","count":13},{"id":"GO:0060315","count":13}]},{"hash":"519613289064936799","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0070682","count":3},{"id":"GO:0098907","count":3},{"id":"GO:0007205","count":3}]},{"hash":"1996007843265114356","title":"RNA Methylation and Transcription Regulation","description":"This cluster is enriched for methylation-related processes (rRNA methylation/processing, peptidyl-arginine, protein, and histone methylation) and for negative regulation of transcription by RNA polymerase II, suggesting a shared theme of epigenetic and RNA-level control of gene expression and ribosome biogenesis. The cobalamin biosynthesis term is less connected but does not override the dominant methylation/transcription-related signals.","confidence":"Medium","size":24,"edges":214,"triangles":1015,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":5},{"id":"GO:0009236","count":4},{"id":"GO:0019919","count":3},{"id":"GO:0016049","count":3},{"id":"GO:0031167","count":3}]},{"hash":"283824775366504227","title":"Unknown","description":"The Top Terms are highly diverse, spanning immune cell homeostasis, endosome trafficking, IGF signaling, plant-specific processes (amyloplast organization, gravitropism), and nuclear activities (DNA integration, histone catabolic). With no edges connecting proteins (Max Degree 0) and no evident shared functional theme, there isn\u2019t a cohesive function linking the cluster. Therefore, Unknown with None confidence. ","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001782","count":2},{"id":"GO:0007032","count":2},{"id":"GO:0048009","count":2},{"id":"GO:0009959","count":2},{"id":"GO:0009660","count":2}]},{"hash":"2039767914834179029","title":"Potassium Ion Transport and Membrane Potential Regulation","description":"The cluster is dominated by terms relating to potassium handling and membrane excitability: multiple GO terms describe K+ transport across membranes, intracellular potassium homeostasis, and regulation of resting membrane potential, including cardiac repolarization. Sensory perception terms (touch and pain) can reflect neuronal excitability where potassium dynamics are critical. Together, these suggest a cohesive theme of potassium-driven membrane potential control.","confidence":"High","size":24,"edges":85,"triangles":46,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0050976","count":9},{"id":"GO:0030007","count":9},{"id":"GO:0030322","count":9},{"id":"GO:0098914","count":9},{"id":"GO:0071805","count":8}]},{"hash":"1227430335126738563","title":"Glutathione-Mediated Detoxification","description":"Top GO terms cluster around detox and antioxidant pathways: cellular oxidant detoxification, glutathione metabolic and derivative biosynthetic processes, toxin/xenobiotic catabolic activity, and related xenobiotic metabolism. This strongly suggests a shared function in redox balance and detoxification, with additional but less central ties to amino acid metabolism and stress responses; occasional calcium-regulation terms are likely ancillary. ","confidence":"High","size":24,"edges":275,"triangles":2002,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":20},{"id":"GO:0009407","count":19},{"id":"GO:0006749","count":19},{"id":"GO:0060316","count":18},{"id":"GO:0006289","count":18}]},{"hash":"1063049360319664631","title":"Unknown","description":"The top GO terms are scattered across diverse processes (tRNA queuosine biosynthesis, proteolysis, deglycosylation, amino-acid catabolism, and organelle targeting/homeostasis) with no dominant function linking the proteins, and there are no edges or triangles to indicate a cohesive interaction pattern.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008616","count":1},{"id":"GO:0006508","count":1},{"id":"GO:0033345","count":1},{"id":"GO:0006517","count":1},{"id":"GO:0006559","count":1}]},{"hash":"1819646475460729455","title":"TGF-\u03b2 signaling and cytoskeletal remodeling in development","description":"This cluster centers on GO terms for TGF-\u03b2 stimulus response, actin bundle assembly, cell migration, epithelial polarity, and development (including brain development and transcription), suggesting proteins that coordinate developmental signaling with cytoskeletal dynamics and cell movement. The presence of proteasome assembly/ERAD references hints at broader cellular regulation during development but does not outweigh the core theme of signaling-driven cytoskeletal remodeling.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071560","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0007420","count":3},{"id":"GO:0006351","count":3}]},{"hash":"664612156255730393","title":"Keratinocyte differentiation and growth signaling","description":"This cluster is dominated by keratinocyte differentiation and key growth-control pathways (hippo signaling and Wnt canonical signaling), along with apoptosis and cell-cycle regulation terms. Together, these terms suggest a cohesive theme of epidermal cell fate decisions governed by Hippo/Wnt signaling that balance proliferation and differentiation. ","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030216","count":17},{"id":"GO:0006915","count":17},{"id":"GO:0035329","count":17},{"id":"GO:0060044","count":17},{"id":"GO:0090263","count":16}]},{"hash":"970916855894048991","title":"RNA splicing and translation initiation regulation","description":"The top GO terms cluster around spliceosome-mediated mRNA processing (alternative splicing, splice site recognition, preinitiation complex formation) and translation initiation (including eIF4F complex assembly and IRES-driven initiation), with several entries mentioning miRNA/siRNA-mediated silencing of translation. This suggests the proteins function in both post-transcriptional RNA processing and control of translation, justifying a label focused on RNA processing and translation initiation control.","confidence":"High","size":24,"edges":17,"triangles":3,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":3},{"id":"GO:0016556","count":3},{"id":"GO:0034462","count":3},{"id":"GO:0000380","count":3},{"id":"GO:0001731","count":3}]},{"hash":"1888148663127608437","title":"Proteasome-mediated protein degradation and metal stress response","description":"This cluster is dominated by ubiquitin-proteasome system terms (ubiquitin-dependent protein catabolic process, SCF-dependent proteasomal ubiquitin-dependent protein degradation, protein polyubiquitination, autoubiquitination) and includes stress-related terms (cellular response to cadmium ion, response to arsenic-containing substance, oxidative stress\u2013related apoptotic signaling, DNA damage checkpoint signaling), indicating a cohesive theme around proteostasis coupled with metal-induced stress and genome maintenance.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042787","count":8},{"id":"GO:0031146","count":8},{"id":"GO:0071276","count":7},{"id":"GO:0000209","count":6},{"id":"GO:1903378","count":6}]},{"hash":"1572029575127113417","title":"Unknown","description":"The GO terms are a mix of spindle assembly, metabolism, transcription and chromatin regulation, translation-related methylation, and organ development; there is no single dominant biological theme tying these proteins together, suggesting no coherent cluster function beyond being diverse. ","confidence":"","size":24,"edges":36,"triangles":0,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0051225","count":2},{"id":"GO:0009102","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0030488","count":2},{"id":"GO:0033697","count":1}]},{"hash":"823270459460472640","title":"Transmembrane nutrient and ion transporters","description":"The top GO terms are dominated by transmembrane transport across membranes for a variety of substrates (nitrate and its assimilation; sugars like galactose and arabinose; sodium and phosphate ions; fucose; 4-hydroxyphenylacetate), with an additional note on neurotransmitter loading into synaptic vesicles. This points to a coherent theme: membrane transporters or transporter-associated functions handling diverse nutrients and ions. The absence of interaction edges among proteins does not undermine this shared functional signal. ","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":6},{"id":"GO:0015757","count":6},{"id":"GO:0098700","count":6},{"id":"GO:0015706","count":6},{"id":"GO:0006004","count":6}]},{"hash":"1391639687852662090","title":"Fungal Cell Wall Catabolism and Biofilm Formation","description":"Top GO terms indicate strong enrichment for degradation and remodeling of fungal cell wall components (beta-glucan, mannan, xylan, cellulose) and for single-species biofilm formation on both host and inanimate substrates, complemented by related lipid/sterol catabolic processes typical of fungi. This combination points to a cohesive theme of fungal cell-wall remodeling linked to biofilm lifestyle.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":4},{"id":"GO:0071555","count":3},{"id":"GO:0019433","count":3},{"id":"GO:0044407","count":3},{"id":"GO:0045493","count":3}]},{"hash":"1162651139132388970","title":"Cell Cycle and Telomere Maintenance","description":"The terms cluster around core cell cycle processes (cell cycle, cell division, spindle assembly) and telomere maintenance/regulation (telomere capping, telomere maintenance via telomerase, cohesion regulation at telomeres), with supportive signals from the Wnt pathway. Ribosome biogenesis and a few regulatory modifications (ADP-ribosylation) appear as ancillary growth-related functions but do not outweigh the dominant theme of cell division coupled to telomere integrity. This supports labeling the cluster as related to cell cycle control and telomere maintenance.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0007049","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0042254","count":3},{"id":"GO:1900383","count":2},{"id":"GO:0070213","count":2}]},{"hash":"1998974857572367344","title":"Ribosome biogenesis and rRNA processing","description":"The cluster is dominated by GO terms tied to ribosome biogenesis: large subunit assembly (GO:0000027), export of the large subunit from the nucleus (GO:0000055), maturation of LSU rRNA from tricistronic transcripts (GO:0000463), maturation of 5.8S rRNA (GO:0000466), and assembly of the large subunit preribosome (GO:1902626), indicating a cohesive theme around ribosome assembly and rRNA maturation. Some terms, such as regulatory ncRNA-mediated post-transcriptional gene silencing and defense response to Gram-negative bacteria, appear peripheral and do not alter the central ribosome-related signal. Therefore, the label reflects the cluster\u2019s core function.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045071","count":2},{"id":"GO:0000055","count":1},{"id":"GO:0000027","count":1},{"id":"GO:0000463","count":1},{"id":"GO:0000466","count":1}]},{"hash":"1959104188602852172","title":"Unknown","description":"The top GO terms are highly diverse, spanning cell cycle, ubiquitination, several development/morphogenesis processes, and multiple post-translational modifications (glycosylation, sialylation). There is no clear, single functional theme linking these proteins, and some terms are obsolete or plant-specific, so a cohesive label is not supported by the data.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0036342","count":1},{"id":"GO:0060349","count":1}]},{"hash":"2040418672975999976","title":"Telomere maintenance and signaling regulation","description":"The GO terms center on telomere regulation (capping, maintenance via telomerase, and telomere length control) and include signaling pathways (Wnt, ephrin signaling, MAPK). This suggests a cluster of proteins that coordinate telomere stability with broader cellular signaling, with spindle assembly and ADP-ribosylation appearing as additional regulatory contexts.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000161","count":2},{"id":"GO:1900383","count":2},{"id":"GO:0070213","count":2},{"id":"GO:0051225","count":2},{"id":"GO:1904355","count":2}]},{"hash":"2076942764234316856","title":"Diverse Biosynthetic and Metabolic Processes","description":"The top terms are dominated by various biosynthetic and metabolic pathways\u2014antibiotic biosynthesis, poly-hydroxybutyrate biosynthesis, very long-chain fatty acid biosynthesis, retinal and retinoic acid biosynthesis, and testosterone biosynthesis\u2014alongside more general terms like regulation of transcription and spindle assembly. This pattern suggests a broad set of proteins involved in multiple biosynthetic/metabolic processes rather than a single, cohesive function. The absence of edges also indicates the proteins may be functionally diverse, aligning with a broad metabolism/biosynthesis theme. ","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0017000","count":4},{"id":"GO:0042619","count":4},{"id":"GO:0046677","count":3},{"id":"GO:0006355","count":3}]},{"hash":"141425074007276655","title":"Innate immune activation and antigen presentation","description":"Interpretation: The top GO terms point to regulation of NF-kappaB signaling (including non-canonical pathway), IL-1 production, antiviral defense, and enhanced dendritic cell antigen processing/presentation, together with proteasomal degradation, all of which are core components of innate immune activation and initiation of adaptive immunity. While a couple of terms (cornea development, defecation rhythm) are less directly tied to immunity, most terms converge on immune signaling and antigen presentation, supporting this label.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042345","count":2},{"id":"GO:0051770","count":2},{"id":"GO:0050701","count":2},{"id":"GO:0002606","count":2},{"id":"GO:0051607","count":2}]},{"hash":"58601233206117848","title":"Neural development and synaptic signaling","description":"This cluster concentrates on cortical development, synaptic potentiation, and neural growth factor responses, with related signaling pathways (GTPase regulation, NFAT/JNK) and myelination context, suggesting a brain development and synaptic function theme.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":3},{"id":"GO:0051534","count":2},{"id":"GO:1900271","count":2},{"id":"GO:0007257","count":2},{"id":"GO:0021819","count":2}]},{"hash":"956670165860742084","title":"Calcium-Driven Signaling in Vascular and Immune Responses","description":"The cluster centers on signaling cascades triggered by stimuli, with calcium release into the cytosol repeatedly appearing as a key node, and includes endothelial/vascular processes, immune-related regulation, and inflammatory signaling (NF-kappaB), as well as sensory responses (thermoception, cold, pain) and endocytic activity. This suggests a theme of calcium-mediated signaling coordinating vascular, immune, and sensory responses, rather than a single highly specific function.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098907","count":5},{"id":"GO:0010745","count":5},{"id":"GO:0070682","count":4},{"id":"GO:0097497","count":4},{"id":"GO:0050955","count":4}]},{"hash":"49395829294614936","title":"Neuronal calcium signaling and secretion","description":"The top GO terms cluster around calcium import and release (calcium signaling), responses to stimuli (mechanical, cold), regulation of synaptic plasticity via receptor localization to synapse, and vasopressin secretion, all pointing to calcium-dependent neuronal signaling and neuropeptide release. Some terms are deprecated or less relevant, but the dominant theme is calcium-driven neuronal signaling and secretion.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":3},{"id":"GO:0098703","count":3},{"id":"GO:0009409","count":3},{"id":"GO:0051209","count":3},{"id":"GO:1900383","count":3}]},{"hash":"1085348556268480851","title":"Signaling and cell-cycle regulation","description":"Top GO terms point to broad signaling involvement (GPCR signaling pathway, kinase activity regulation, GTPase activity) along with cell-cycle processes (mitotic cell cycle) and various regulatory functions (autophosphorylation, mRNA transport, hypoxia response, ADP-ribosylation). The cluster appears to collect diverse signaling and regulatory roles rather than a single specific pathway, so a broad label like this is appropriate.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007205","count":5},{"id":"GO:0000278","count":4},{"id":"GO:0051028","count":4},{"id":"GO:0071456","count":4},{"id":"GO:0031954","count":4}]},{"hash":"1915887971960632057","title":"Cardiac function and stress-induced hypertrophy","description":"Top GO terms point to direct cardiac signals: regulation of heart rate and positive regulation of cardiac muscle hypertrophy in response to stress. These cardiac-focused terms are complemented by development-related terms and by general cellular processes (mitotic cell cycle, ribosome biogenesis, protein homooligomerization). The strongest, most specific theme is heart function and stress-induced hypertrophy, suggesting a cluster that centers on cardiac regulation with ancillary housekeeping processes.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0002027","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0008284","count":3},{"id":"GO:1903244","count":3},{"id":"GO:0000278","count":2}]},{"hash":"1023378176519333850","title":"Bacterial cell wall and envelope biosynthesis","description":"This cluster is enriched for GO terms related to biosynthesis of envelope components such as peptidoglycan and lipopolysaccharide, plus membrane lipids and related dephosphorylation processes. The presence of peptidoglycan and LPS biosynthesis signals a shared theme of cell envelope construction and remodeling, with supporting carbohydrate metabolism and membrane-associated activities. Some terms reference broader metabolic or secondary processes (antibiotic biosynthesis, stilbene catabolic process), but the envelope-focused terms provide the strongest, coherent thread.","confidence":"Medium","size":23,"edges":71,"triangles":69,"max_degree":18,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0005975","count":5},{"id":"GO:0017000","count":4},{"id":"GO:0009103","count":3},{"id":"GO:0016311","count":3},{"id":"GO:0046272","count":3}]},{"hash":"236811494758249686","title":"Neural and muscular development with synaptic maturation","description":"The top terms point to broad developmental processes across multiple tissues (myoblast fusion, heart development, Schwann cell development, multicellular organism development) and neural maturation (axonogenesis, long-term synaptic potentiation, excitatory postsynaptic potential), with regulation of apoptosis during development. This suggests a cohesive theme of neural and muscular differentiation and synaptic maturation within an embryonic/organismal development context, despite one plant-specific term appearing in the list. Confidence: Medium","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043065","count":11},{"id":"GO:0007520","count":11},{"id":"GO:0060291","count":11},{"id":"GO:0000278","count":11},{"id":"GO:0060079","count":11}]},{"hash":"332085453482793109","title":"Proteostasis and mitochondrial import during cell cycle","description":"This cluster centers on GO terms spanning mitochondrial intermembrane space protein import, proteasome assembly, chaperone-mediated assembly, protein oligomerization, and cell-cycle processes such as leading-strand elongation and centriole elongation, plus ubiquitin-proteasome\u2013related regulation. Taken together, the terms point to a theme of coordinating protein quality control and folding with mitochondrial targeting and cell-division machinery, rather than a single narrow process, hence a proteostasis-and-cell-cycle-focused label.","confidence":"Medium","size":23,"edges":25,"triangles":4,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0045041","count":6},{"id":"GO:0051301","count":6},{"id":"GO:0051131","count":6},{"id":"GO:0051260","count":5},{"id":"GO:0006272","count":4}]},{"hash":"1357206123131737900","title":"Plant cell wall biosynthesis and root hair development","description":"This cluster is dominated by GO terms related to plant cell wall formation and modification, such as cell wall organization, plant-type secondary cell wall biogenesis, and glucuronoxylan biosynthesis, plus root hair cell development. The presence of glycosylation-related terms (poly-N-acetyllactosamine biosynthesis, Lewis a epitope biosynthesis) suggests surface glycan modifications associated with cell wall\u2013related proteins. Together, these indicate a cohesive plant-specific theme centered on cell wall construction/remodeling and its role in root hair development, with a minor presence of unrelated terms that do not override the main signal.","confidence":"High","size":23,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":4},{"id":"GO:0080147","count":4},{"id":"GO:0010417","count":3},{"id":"GO:0009834","count":3},{"id":"GO:0005978","count":3}]},{"hash":"1418816909081500756","title":"Cell cycle with inflammatory and metabolic signaling","description":"The cluster prominently features cell division and cell cycle terms, but also includes inflammatory-related processes (IL-6 production, prostaglandin secretion) and metabolic/redox-associated terms (hydrogen sulfide biosynthesis, L-cysteine biosynthesis, xenobiotic response, demethylation). This suggests a broad functional grouping that links cell cycle regulation with metabolic signaling and inflammatory responses, rather than a single tightly defined pathway.","confidence":"Medium","size":23,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0007049","count":4},{"id":"GO:0070814","count":4},{"id":"GO:0019344","count":4},{"id":"GO:0055114","count":3}]},{"hash":"511713034767804541","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by GO terms for ribosome biogenesis and translation (ribosome biogenesis, translation, cytoplasmic translation, ribosomal subunit biogenesis, ribosomal large subunit export from nucleus, tRNA modification), indicating a core set of proteins involved in ribosome assembly and protein synthesis. The inclusion of cell division and septum assembly terms likely reflects growth coordination with ribosome production, reinforcing the theme of a translational machinery-focused cluster.","confidence":"High","size":23,"edges":95,"triangles":137,"max_degree":15,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":9},{"id":"GO:0006412","count":7},{"id":"GO:0051301","count":6},{"id":"GO:0042274","count":4},{"id":"GO:0000747","count":4}]},{"hash":"336343393629142455","title":"Neuroimmune Regulation of Synapses","description":"The terms show a blend of innate immune signaling (innate immune response, response to dsRNA, LPS signaling, interferon-beta production) with neural/synaptic processes (positive regulation of synapse assembly, trans-synaptic signaling, corpus callosum development, cell morphogenesis). This points to a cluster of proteins involved in neuroimmune interactions that modulate synapse formation and transmission, rather than a single isolated pathway. Ribosome biogenesis appears as a broader cellular process accompanying these functions.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051965","count":3},{"id":"GO:0022038","count":3},{"id":"GO:0045359","count":3},{"id":"GO:0043330","count":3},{"id":"GO:0045087","count":3}]},{"hash":"1589158032587341481","title":"Organelle trafficking and cytoskeletal dynamics","description":"This cluster centers on intracellular transport and organelle dynamics, highlighted by mitochondrial fission, endosome-to-lysosome trafficking, vacuole targeting, tubulin complex assembly, and phagophore localization, all tied together by small GTPase signaling. While it also includes cell division and signaling terms, the dominant pattern is cytoskeleton\u2011driven trafficking and organelle maintenance.","confidence":"High","size":23,"edges":4,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000266","count":10},{"id":"GO:0007264","count":10},{"id":"GO:0051301","count":10},{"id":"GO:1902824","count":9},{"id":"GO:1902307","count":9}]},{"hash":"388407915435581446","title":"Steroid, Prostaglandin, and Retinoid Metabolism","description":"This cluster is driven by biosynthetic and metabolic processes for lipid-derived signaling molecules: prostaglandins, androgens/testosterone, and retinoids (retinol/retinal). The presence of PI3K/AKT signaling regulation and smooth muscle proliferation terms suggests related hormonal or signaling roles, tying these metabolism pathways together. A few terms like fructose biosynthesis appear as noise, but the core theme remains steroid, prostaglandin, and retinoid metabolism.","confidence":"Medium","size":23,"edges":241,"triangles":1535,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":13},{"id":"GO:0042572","count":12},{"id":"GO:0046370","count":11},{"id":"GO:0001516","count":10},{"id":"GO:0042574","count":10}]},{"hash":"1912901547320355338","title":"Steroid Hormone and Cholesterol Metabolism","description":"The top GO terms cluster around steroid-related metabolism (progesterone, testosterone, androgen biosynthesis/metabolism), prostaglandin biosynthesis, and cholesterol-derived pathways (cholesterol catabolic, bile acid biosynthesis). This points to a lipid/steroid metabolism module. Redox/oxidative stress terms (response to hydrogen peroxide, methylglyoxal) are also present, suggesting oxidative context within this metabolic theme. Therefore, the label Steroid Hormone and Cholesterol Metabolism reflects the core functional connection of the cluster.","confidence":"Medium","size":23,"edges":10,"triangles":5,"max_degree":4,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0042448","count":4},{"id":"GO:0001516","count":4},{"id":"GO:0061370","count":4},{"id":"GO:0006699","count":4}]},{"hash":"1383486046558098718","title":"Cell Cycle Regulation and Stress Response","description":"This cluster centers on core growth and division processes (cell cycle, cell division) with links to ribosome biogenesis (ribosomal large subunit export from nucleus) and transcriptional control, alongside multiple stress-related responses (oxidative stress, amino acid starvation, salt stress). Together, these terms point to a module coordinating cell growth, division, and adaptive stress responses, justifying the label \"Cell Cycle Regulation and Stress Response.\"","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0000055","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0034599","count":2},{"id":"GO:0000122","count":2}]},{"hash":"507943959081926878","title":"Cardiac morphogenesis and conduction","description":"The top GO terms center on heart morphogenesis, ventricular cardiac muscle tissue morphogenesis, and cell communication by electrical coupling involved in cardiac conduction, indicating a cluster of proteins tied to heart development and cardiac electrical signaling. Some obsolete or metabolic terms appear, likely annotation noise, but the core theme remains cardiac development and conduction.","confidence":"High","size":23,"edges":23,"triangles":1,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0022417","count":3},{"id":"GO:0042208","count":3},{"id":"GO:0042619","count":3},{"id":"GO:1901710","count":2}]},{"hash":"1873582199641308720","title":"Plant cell wall biosynthesis and root hair development","description":"These proteins are enriched for GO terms tied to plant cell wall biosynthesis (rhamnogalacturonan II biosynthetic process; cell wall organization) and root hair development, indicating a module focused on cell wall construction and root hair formation in plants. A few low-count terms related to animal processes or circadian rhythms appear as potential noise, but the dominant signals align with plant cell wall biogenesis and root hair differentiation.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010306","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0080147","count":3},{"id":"GO:0060576","count":2},{"id":"GO:0043380","count":1}]},{"hash":"1497287595043621025","title":"Neural development and CSF ion transport","description":"The top GO terms converge on brain development and cerebrospinal fluid homeostasis: pyramidal neuron development, brain morphogenesis, cerebrospinal fluid secretion, and various ion (chloride, bicarbonate) and pH-regulating transport processes. This suggests a cluster of neural development proteins linked to CSF production/ion transport and neural function, with some behavioral association (locomotory exploration). Overall, a coherent theme around brain development coupled with CSF ion transport.","confidence":"Medium","size":23,"edges":19,"triangles":0,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":3},{"id":"GO:1902476","count":3},{"id":"GO:0021860","count":3},{"id":"GO:0035641","count":3},{"id":"GO:0015701","count":3}]},{"hash":"333577651664888688","title":"Chloroplast Photosynthesis and Light Response","description":"The top GO terms are dominated by photosynthesis-related processes, including photosynthesis itself, photosystem II assembly and repair, and cellular response to light intensity, which together point to chloroplast energy capture and light-driven functions as the central theme of this cluster. A few other terms appear at very low frequency (nitrate assimilation, mitochondrion inheritance, etc.), suggesting some noise or incidental associations, but the primary signal aligns with chloroplast photosynthetic activity.","confidence":"Medium","size":23,"edges":22,"triangles":0,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":2},{"id":"GO:0071484","count":1},{"id":"GO:0010207","count":1},{"id":"GO:0010206","count":1},{"id":"GO:0042128","count":1}]},{"hash":"1940481131466197015","title":"Post-transcriptional RNA processing and translation regulation","description":"The cluster is enriched for GO terms related to mRNA splicing (spliceosome, splice site recognition, mRNA processing/modification) and translation initiation/reinitiation, plus stress-related mRNA stability regulation. Together these point to proteins involved in post-transcriptional gene expression control, linking RNA maturation and translation initiation with stress-responsive regulation.","confidence":"High","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0001731","count":6},{"id":"GO:0002188","count":6},{"id":"GO:0010610","count":5},{"id":"GO:0000381","count":4},{"id":"GO:0006376","count":4}]},{"hash":"1558617873295765012","title":"Mitotic Regulation and Neural Development","description":"Based on top GO terms, the cluster shows strong signals for cell division, mitosis, APC-dependent catabolic processes, and microtubule-based movement, coupled with nervous system development and neuron projection morphogenesis. The presence of K11-linked ubiquitination indicates ubiquitin-mediated regulation common to both cell cycle control and neural remodeling. This combination suggests proteins involved in coordinating mitotic processes with neural development/morphogenesis.","confidence":"High","size":23,"edges":46,"triangles":39,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0045792","count":3},{"id":"GO:0070979","count":2},{"id":"GO:0048692","count":2}]},{"hash":"1840701736367819962","title":"Ubiquitin-dependent protein degradation (ERAD)","description":"The top GO terms cluster around ubiquitin-mediated proteolysis and ER-associated degradation (e.g., ubiquitin-dependent ERAD, ubiquitin-dependent protein catabolic process, and K6-linked ubiquitination), with autoubiquitination and related degradation processes also present. Some terms are peripheral, but the dominant theme is ubiquitin-driven protein turnover, including connection to broader signaling like NF-kappaB via ubiquitination pathways. ","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030433","count":8},{"id":"GO:0042787","count":6},{"id":"GO:0051865","count":6},{"id":"GO:0036205","count":4},{"id":"GO:0009048","count":4}]},{"hash":"109552440100597342","title":"Unknown","description":"The terms mix vertebrate developmental processes (embryonic pectoral fin morphogenesis, endoderm development, BMP signaling, embryonic skeletal joint development) with plant-specific biosynthetic processes (glucuronoxylan, arabinan, xylogalacturonan, plant-type secondary cell wall biosynthesis) and signaling. Because there is no single cohesive function linking all terms across kingdoms, a consistent cluster label cannot be inferred from the GO profile.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"wound healing","top_go_terms":[{"id":"GO:0035118","count":7},{"id":"GO:0010417","count":7},{"id":"GO:0009863","count":7},{"id":"GO:0035884","count":7},{"id":"GO:0008101","count":7}]},{"hash":"2070255774747761227","title":"Epithelial Actin Cytoskeleton Remodeling","description":"The top GO terms cluster around actin dynamics (filament severing, nucleation, capping, and depolymerization) and epithelial-specific processes (terminal web assembly, intestinal glucose absorption, and response to growth factors), indicating coordinated actin remodeling in epithelial cells, with a reasonable link to related growth and adhesion processes.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051014","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0045010","count":1},{"id":"GO:1900025","count":1},{"id":"GO:1901731","count":1}]},{"hash":"363603305807760548","title":"Phosphatase-driven signaling and cytoskeletal dynamics","description":"This cluster is dominated by GO terms tied to dephosphorylation and kinase regulation (protein dephosphorylation, negative regulation of protein kinase activity), alongside phosphatidylinositol and calcium\u2013calcineurin signaling, all of which converge on controlling cytoskeletal organization, cell shape, cytokinesis, and apoptotic outcomes. The combination suggests a coherent theme of phosphorylation-state\u2013dependent signaling pathways that regulate cell morphology and division, with a possible developmental role indicated by the ureteric bud term. The presence of calcium/NFAT signaling further supports a central role for calcium-dependent signaling in coordinating these processes. Overall, the label captures the core functional axis of signaling and cytoskeletal control, with a potential developmental angle.","confidence":"Medium","size":23,"edges":87,"triangles":138,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006469","count":11},{"id":"GO:0008360","count":10},{"id":"GO:0006470","count":10},{"id":"GO:0043065","count":10},{"id":"GO:0035502","count":10}]},{"hash":"1841841914494693012","title":"Development and Protein Quality Control","description":"The dominant terms are multicellular organism development and cell differentiation, suggesting developmental roles; accompanying terms include protein polyubiquitination and ERAD (protein quality control/turnover), ER-to-Golgi transport (protein trafficking), and translation initiation. These together point to a cluster of proteins involved in developmental regulation coupled with cellular protein processing and trafficking.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0030154","count":2},{"id":"GO:0001731","count":1},{"id":"GO:2000601","count":1}]},{"hash":"50775534816596868","title":"Unknown","description":"This cluster shows a mix of translation-related terms (formation of translation preinitiation complex, translation reinitiation), microtubule dynamics (severing, movement), transcription, cell division, and sporulation/development terms, with no unifying process. The absence of edges and the diverse GO terms suggest functionally heterogeneous proteins rather than a coherent protein function module.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0051013","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0007018","count":2}]},{"hash":"1779934743857452741","title":"Transcriptional regulation and chromatin modification","description":"This cluster is enriched for DNA-templated transcription and histone-related modification terms, suggesting a core of transcriptional control and chromatin remodeling. Additional signals for muscle differentiation, vasculogenesis, and Notch signaling modulation point to roles in developmental gene regulation, even though some terms are obsolete. Overall, the common theme is transcriptional regulation with chromatin context in differentiation processes.","confidence":"Medium","size":23,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0042264","count":5},{"id":"GO:0042265","count":5},{"id":"GO:0045663","count":5},{"id":"GO:0070544","count":5}]},{"hash":"443725642232716746","title":"Vesicle trafficking and vacuole fusion regulation","description":"The terms cluster around intracellular vesicle trafficking, including vesicle tethering, non-autophagic vacuole fusion, SNARE complex regulation, and endosome-to-lysosome transport, with supporting processes like endocytic recycling, actin dynamics, and calcium signaling\u2014indicating a cohesive vesicle trafficking/fusion module.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0099022","count":2},{"id":"GO:0042144","count":2},{"id":"GO:0035542","count":2},{"id":"GO:0032889","count":2},{"id":"GO:0035556","count":2}]},{"hash":"7637383685011861","title":"ERK/MAPK Signaling and Transcription Regulation","description":"The top GO terms center on the ERK1/ERK2 cascade and negative regulation of transcription by RNA polymerase II, suggesting a functional theme where MAPK signaling modulates transcriptional activity. Some other terms hint at broader signaling roles (e.g., membrane proteolysis regulation, hormone secretion), but the core connection remains signaling via ERK/MAPK influencing transcription.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0051044","count":2},{"id":"GO:0070371","count":2},{"id":"GO:0033697","count":1},{"id":"GO:0036091","count":1}]},{"hash":"1074221011447996366","title":"RNA processing and modification","description":"Most top GO terms center on RNA biology (tRNA wobble uridine modification, tRNA methylation, 7-methylguanosine mRNA capping, ribosomal small subunit export), indicating a cluster tied to RNA maturation and translation readiness. While some terms relate to methylation of proteins and metabolite biosynthesis, the dominant theme is RNA processing/modification, supporting this label.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:0019919","count":2},{"id":"GO:0009102","count":2},{"id":"GO:0002098","count":2},{"id":"GO:0016049","count":2}]},{"hash":"1982300366952816163","title":"Bacterial cell wall synthesis and division","description":"The top terms cluster around peptidoglycan biosynthesis and turnover, cell wall organization, and processes related to cell division and cell shape, suggesting the proteins function together in bacterial cell growth and cell wall remodeling. Some terms (e.g., mRNA splicing, cellulose catabolic process, cobalamin biosynthesis) are less coherent with this theme, but the dominant signal points to bacterial cell wall synthesis and division.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0051301","count":1},{"id":"GO:0008360","count":1},{"id":"GO:0030245","count":1},{"id":"GO:0009252","count":1}]},{"hash":"300621862466043486","title":"Plant Cell Wall Biosynthesis and Root Hair Development","description":"The dominant GO terms point to plant-specific processes: cell wall organization, UDP-D-xylose metabolism, and RG-II biosynthesis, all tied to cell wall construction, plus root hair cell development. A few terms related to axon/cilia may be incidental annotations, but they do not outweigh the plant cell wall/root hair theme.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":3},{"id":"GO:0033319","count":2},{"id":"GO:0010306","count":2},{"id":"GO:0080147","count":2},{"id":"GO:0006508","count":1}]},{"hash":"476106403181362530","title":"Epithelial glycosylation and cell-surface adhesion","description":"The set emphasizes glycan biosynthesis (poly-N-acetyllactosamine, Lewis A, O-linked glycosylation) together with terms about follicle epithelium polarity and adhesion, insect eye-development structures, and plant cell-wall glycoproteins (arabinogalactan proteins, seed coat mucilage). This points to a common theme of glycan-modified cell-surface components shaping epithelial cell interactions and polarity.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007299","count":4},{"id":"GO:0075015","count":4},{"id":"GO:0001744","count":4},{"id":"GO:0042248","count":4},{"id":"GO:0030311","count":3}]},{"hash":"1333956725545160710","title":"Mitochondrial Translation and Cristae Formation","description":"This cluster is dominated by GO terms tied to mitochondria: translation and especially positive regulation of mitochondrial translation, assembly of the respiratory chain (complex I), and cristae formation, along with protein insertion into the mitochondrial membrane. These indicate a coherent function related to mitochondrial gene expression and organelle biogenesis/structure, with accompanying ion homeostasis terms that are commonly associated with mitochondrial membranes. Therefore, the label captures the core theme of mitochondrial translation and membrane/CRISSA formation activities.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902476","count":2},{"id":"GO:0032981","count":1},{"id":"GO:0019918","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0030007","count":1}]},{"hash":"1973782558052681560","title":"Cardiac ion transport and action potential regulation","description":"The cluster is dominated by GO terms related to potassium and sodium ion transport across the plasma membrane, intracellular potassium homeostasis, and regulation of cardiac action potentials (AV node and ventricular). These points together strongly indicate a cohesive theme of cardiac electrophysiology and ion handling, with a few ancillary terms (e.g., cGMP signaling, hypoxia detection) that are less central to the core function. ","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097623","count":4},{"id":"GO:0098719","count":4},{"id":"GO:0010754","count":3},{"id":"GO:0071321","count":3},{"id":"GO:0051260","count":3}]},{"hash":"2104208357360299114","title":"Phosphatase-Driven Signaling Suppression","description":"This cluster centers on dephosphorylation (peptidyl-tyrosine and peptidyl-threonine) and negative regulation of signaling pathways (T cell receptor signaling, ERK/MAPK cascade), with related effects on apoptosis and immune signaling; the mix suggests phosphatase-mediated downregulation of signaling in immune and cellular processes, despite some cell division and RNA processing terms that are less central. ","confidence":"High","size":22,"edges":144,"triangles":475,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0035335","count":18},{"id":"GO:0050860","count":14},{"id":"GO:0070373","count":14},{"id":"GO:0000200","count":14},{"id":"GO:0006370","count":13}]},{"hash":"313166906968164781","title":"N-terminal acetylation cluster","description":"Top GO terms are dominated by N-terminal acetylation and related modifications (N-terminal methionine/glutamate/lysine acetylation, propionylation, spermidine acetylation), indicating a cohesive theme of post-translational acetylation. Other processes like angiogenesis and melatonin biosynthesis appear but are less central to the core function.","confidence":"High","size":22,"edges":8,"triangles":1,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001525","count":14},{"id":"GO:0061606","count":13},{"id":"GO:0030187","count":13},{"id":"GO:0017196","count":13},{"id":"GO:0018003","count":13}]},{"hash":"508946801659887015","title":"Transcription and Neuronal Morphogenesis","description":"The top GO terms cluster around DNA-templated transcription, dendrite morphogenesis, and potassium ion transport, with several neuronal and signaling-related terms (e.g., response to cocaine, cellular response to arsenite, PI3K activity regulation, nucleus translocation). This suggests a coherent theme where transcriptional regulation interfaces with neuronal development and signaling functions, rather than a purely metabolic or structural set. Confidence: Medium","confidence":"","size":22,"edges":224,"triangles":1407,"max_degree":21,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":22},{"id":"GO:0006935","count":21},{"id":"GO:0048813","count":21},{"id":"GO:0006813","count":21},{"id":"GO:0043552","count":21}]},{"hash":"1930801338296843770","title":"Biosynthesis and Methylation Enzymes","description":"The terms span several biosynthetic processes (antibiotic, biotin, cobalamin, chlorophyll biosynthesis) and several methylation/modification processes (peptidyl-arginine methylation, N-terminal glycine methylation, tRNA wobble modification). This suggests a cluster of enzymes involved in producing biomolecules and in various modifications, rather than a single specific pathway. Therefore, the label reflects both biosynthetic capacity and modification activity.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":2},{"id":"GO:0002098","count":1},{"id":"GO:0019919","count":1},{"id":"GO:1901052","count":1},{"id":"GO:0009102","count":1}]},{"hash":"967005885802151422","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":138,"triangles":485,"max_degree":18,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042273","count":5},{"id":"GO:0006369","count":5},{"id":"GO:0006412","count":5},{"id":"GO:0006605","count":4},{"id":"GO:0019079","count":4}]},{"hash":"801832411014665658","title":"Glycan biosynthesis and epithelial polarity in development","description":"The top GO terms cluster around glycosylation processes (poly-N-acetyllactosamine biosynthesis, Lewis a epitope biosynthesis, O-linked glycosylation) and maintenance of epithelial polarity and adhesion ( follicle epithelium polarity, egg chamber adhesion, root hair-like development references). This points to a theme where glycan modifications influence cell\u2013cell/matrix interactions and polarity during developmental epithelia formation. Some plant-specific terms appear, but the recurring signal is glycosylation-linked regulation of epithelial development.","confidence":"High","size":22,"edges":46,"triangles":13,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0080147","count":5},{"id":"GO:0007299","count":4},{"id":"GO:0075015","count":4},{"id":"GO:0001744","count":4},{"id":"GO:0042248","count":4}]},{"hash":"290618947193604502","title":"Central metabolism and metal ion response","description":"Based on the top GO terms, the cluster centers on core metabolic pathways (glycolysis, fructose metabolism, PPP shunt) and cobalt/cobalamin-related processes (cobalamin biosynthesis, cellular response to cobalt ion). Additional terms related to autophagy and xenobiotic response suggest general stress adaptation that can accompany metabolic shifts. With no observed edges, the connection is not tightly cohesive, but the dominant signal is metabolic processing linked to metal ion/cofactor biology, justifying the label. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0009236","count":5},{"id":"GO:0007585","count":4},{"id":"GO:0006000","count":4},{"id":"GO:0006096","count":4},{"id":"GO:0016311","count":4}]},{"hash":"1876386147374833850","title":"Potassium Homeostasis and Membrane Potential Regulation","description":"The cluster is dominated by GO terms related to potassium ion homeostasis and membrane potential control (intracellular potassium homeostasis, potassium ion transmembrane transport, stabilization and regulation of membrane potential, and membrane repolarization in cardiac tissue), pointing to proteins involved in maintaining cellular excitability. While sensory perception (touch and pain) and development appear among the top terms, their presence is secondary to the core theme of ionic balance and electrical membrane properties.","confidence":"High","size":22,"edges":82,"triangles":106,"max_degree":20,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050976","count":16},{"id":"GO:0030007","count":16},{"id":"GO:0098914","count":16},{"id":"GO:0060075","count":16},{"id":"GO:0071805","count":16}]},{"hash":"315726315589433257","title":"Central carbon metabolism and cofactor biosynthesis","description":"The cluster shows strong representation of core metabolic pathways (glycolysis, gluconeogenesis, and the TCA cycle) along with biosynthetic processes for cofactors such as biotin and porphyrin derivatives, and fatty acid biosynthesis. This pattern points to a cohesive metabolism-focused module centered on energy production and precursor synthesis. Occasional lysine-related annotations are present but do not override the dominant energy/biomolecule-assembly themes. ","confidence":"High","size":22,"edges":192,"triangles":1036,"max_degree":21,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0033512","count":8},{"id":"GO:0006094","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0006107","count":5},{"id":"GO:0006099","count":5}]},{"hash":"392674970700207881","title":"Vitamin Cofactor Metabolism and Xenobiotic Response","description":"Based on the top GO terms, the cluster is enriched for vitamin cofactor metabolism (thiamine biosynthesis; tetrahydrofolate metabolism) and for cellular stress/detoxification responses (redox homeostasis, response to xenobiotics, ethanol, LPS, and metal ions). The combination suggests a functional module where vitamin metabolism interfaces with redox balance and detox pathways, rather than a single dedicated biological process.","confidence":"Medium","size":22,"edges":167,"triangles":648,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0009228","count":10},{"id":"GO:0043046","count":10},{"id":"GO:0045454","count":10},{"id":"GO:0046653","count":10},{"id":"GO:0042493","count":9}]},{"hash":"1677281133341765306","title":"Growth and Cytoskeleton Remodeling with Trafficking","description":"This cluster is dominated by terms related to growth (multicellular organism growth), cytoskeletal dynamics (positive regulation of Arp2/3 actin nucleation and GTPase activity), and intracellular trafficking (ER to Golgi transport) along with protein modification (ubiquitination) and translation initiation, suggesting a cohesive theme around growth signaling, cytoskeleton remodeling, and vesicular trafficking; some methylation terms are obsolete, but the core signals point to these interconnected processes.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0035264","count":5},{"id":"GO:0050830","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0001731","count":4},{"id":"GO:2000601","count":4}]},{"hash":"874730460481686871","title":"Telomere maintenance and shelterin assembly","description":"The top GO terms strongly point to telomere biology, including telomeric loop formation, positive regulation of shelterin complex assembly, and G-quadruplex DNA formation, with other telomere-related processes and protein localization aspects. Some terms seem unrelated (bone ossification, ethylene response), but the core signal centers on telomere maintenance and genome stability, justifying a telomere-focused label.","confidence":"Medium","size":22,"edges":21,"triangles":0,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0043931","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0021762","count":2},{"id":"GO:0031087","count":2}]},{"hash":"2267433770761122517","title":"Amino acid catabolism and central metabolism","description":"The cluster focuses on amino acid degradation (lysine, kynurenine, alanine) feeding core energy pathways such as gluconeogenesis, glycolysis, and the TCA cycle, indicating a theme of amino-acid\u2013driven central metabolism. Notch signaling and antibiotic biosynthesis appear less central, possibly as shared or incidental associations.","confidence":"Medium","size":22,"edges":228,"triangles":1481,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0033512","count":6},{"id":"GO:0006094","count":6},{"id":"GO:0006086","count":5},{"id":"GO:0006099","count":5},{"id":"GO:0097053","count":4}]},{"hash":"2116375767412804897","title":"Skin and hippocampus development with protein trafficking","description":"This cluster includes GO terms for skin development and keratinocyte differentiation, alongside hippocampus development, indicating tissue-specific developmental processes. The presence of protein targeting, Golgi localization, and regulation of protein phosphorylation/trafficking terms suggests these proteins also share roles in intracellular transport and signaling essential for development. The combination of epidermal/neural development signals with trafficking-related terms supports a label capturing both tissue contexts and the cellular mechanisms involved.","confidence":"Medium","size":22,"edges":45,"triangles":37,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0021766","count":3},{"id":"GO:0071901","count":3},{"id":"GO:0006605","count":3},{"id":"GO:0051683","count":3},{"id":"GO:1902309","count":3}]},{"hash":"1497004195159891643","title":"Ubiquitin-Dependent Proteolysis & ERAD","description":"The top GO terms indicate a strong focus on ubiquitin-mediated protein degradation, including autoubiquitination and K48/K6 linkages, ERAD pathways, and related peroxisomal import processes, pointing to a cluster of proteins involved in ubiquitin-dependent quality control and turnover.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":12},{"id":"GO:0051865","count":11},{"id":"GO:0030433","count":10},{"id":"GO:2000620","count":10},{"id":"GO:0070512","count":10}]},{"hash":"2088846678354646555","title":"Neuronal actin remodeling and spine formation","description":"Top terms center on actin cytoskeleton organization and dendritic spine morphogenesis, indicating roles in neuronal structural changes and synapse formation. Additional terms related to membrane targeting and trafficking align with spine remodeling processes, while splicing regulation hints at neuron-specific transcript regulation. Some terms (sound perception, DNA replication) are less directly connected, but the dominant theme is neuronal actin-driven remodeling.","confidence":"Medium","size":22,"edges":4,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070389","count":4},{"id":"GO:0060997","count":4},{"id":"GO:0030036","count":4},{"id":"GO:0000380","count":3},{"id":"GO:0000381","count":3}]},{"hash":"1313088761133767053","title":"Developmental Processes","description":"The proteins are associated with multiple development- and differentiation-related GO terms (leaf development, multicellular organism development, inner cell mass proliferation, osteoblast differentiation, fat cell differentiation), with additional signals pointing to growth and cell division (mitotic spindle elongation) and translation-related processes (regulation of translational fidelity, tRNA modification). Taken together, the shared theme appears to be developmental biology and growth, rather than a single, tightly defined pathway, justifying the Developmental Processes label.","confidence":"Medium","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006450","count":1},{"id":"GO:0046944","count":1},{"id":"GO:0002949","count":1},{"id":"GO:0048366","count":1},{"id":"GO:0000022","count":1}]},{"hash":"567811512980837297","title":"Innate immune sensing and antigen presentation","description":"The GO terms cluster around detection of LPS, cytokine production (IL-1), regulation of dendritic cell antigen processing and presentation, and NF-kappaB signaling, all hallmark processes of innate immune activation and downstream antigen presentation. Autophagy regulation also aligns with immune processing. While a few terms touch neural or obsolete processes, the dominant theme is innate immune sensing leading to inflammatory signaling and antigen presentation.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032497","count":1},{"id":"GO:0071260","count":1},{"id":"GO:0060007","count":1},{"id":"GO:0019800","count":1},{"id":"GO:0042345","count":1}]},{"hash":"1253056083885287932","title":"Nutrient and Ion Transmembrane Transport","description":"The cluster is dominated by GO terms describing transport across membranes for a variety of substrates (nitrate, galactose, phosphate ions, sodium ions, fucose, 4-hydroxyphenylacetate) and even neurotransmitter loading into synaptic vesicles, indicating a cohesive role in transmembrane and vesicular transport. Some terms like obsolete antibiotic transport seem noisy, but the overall pattern points to diverse transport functions rather than a single metabolism or signaling pathway. The absence of edges or triangles suggests relationships are functional, not interaction-based in this dataset.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046726","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0015757","count":2},{"id":"GO:0098700","count":2},{"id":"GO:0015706","count":2}]},{"hash":"998709442026619167","title":"Sensory signaling and mechanotransduction in development","description":"The top GO terms center on sensory perception (pain, touch) and signaling processes (cGMP/cAMP, calcium release), along with mechanosensory detection and ion transport, suggesting a cluster tied to sensory signaling and mechanotransduction in a developmental context. Some terms are broad (development) but the dominant theme is sensory signaling and mechanotransduction.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":7},{"id":"GO:0019233","count":6},{"id":"GO:0010754","count":5},{"id":"GO:0051262","count":5},{"id":"GO:0009454","count":5}]},{"hash":"1503224608439423094","title":"Endosome-to-vacuole transport and autophagy","description":"The cluster shows strong enrichment for endosomal trafficking (early to late endosome transport, endocytic recycling) and targeting to the vacuole via the Cvt pathway, along with autophagy-related processes (autophagy of peroxisome, vacuole fusion), indicating a cohesive module focused on endosome maturation and autophagic/vacuolar degradation. Some terms like Wnt signaling or transcriptional regulation appear less connected to this core theme and may reflect noise or secondary associations.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:1990126","count":2},{"id":"GO:0045022","count":2},{"id":"GO:0032258","count":2},{"id":"GO:1903071","count":2}]},{"hash":"490116534481603477","title":"Unknown","description":"The Top Terms span immune signaling (GM-CSF response), neuronal signaling (glutamatergic transmission and short-term memory), sensory perception (visual light detection), development-related cytoskeleton polarity, metabolism (propylene), ethanol response, and mitochondrial energy pathways, with no single dominant function or interaction pattern. The cluster has no edges linking proteins, so there is no cohesive biological theme to name more specifically than Unknown.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097011","count":2},{"id":"GO:0051967","count":1},{"id":"GO:0007196","count":1},{"id":"GO:0018964","count":1},{"id":"GO:0050908","count":1}]},{"hash":"538181658870001627","title":"Epigenetic DNA Methylation and Heterochromatin Formation","description":"This cluster is dominated by GO terms linking DNA methylation to heterochromatin establishment and epigenetic control of gene expression, suggesting methylation-based regulation as the common theme. A few terms are obsolete or prokaryotic-related (restriction-modification), but the prevailing signal centers on methylation-driven chromatin states in eukaryotes.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090116","count":1},{"id":"GO:0006346","count":1},{"id":"GO:0009307","count":1},{"id":"GO:0043045","count":1},{"id":"GO:0010425","count":1}]},{"hash":"1782886925519161073","title":"Protein folding, assembly, and secretory trafficking","description":"This cluster is enriched for protein assembly (protein homooligomerization), folding (protein unfolding), and trafficking through the secretory pathway (ER to Golgi transport) plus import into peroxisomes and related quality-control processes (SCF complex dynamics). These collectively suggest a theme of protein maturation and trafficking, though a few terms (nitrogen fixation, leading strand elongation) seem unrelated noise.","confidence":"Medium","size":21,"edges":66,"triangles":87,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051260","count":9},{"id":"GO:0009405","count":8},{"id":"GO:0009399","count":5},{"id":"GO:0051968","count":5},{"id":"GO:0006272","count":4}]},{"hash":"805652314728203957","title":"Mitotic cell cycle control and transcription","description":"The panel is dominated by terms related to DNA-templated transcription and key cell cycle transitions (G1/S, G2/M), plus mitotic regulation (spindle pole separation) and epithelial cell proliferation, especially in the mammary gland. An ER unfolded protein response and insulin signaling linkage suggest stress and metabolic modulation accompanying proliferation, but the core theme is coordinated transcriptional control of cell-cycle progression in proliferating epithelial cells. ","confidence":"High","size":21,"edges":46,"triangles":30,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":10},{"id":"GO:0051301","count":10},{"id":"GO:0030968","count":9},{"id":"GO:0033598","count":9},{"id":"GO:0000086","count":9}]},{"hash":"1739231547090128755","title":"Cellular stress responses and trafficking","description":"The top GO terms point to stress-related cellular adaptation (xenobiotic response, ethanol response, and stress-induced cardiac hypertrophy) and intracellular protein movement (ER to Golgi transport), suggesting a cluster centered on how cells respond to stress while managing protein trafficking. A few terms like DNA recombination and aging appear less central, but the core theme ties to stress response and vesicle transport mechanisms.","confidence":"Medium","size":21,"edges":13,"triangles":7,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0043029","count":2},{"id":"GO:1903244","count":2},{"id":"GO:0042493","count":1},{"id":"GO:0043066","count":1}]},{"hash":"2277567823833336783","title":"Unknown","description":"The top GO terms span lipid metabolism, RNA modification, amino acid catabolism, and neuronal development with no coherent shared function, and there are no edges linking the proteins. This lack of a unifying theme justifies labeling the cluster Unknown with no confidence. ","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006633","count":3},{"id":"GO:0035336","count":3},{"id":"GO:0031119","count":2},{"id":"GO:0000455","count":2}]},{"hash":"41479966720094554","title":"Genome maintenance and RNA quality control","description":"The top GO terms cluster around core genome maintenance activities: DNA replication, unwinding, recombination, and repair (including SOS response and SDSA). In addition, several RNA quality-control processes are present (nonsense-mediated decay, nuclear mRNA surveillance, rRNA catabolic processes) and there is some protein oligomerization. Taken together, these terms point to a functional module centered on preserving genomic integrity and ensuring RNA quality, hence the label Genome maintenance and RNA quality control.","confidence":"High","size":21,"edges":154,"triangles":580,"max_degree":20,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":9},{"id":"GO:0006268","count":8},{"id":"GO:0009432","count":7},{"id":"GO:0006310","count":7},{"id":"GO:0045003","count":6}]},{"hash":"298359946641503417","title":"Epigenetic methylation and chromatin regulation","description":"The cluster\u2019s top GO terms are dominated by various methylation processes (DNA, rRNA, tRNA, histone, peptidyl-arginine methylation) and linked transcriptional regulation, plus growth/senescence processes. This suggests a cohesive theme around methylation-based epigenetic regulation and chromatin state control.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043046","count":2},{"id":"GO:0019919","count":2},{"id":"GO:0070476","count":2},{"id":"GO:0090398","count":2},{"id":"GO:0016049","count":2}]},{"hash":"197103593232585109","title":"GPCR Signaling and Vesicle Exocytosis","description":"The terms cluster around receptor-mediated signaling (GPCR internalization, thrombin-activated receptor signaling), cytoskeletal regulation (Rho signaling, filopodium assembly), and secretion/exocytosis (dense core granule exocytosis, synaptic vesicle priming), with supportive immune and metabolic signaling (IL-18, insulin signaling, B cell homeostasis). This points to a common theme of signal transduction that governs vesicle trafficking and release across cell types.","confidence":"Medium","size":21,"edges":24,"triangles":0,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":4},{"id":"GO:0051489","count":3},{"id":"GO:0070493","count":3},{"id":"GO:0032094","count":2},{"id":"GO:0035655","count":2}]},{"hash":"1348622748899052498","title":"Transcription Regulation and Histone Modification","description":"This cluster is driven by GO terms for DNA-templated transcription and histone H3-K4 demethylation, indicating a core theme of transcription control via chromatin modification. The presence of multiple protein hydroxylation terms suggests associated post-translational modifications that can modulate transcription or differentiation, with notes of myoblast differentiation and vasculogenesis pointing to developmental regulation. Taken together, the proteins likely function in controlling gene expression through chromatin state and related modifications.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0006351","count":6},{"id":"GO:0034720","count":5},{"id":"GO:0045663","count":4},{"id":"GO:0042264","count":4}]},{"hash":"1938291846577024342","title":"Nematode cuticle formation and collagen modification","description":"The top GO terms point to nematode molting and cuticle assembly, including the molting cycle and collagen/cuticulin-based cuticle, with prolyl hydroxylation linked to collagen modification. Some biosynthetic terms for glycosphingolipids (globoside, mannosyl-inositol phosphorylceramide) may relate to membrane components during cuticle formation, though several terms are obsolete or less directly connected. Overall, the shared theme appears to be nematode cuticle biosynthesis and collagen post-translational modification, with ancillary lipid biosynthesis terms. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036210","count":3},{"id":"GO:0051999","count":3},{"id":"GO:0001576","count":3},{"id":"GO:0018996","count":2},{"id":"GO:0018401","count":2}]},{"hash":"98928601032066446","title":"Biosynthesis and Modification Processes","description":"The top GO terms cluster around biosynthetic activities (cobalamin, carnitine, antibiotic biosynthesis) and biochemical modifications (tRNA wobble uridine modification, methylation, peptidyl-prolyl isomerization, tyrosine phosphorylation). While other terms (innate immune response, mitotic cell cycle) appear, the common thread is enzymes involved in constructing or altering biomolecules, justifying a broad label focused on biosynthesis and modification.","confidence":"Medium","size":21,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002098","count":2},{"id":"GO:0018108","count":2},{"id":"GO:0032259","count":2},{"id":"GO:0009236","count":2},{"id":"GO:0055114","count":2}]},{"hash":"51122983515976098","title":"Epidermal differentiation and growth signaling","description":"The dominant GO term is keratinocyte differentiation, complemented by multiple growth-regulatory pathways (Wnt, Hippo, TGF-\u03b2 signaling) and processes like cell cycle, apoptosis, and JNK cascade regulation. This points to a cluster centered on epidermal differentiation with interconnected growth-control and stress-response signaling, rather than a single pathway. The other terms fit into this broader theme, even if not exclusively epidermal. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0030216","count":8},{"id":"GO:0006915","count":8},{"id":"GO:0090263","count":8},{"id":"GO:0035329","count":8},{"id":"GO:0060044","count":8}]},{"hash":"1995778311927364692","title":"Developmental Regulation and Morphogenesis","description":"This cluster centers on GO terms related to development and tissue morphogenesis, including embryonic body morphogenesis, mesenchymal proliferation in organ development, neuron differentiation, cardiac action potential regulation, and oocyte localization; it also includes related cellular architecture processes such as desmosome assembly and vacuole inheritance/fusion, as well as cell cycle regulation and apoptosis. The common thread is broad developmental programs and maintenance of cell-cell junctions and organogenesis, rather than a single specific function.","confidence":"Medium","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0007050","count":13},{"id":"GO:1904948","count":12},{"id":"GO:0098911","count":12},{"id":"GO:0030720","count":12},{"id":"GO:0060916","count":12}]},{"hash":"1065022626290540326","title":"Ribosome Translation Initiation and Quality Control","description":"The top terms cluster around translation initiation, formation of initiation complexes, and ribosome-associated quality control (rescue and ubiquitin-mediated degradation), indicating a shared focus on ribosome function and translational regulation. Some terms about glial development appear as potential outliers, but the dominant signal supports ribosome-related processes.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072344","count":1},{"id":"GO:1990116","count":1},{"id":"GO:1905618","count":1},{"id":"GO:0045947","count":1},{"id":"GO:0014003","count":1}]},{"hash":"725572372163336421","title":"Unknown","description":"The top GO terms cover disparate processes (B cell homeostasis, ERAD, septin ring assembly, histone catabolism, peroxisome import, dosage compensation, etc.) with no clear shared function, suggesting this cluster is a heterogeneous mix rather than a single pathway.","confidence":"","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001782","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0000921","count":1},{"id":"GO:0036205","count":1},{"id":"GO:0046597","count":1}]},{"hash":"871701568430216202","title":"Protein and polyamine acetylation","description":"The top GO terms are dominated by various acetylation events (N-terminal and peptidyl acetylation, peptidyl-lysine acetylation, spermidine/putrescine acetylation) and related metabolic processes, suggesting the cluster centers on acetylation-modifying pathways and their metabolic connections, with melatonin biosynthesis and angiogenesis as downstream associations via acetyltransferase activity.","confidence":"High","size":21,"edges":31,"triangles":13,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0061606","count":8},{"id":"GO:0030187","count":8},{"id":"GO:0017196","count":8},{"id":"GO:0001525","count":8},{"id":"GO:0018003","count":8}]},{"hash":"772143867919862011","title":"Calcium signaling in stress and development","description":"The cluster shows a clear imprint of calcium-related processes: calcium import across the plasma membrane, regulation of ryanodine receptor\u2013mediated calcium release, and responses linked to TRP channel\u2013associated stimuli (cold, capsazepine). Cardiac stress\u2013related growth signaling and vasopressin secretion further point to Ca2+-dependent signaling pathways, while development terms suggest calcium\u2019s role in morphogenesis. Some terms (like general cell cycle) are broader but do not override the dominant calcium-centric theme.","confidence":"Medium","size":21,"edges":4,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1903244","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0098703","count":3},{"id":"GO:0009409","count":3},{"id":"GO:0035502","count":3}]},{"hash":"531974440119732845","title":"Large subunit ribosome biogenesis and rRNA processing","description":"This cluster is driven by ribosome biogenesis signals: multiple terms point to large subunit assembly/export and rRNA maturation (LSU rRNA, 5.8S rRNA, preribosome maturation), suggesting a cohesive theme around large ribosomal subunit biogenesis. A few outlier terms (lipopolysaccharide biosynthesis, stem cell maintenance, histone exchange) may reflect annotation noise rather than true functional clustering.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0000027","count":1},{"id":"GO:0000463","count":1},{"id":"GO:0000466","count":1}]},{"hash":"977662917095861839","title":"RNA processing and ribosome biogenesis","description":"The terms show a clear emphasis on RNA maturation and processing (spliceosome assembly, mRNA splicing, 5S rRNA maturation), which together point to RNA processing and ribosome assembly. Other terms related to protein folding and stress responses are present but less prominent, so the core theme remains RNA processing and ribosome biogenesis.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010588","count":1},{"id":"GO:0000387","count":1},{"id":"GO:0045585","count":1},{"id":"GO:0045292","count":1},{"id":"GO:0000481","count":1}]},{"hash":"417422092291712985","title":"Neural development and receptor signaling","description":"The Top Terms include FGFR/VEGFR signaling, serine/threonine kinase signaling, trans-synaptic signaling, and retinal axon guidance, all tied to neural development and synaptic modulation. While a single term touches on immune differentiation, the dominant pattern is receptor-mediated signaling in neural development and synaptic function. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070926","count":1},{"id":"GO:0042523","count":1},{"id":"GO:0035607","count":1},{"id":"GO:0002651","count":1},{"id":"GO:0099557","count":1}]},{"hash":"575935135498478799","title":"Fe-S cluster biogenesis and maturation","description":"The top GO terms are dominated by iron-sulfur (Fe-S) cluster biology, including [2Fe-2S] cluster assembly and maturation via Fe-S cluster transfer, plus related iron-responsive transcription/regulation terms. Although a few broader metabolic terms appear, the strongest and most specific signal points to Fe-S cluster biogenesis and protein maturation as the cluster\u2019s theme.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009190","count":1},{"id":"GO:0044238","count":1},{"id":"GO:0045900","count":1},{"id":"GO:0030488","count":1},{"id":"GO:0034396","count":1}]},{"hash":"1998820505259759987","title":"Developmental calcium signaling and deubiquitination","description":"The cluster is enriched for both calcium signaling terms (calcium import, Ryanodine receptor regulation) and three distinct ubiquitin deubiquitination terms (K11-, K48-, K63-linked), alongside development-related GO terms (metanephric ureteric bud development, ossification, multicellular development, neuron-related regulation). This points to a theme of coordinated calcium signaling and ubiquitin-mediated regulation in developmental contexts, potentially across neural and tissue differentiation processes.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043524","count":2},{"id":"GO:0035871","count":2},{"id":"GO:0071108","count":2},{"id":"GO:0070536","count":2},{"id":"GO:0098703","count":2}]},{"hash":"797318087068183936","title":"Diverse membrane solute transporters","description":"The top GO terms point to transport of various solutes across membranes (sialic acid, galactose, nitrate, sodium, phosphate, 4-hydroxyphenylacetate), plus a vesicle-related transport term for neurotransmitter loading, indicating a cluster of membrane transporter proteins with broad substrate specificity rather than a single substrate or pathway.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":4},{"id":"GO:0042128","count":3},{"id":"GO:0015757","count":3},{"id":"GO:0098700","count":3},{"id":"GO:0015706","count":3}]},{"hash":"652716482024972190","title":"Developmental signaling and actin cytoskeleton dynamics","description":"These proteins cluster around developmental processes (skin development; multicellular organism development) and signaling pathways (Wnt signaling; peptidyl-tyrosine phosphorylation; GPCR-associated signaling terms), with a strong emphasis on actin cytoskeleton remodeling (positive regulation of Arp2/3-mediated actin nucleation) and vesicle uptake (pinocytosis). The combination suggests a role in coordinating developmental signaling with cytoskeletal changes and endocytic processes, rather than a single specialized function. Confidence: Medium","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043588","count":8},{"id":"GO:0010745","count":7},{"id":"GO:0098907","count":6},{"id":"GO:0007205","count":6},{"id":"GO:0000278","count":6}]},{"hash":"1264730521579669722","title":"Calcium-Dependent Neuronal Signaling and Plasticity","description":"The GO terms cluster around calcium handling (calcium import, release of sequestered calcium) and neuronal signaling processes (synaptic plasticity regulation, vasopressin secretion), with a tangential link to Wnt signaling known to influence synaptic function. This suggests a coherent theme of calcium-mediated signaling driving synaptic plasticity, even though the interaction network is sparse and some terms are obsolete. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016055","count":2},{"id":"GO:0071260","count":1},{"id":"GO:0098703","count":1},{"id":"GO:0009409","count":1},{"id":"GO:0051209","count":1}]},{"hash":"2305594514962524355","title":"Cell Cycle and RNA Processing","description":"The top GO terms are dominated by cell division and cell cycle, indicating a core association with cell cycle functions. Supporting signals include RNA processing steps (mRNA capping, SSU-rRNA maturation) and regulatory ncRNA-mediated gene silencing, which often accompany cell-cycle\u2013related gene expression control. Other terms like protein targeting, meiotic gene conversion, and SOS response are less central, suggesting a broader, cycle-focused theme with some peripheral processes. Overall, the cluster seems centered on cell cycle activity with linked RNA processing roles.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0006370","count":2},{"id":"GO:0000462","count":1},{"id":"GO:0031047","count":1}]},{"hash":"2094359064648806418","title":"Ribosome biogenesis and RNA modification","description":"Reason: Most terms point to ribosome biogenesis, rRNA maturation/assembly, and RNA methylation (rRNA and tRNA), with a note of mitochondrial translation; a few outliers like mRNA capping and transcription regulation are secondary and do not override the core ribosome/RNA processing theme.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006370","count":2},{"id":"GO:2001246","count":2},{"id":"GO:0070475","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0042256","count":1}]},{"hash":"1825759082162692194","title":"Developmental processes and cytoskeletal dynamics","description":"The top GO terms point to development across multiple tissues (brain, spinal cord, seminiferous tubules) and cytoskeleton-related activities (microtubule severing, movement, spindle orientation, filopodium assembly). This suggests a cluster of proteins involved in developmental progression governed by cytoskeletal remodeling, rather than a single pathway. Some terms are outdated or unrelated (ERAD), but the dominant pattern is development with cytoskeletal modulation.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0071044","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0051013","count":2},{"id":"GO:0072520","count":2}]},{"hash":"213839069910574598","title":"Epithelial Differentiation and Cell Cycle Regulation","description":"The cluster is dominated by epithelial differentiation signals (intestinal epithelial cell differentiation, keratinocyte differentiation) and related regulation of differentiation, with additional hints of cell division control (regulation of cytokinesis) and proteostasis (ubiquitin-dependent protein degradation). This suggests a cohesive theme around epithelial lineage specification coupled with cell-cycle and protein turnover processes.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060575","count":1},{"id":"GO:0080182","count":1},{"id":"GO:2000146","count":1},{"id":"GO:0097198","count":1},{"id":"GO:0010957","count":1}]},{"hash":"1207569322728519343","title":"Immune-Endocrine Signaling and Vesicle Trafficking","description":"The top GO terms span immune cytokine signaling (B cell homeostasis, GM-CSF stimulus, IL-18 signaling), growth factor and endocrine signaling (EGF stimulus, insulin receptor signaling), developmental context (heart development), plus secretory and trafficking processes (dense core granule exocytosis, synaptic vesicle priming, GPCR internalization). This suggests a core theme of signaling and regulated secretion across immune, metabolic, and developmental contexts, centered on receptor trafficking and vesicle-mediated release.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001782","count":2},{"id":"GO:0097011","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0071364","count":2},{"id":"GO:0032094","count":1}]},{"hash":"2223180076931805081","title":"Keratinocyte differentiation and growth signaling","description":"This cluster combines terms centered on epidermal biology and growth control: keratinocyte differentiation, mitotic cell cycle, and regulatory signaling pathways (Wnt, Hippo, and TGF-beta receptor signaling) with both positive and negative regulation components. The convergence of differentiation, proliferation, apoptosis, and signaling modulation suggests a cohesive module governing epidermal development and cell fate decisions, rather than a random mix of unrelated processes. Confidence: High","confidence":"","size":20,"edges":159,"triangles":676,"max_degree":19,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":11},{"id":"GO:0000278","count":10},{"id":"GO:0046827","count":10},{"id":"GO:0043547","count":9},{"id":"GO:0030216","count":8}]},{"hash":"1852805762329127705","title":"Unknown","description":"The GO terms include immune cytokine production regulation, insulin receptor signaling, axon regeneration regulation, PMA response, sorbitol response, mitotic spindle organization, sperm capacitation, regulation of nuclear migration during mitotic telophase, positive regulation of sodium transport, and serine/threonine kinase signaling. This spread across immune, metabolic, neuronal, reproductive, and cell-cycle processes does not point to a single cohesive biological theme for this cluster, so I cannot assign a specific, representative function label.","confidence":"","size":20,"edges":183,"triangles":1025,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0002741","count":20},{"id":"GO:0008286","count":20},{"id":"GO:0048679","count":20},{"id":"GO:1904628","count":20},{"id":"GO:0072709","count":20}]},{"hash":"1768960345010023651","title":"Androgen signaling and prostate development","description":"The top GO terms\u2014male sex differentiation, steroid hormone receptor complex assembly, and prostate gland development\u2014strongly point to an androgen-driven program of male reproductive development. While other terms (interferon response, heart morphogenesis) appear, they are less represented and do not define the cluster, so the reproductive/hormonal theme is most representative.","confidence":"High","size":20,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046661","count":6},{"id":"GO:0006463","count":6},{"id":"GO:0030850","count":6},{"id":"GO:0071357","count":4},{"id":"GO:0051301","count":4}]},{"hash":"1464526509493480283","title":"Ubiquitination-Driven Proteasomal Degradation","description":"This cluster is dominated by GO terms for ubiquitination (including K48-, K11-, and K6-linked chains), autoubiquitination, ER-associated degradation, and SCF/APC-mediated proteolysis, plus proteasomal catabolic processes and even links to NF-kappaB signaling. Together these terms define a coherent proteostasis module centered on tagging proteins for degradation via the ubiquitin-proteasome system and related quality-control pathways, with some connections to cell-cycle regulators.","confidence":"High","size":20,"edges":109,"triangles":317,"max_degree":18,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051865","count":12},{"id":"GO:0030433","count":12},{"id":"GO:0016558","count":10},{"id":"GO:0070936","count":10},{"id":"GO:0085020","count":10}]},{"hash":"1917871703639260099","title":"Nucleic Acid Repair and RNA Modification","description":"The top GO terms cluster around DNA repair (base-excision repair), DNA-templated transcription, and DNA recombination, along with RNA pseudouridine synthesis (tRNA and rRNA), plus nucleotide salvage pathways. Together these indicate a module focused on nucleic acid metabolism, DNA repair, and RNA processing/modification. Some outliers ( xenobiotic response, cytolysis, salvage terms) are present but do not outweigh the central theme.","confidence":"Medium","size":20,"edges":35,"triangles":17,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006284","count":5},{"id":"GO:0007568","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0006310","count":3},{"id":"GO:0031119","count":3}]},{"hash":"67972798739045760","title":"Microtubule Dynamics and Spindle Assembly","description":"This cluster is enriched for GO terms about microtubule behavior (plus/minus end depolymerization and sliding), spindle function (centrosome separation, kinetochore attachments), and microtubule cytoskeleton polarity, with supporting signals from actomyosin ring formation and dendritic transport\u2014together pointing to microtubule-based organization and spindle apparatus roles.","confidence":"High","size":20,"edges":110,"triangles":316,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0070462","count":13},{"id":"GO:0000915","count":13},{"id":"GO:0098971","count":13},{"id":"GO:0031534","count":13},{"id":"GO:0031535","count":13}]},{"hash":"1692110552875415112","title":"Unknown","description":"The top GO terms mix neuronal signaling (sensory perception of sound, neurotransmitter loading into synaptic vesicle) with a variety of transport and metabolic processes (nitrate, galactose, phosphate, fucose, and 4-hydroxyphenylacetate transport) and have no clear common function or pathway binding the proteins together. With no edges or cohesive theme, there isn\u2019t a single interpretable label that accurately represents the cluster.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070493","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0007605","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0015757","count":2}]},{"hash":"266750939001878226","title":"Diverse Solute Transporters","description":"These proteins appear to function as membrane transporters for a broad set of solutes, including nitrate/nitrite, glucose, phosphate, urate, selenite, and xenobiotics, as well as vesicular loading of neurotransmitters. The common thread is transmembrane transport of diverse substrates, spanning both plasma membrane and vesicular systems, rather than a single substrate-specific function.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":6},{"id":"GO:0006855","count":5},{"id":"GO:1904659","count":5},{"id":"GO:0015707","count":5},{"id":"GO:0098700","count":4}]},{"hash":"1901298137079031173","title":"Unknown","description":"The top GO terms are highly diverse, covering forebrain development, trophoblast differentiation, ovarian axis specification, various apoptotic processes, cell cycle regulation, and even metabolism/redox. There isn\u2019t a clear, shared function or pathway tying these proteins together, and the annotations appear scattered rather than converging on a single theme. Therefore, no coherent label can be assigned. ","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0009236","count":2},{"id":"GO:0030900","count":1},{"id":"GO:0033301","count":1},{"id":"GO:1990086","count":1}]},{"hash":"1151200981225060900","title":"Chromatin Regulation and Differentiation","description":"The top GO terms point to chromatin remodeling and transcriptional control (histone demethylation, DNA-templated transcription, positive regulation of chromatin binding) and differentiation processes (myoblast differentiation, vasculogenesis), suggesting these proteins collectively regulate gene expression to drive cell fate decisions. While a couple of terms (response to cold, oxidation-reduction) are broader stress-related processes, the core signal centers on chromatin regulation and differentiation pathways.","confidence":"Medium","size":20,"edges":16,"triangles":2,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0034720","count":6},{"id":"GO:0042264","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0070544","count":4},{"id":"GO:0009409","count":3}]},{"hash":"549783747269781511","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":3,"triangles":1,"max_degree":2,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000462","count":4},{"id":"GO:0031047","count":4},{"id":"GO:0071894","count":4},{"id":"GO:0042273","count":4},{"id":"GO:0048026","count":4}]},{"hash":"68330155116008822","title":"Unknown","description":"The GO terms are highly heterogeneous (epigenetic regulation, catabolic processes, diverse signaling and developmental processes) and there are no network connections among the proteins, so there isn\u2019t a single cohesive function that ties the cluster together. A single, meaningful label cannot be assigned.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051573","count":2},{"id":"GO:0043046","count":2},{"id":"GO:0019608","count":2},{"id":"GO:0006212","count":2},{"id":"GO:0034720","count":2}]},{"hash":"1114252931085296496","title":"Cell wall biosynthesis and organization","description":"The top GO terms point to cell wall biology\u2014biosynthesis, remodeling, and organization (including rhamnogalacturonan II and xyloglucan biosynthesis, fungal-type cell wall biogenesis), plus plant-specific root hair development and related growth/division processes. This combo suggests a cohesive cluster of proteins involved in cell wall construction and modification across plants and fungi.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":3},{"id":"GO:0010306","count":2},{"id":"GO:0080147","count":2},{"id":"GO:0005992","count":2},{"id":"GO:0005983","count":2}]},{"hash":"927217404799450336","title":"Ribosome biogenesis and translation","description":"This cluster is strongly enriched for translation and ribosome-related processes, with terms for translation (GO:0006412), ribosome assembly/biogenesis (GO:0042254, GO:0042255, GO:0000027), and rRNA processing (GO:0000447). The pattern indicates proteins involved in ribosome construction and protein synthesis, with a secondary signal of antibiotic response likely linked to translation-targeting mechanisms.","confidence":"High","size":20,"edges":190,"triangles":1140,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":17},{"id":"GO:0046677","count":5},{"id":"GO:0006415","count":3},{"id":"GO:0000027","count":3},{"id":"GO:0015968","count":2}]},{"hash":"2145353511514059283","title":"Thermal stress response with DNA repair and calcium signaling","description":"The cluster\u2019s top GO terms cluster around responses to temperature (heat and cold), DNA repair and transcription, redox homeostasis, and calcium signaling, pointing to a general theme of stress management and genome maintenance with calcium-mediated signaling. A single brain development term appears but is not central to the overall pattern; the dominant signal is cellular stress response, DNA repair, and calcium dynamics.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":3},{"id":"GO:0009408","count":3},{"id":"GO:0006281","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0045454","count":2}]},{"hash":"704891244572252357","title":"Calcium signaling and synaptic plasticity","description":"The top GO terms cluster around calcium dynamics (import across the membrane and release from stores) and synaptic regulation (receptor localization to synapse) plus vasopressin secretion, which together point to Ca2+-dependent neuronal signaling and modulation of synaptic plasticity and neuropeptide release. Some terms are less coherent (e.g., cell cycle, cold response), but the calcium/synaptic terms are the predominant theme. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0071260","count":2},{"id":"GO:0098703","count":2},{"id":"GO:0009409","count":2},{"id":"GO:0051209","count":2}]},{"hash":"908066233470961264","title":"Synapse Formation and Protein Quality Control","description":"The cluster is enriched for neuronal-related terms such as positive regulation of synapse assembly and cell surface receptor signaling, suggesting a role in synapse formation or maintenance. At the same time, several terms point to protein homeostasis, including ubiquitin-dependent protein catabolic processes and ER-associated degradation (ERAD), implying coordinated proteostasis mechanisms in neurons. Although some terms like nitroglycerin metabolism and TNT catabolism are less related, the dominant theme appears to be synaptic regulation linked with protein quality control. ","confidence":"Medium","size":20,"edges":17,"triangles":0,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0051965","count":2},{"id":"GO:0042220","count":1},{"id":"GO:0007166","count":1},{"id":"GO:1904153","count":1},{"id":"GO:1903061","count":1}]},{"hash":"512405997447289020","title":"Gene Expression Regulation and TORC1 Signaling","description":"This cluster centers on multiple facets of gene expression control, including DNA-templated transcription, translation initiation/reinitiation, and mRNA transport, with additional links to ncRNA-mediated gene silencing, ubiquitin-dependent proteolysis, GTPase regulation, and TORC1 signaling, indicating a cohesive theme of transcription/translation regulation and related post-translational regulation.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0001731","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0006355","count":2},{"id":"GO:0070262","count":2}]},{"hash":"2125907380909656263","title":"ER Protein Folding and Quality Control","description":"The cluster is dominated by GO terms pointing to ER-based proteostasis: protein folding in the endoplasmic reticulum, response to unfolded protein, redox homeostasis, and ubiquitin-proteasome\u2013mediated quality control, with related terms on post-translational targeting and maturation. This suggests a cohesive theme of ER-associated protein folding and quality control under stress, though a mesoderm formation term appears as an outlier. ","confidence":"High","size":20,"edges":23,"triangles":0,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0034975","count":7},{"id":"GO:0045454","count":7},{"id":"GO:0006986","count":6},{"id":"GO:0071630","count":6},{"id":"GO:0070389","count":6}]},{"hash":"239979670878727427","title":"Mitotic cell cycle and telomere maintenance","description":"The cluster features several GO terms centered on cell division and chromosome stability, such as mitotic cell cycle, spindle assembly, and various telomere maintenance/capping processes, plus related cohesion regulation. While there are ancillary terms related to signaling (Wnt) and receptor localization, the dominant theme ties to mitosis and telomere integrity, suggesting these proteins broadly coordinate cell-cycle progression and genome stability.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007205","count":6},{"id":"GO:0000278","count":4},{"id":"GO:1900383","count":4},{"id":"GO:0070213","count":4},{"id":"GO:0051225","count":4}]},{"hash":"1741281636661348206","title":"Synaptic signaling and memory","description":"The cluster is dominated by GO terms related to neural communication and memory, including excitatory postsynaptic potential, short-term and long-term memory, and response to amphetamine, pointing to proteins involved in synaptic signaling and memory formation. The heart-related terms (heart development, cardiac muscle contraction) are less consistent with this theme and may reflect broader or overlapping roles or annotation noise. Overall, the neural/synaptic theme best explains the enrichment pattern.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":3},{"id":"GO:0060048","count":3},{"id":"GO:0007281","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0008360","count":3}]},{"hash":"1880946633453707618","title":"Cell signaling and mechanotransduction","description":"The top GO terms point to broad signal transduction activities (Wnt signaling, GPCR-related signaling, and GTPase regulation) with accompanying calcium signaling (calcium import) and responses to mechanical stimuli, suggesting a cluster of proteins involved in signaling and mechanotransduction rather than a single pathway. Some terms touch on stress or cardiac-specific contexts, but the common theme is intracellular communication and response to cues.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0016055","count":6},{"id":"GO:0048549","count":6},{"id":"GO:0098907","count":6},{"id":"GO:0007205","count":6},{"id":"GO:0048265","count":6}]},{"hash":"1365328306642165766","title":"Cardiac and skeletal muscle development","description":"The cluster is dominated by terms tied to muscle biology, especially heart development and cardiac muscle contraction, along with skeletal muscle fiber development. It also shows related signaling activities (protein phosphorylation and GTPase/kinase regulation) that commonly govern muscle differentiation and function. A couple of terms like visual perception and fat cell differentiation appear as outliers, likely reflecting pleiotropy or annotation noise, but do not obscure the muscle-focused theme.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007205","count":6},{"id":"GO:0007507","count":5},{"id":"GO:0048741","count":5},{"id":"GO:0031954","count":4},{"id":"GO:0043547","count":4}]},{"hash":"2161963320593525564","title":"Telomere maintenance regulation","description":"This cluster shows multiple GO terms centered on telomere maintenance and telomerase regulation (telomere capping, maintenance via telomerase, and overall regulation), indicating a cohesive telomere biology theme. Additional terms cover broader signaling and cell cycle processes, but the telomere-related terms dominate the functional signal.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900383","count":3},{"id":"GO:0070213","count":3},{"id":"GO:0051225","count":3},{"id":"GO:1904355","count":3},{"id":"GO:1904908","count":3}]},{"hash":"946659230637565026","title":"Unknown","description":"The top GO terms span endocytic trafficking, PI catabolism, ciliary/flagellar dynein arm assembly, ribosome assembly, and organismal phenotypes, with no clear, single shared function linking the proteins. No edges or cohesive functional signal to tie them into a specific theme. ","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031161","count":1},{"id":"GO:0001921","count":1},{"id":"GO:2001135","count":1},{"id":"GO:0008344","count":1},{"id":"GO:0014898","count":1}]},{"hash":"373155182386912051","title":"Meiosis and Germline RNA Processing","description":"The terms strongly cluster around meiotic progression (meiotic cell cycle, karyogamy) and germline development (germarium-derived germ-line cyst encapsulation), with supporting RNA-level regulation (adenosine-to-Inosine editing, mRNA destabilization, and regulation of cap-independent translation). Although some GO terms are obsolete, the shared theme appears to be meiosis/germline processes coupled with post-transcriptional control of RNA. This suggests a cohesively functioning group of proteins involved in meiotic events and RNA processing/translation regulation in a fungal/germline context.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080009","count":1},{"id":"GO:0007329","count":1},{"id":"GO:0000742","count":1},{"id":"GO:0030708","count":1},{"id":"GO:0051321","count":1}]},{"hash":"968180591834212196","title":"Calcium signaling and synaptic plasticity","description":"Several top GO terms point to calcium dynamics (calcium import across the plasma membrane, release of sequestered calcium into cytosol) and vasopressin secretion, which are tightly linked to Ca2+-dependent signaling. The presence of a term relating to regulation of synaptic plasticity by receptor localization to the synapse further supports a neuronal/synaptic function centered on calcium signaling. Some terms about responses to mechanical stimulus or cold can invoke Ca2+-mediated stress signaling, reinforcing the Ca2+\u2013driven theme. Thus, the cluster appears to reflect Ca2+-mediated signaling coordinating neuroendocrine secretion and synaptic plasticity.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":1},{"id":"GO:0098703","count":1},{"id":"GO:0009409","count":1},{"id":"GO:0051209","count":1},{"id":"GO:1900383","count":1}]},{"hash":"1626065708626203750","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007114","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0009245","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0031126","count":2}]},{"hash":"1135322643068738979","title":"Protein methylation and chromatin regulation","description":"Top GO terms cluster around various methylation processes (rRNA methylation; peptidyl-lysine/arginine/glycine methylation; N-terminal methylation) and chromatin regulation (rDNA heterochromatin formation, negative regulation of transcription by RNA Pol II). This pattern points to enzymes and factors involved in methylation-driven chromatin control of gene expression and ribosome biogenesis.","confidence":"High","size":19,"edges":168,"triangles":919,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0031167","count":9},{"id":"GO:0018027","count":9},{"id":"GO:0000183","count":9},{"id":"GO:0000122","count":8},{"id":"GO:0009236","count":8}]},{"hash":"619408698896929394","title":"Oxidant detoxification and lipid catabolism","description":"The top GO terms cluster around cellular oxidant detoxification and several lipid/aromatic compound catabolic processes (triglyceride catabolic process, monoacylglycerol catabolic process, beta-ketoadipate pathway, 3-phenylpropionate catabolic process), with some redox-related terms. This points to a shared theme of detoxifying oxidants while degrading lipids and aromatic substrates, rather than a single narrow function. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":6},{"id":"GO:0055114","count":6},{"id":"GO:2000124","count":6},{"id":"GO:0019433","count":6},{"id":"GO:0009086","count":5}]},{"hash":"445471346992344225","title":"Primary Metabolism and Cofactor Biosynthesis","description":"This cluster is dominated by core metabolic and biosynthetic processes, including the tricarboxylic acid cycle and the biosynthesis of vitamins and cofactors (biotin, thiamine) as well as porphyrinogen synthesis. Also present are RNA modification pathways (rRNA base methylation, tRNA queuosine biosynthesis) and fermentation, which are all linked to growth and energy production. Together, these terms point to a cohesive theme of primary metabolism and biosynthetic capacity that supports cellular growth and function, with some RNA biogenesis aspects accompanying the metabolic state.","confidence":"Medium","size":19,"edges":95,"triangles":186,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006099","count":5},{"id":"GO:0006782","count":4},{"id":"GO:0009102","count":4},{"id":"GO:0046677","count":4},{"id":"GO:0009228","count":4}]},{"hash":"433423586326695188","title":"Neuronal Translation and Stress Response","description":"The cluster features protein-synthesis terms (cytoplasmic translation, ribosomal export) along with several stress-related and neuronal terms (hyperosmotic/salt stress, amino acid starvation, xenobiotic response, endocytosis, nervous system development, regulation of excitatory postsynaptic potential). This combination suggests neuronal proteins that link translation machinery with stress signaling and synaptic function, justifying a name centered on neuronal translation and stress responses.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0002181","count":4},{"id":"GO:0000056","count":3},{"id":"GO:0006972","count":3},{"id":"GO:0035690","count":3},{"id":"GO:0006367","count":3}]},{"hash":"2228322924173024531","title":"Mitochondrial translation and respiration","description":"This cluster is enriched for translation-related GO terms, including mitochondrial and cytoplasmic translation, plus mitochondrial tRNA aminoacylation (prolyl-, glycyl-, alanyl-tRNA), and it also includes the respiratory electron transport chain term. The combination points to proteins involved in mitochondrial protein synthesis and energy production pathways.","confidence":"High","size":19,"edges":161,"triangles":814,"max_degree":18,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0002181","count":4},{"id":"GO:0070584","count":3},{"id":"GO:0022904","count":3},{"id":"GO:0009245","count":2}]},{"hash":"1359884517572243297","title":"Neural development and transcriptional regulation","description":"The cluster shows strong signals for neural development terms (midbrain development, forebrain-midbrain boundary formation, trigeminal ganglion development, muscle organ development) alongside negative regulation of transcription by RNA polymerase II, suggesting a theme of transcriptional control during neural development. A couple of immune/secondary metabolism terms appear less coherent with the core theme, possibly reflecting broader gene functions. Overall, this cluster is best described as neural development with transcriptional regulatory involvement.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":4},{"id":"GO:0030901","count":2},{"id":"GO:0050832","count":2},{"id":"GO:0014909","count":2},{"id":"GO:0021905","count":2}]},{"hash":"2223222509379198752","title":"Unknown","description":"Top GO terms span neural behavior, protein turnover, detoxification, immune signaling, and vascular processes, with no single unifying function linking them and no edges connecting the proteins; therefore there is no coherent cluster theme to name.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035641","count":2},{"id":"GO:0008284","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0001662","count":1},{"id":"GO:0098869","count":1}]},{"hash":"1135973687090602695","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":31,"triangles":3,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0046661","count":2},{"id":"GO:0048680","count":2}]},{"hash":"245649210850189071","title":"Brain and neural development","description":"The proteins show strong enrichment for neural- and development-related terms (brain development, forebrain development, retina development) alongside broader developmental processes. While transcriptional regulation and microtubule-related terms are present, the clearest shared theme is neural tissue formation and development, justifying a label focused on brain/ neural development.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0061087","count":3},{"id":"GO:0051225","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0007338","count":3}]},{"hash":"932951805124574089","title":"ER Stress Response and Protein Quality Control","description":"This cluster centers on processes managing misfolded or stressed proteins in the endoplasmic reticulum, including protein folding in the ER, unfolded protein response, translation upregulation during ER stress, and ubiquitin-dependent degradation via ERAD and MVB/lysosomal pathways, plus redox homeostasis that supports ER function. A few terms reflect broader anti-apoptotic responses during stress. Overall, the terms cohere around ER quality control and stress adaptation.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043524","count":3},{"id":"GO:0043162","count":2},{"id":"GO:0043328","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0045454","count":2}]},{"hash":"866111714891634425","title":"Sterol and Prostaglandin Biosynthesis with Antibiotic Stress Response","description":"This cluster is dominated by biosynthetic processes (sterol, prostaglandin, antibiotic, and other lipid-related pathways) and includes stress- and growth-related responses. The recurring theme is production of lipid- and metabolite-related compounds, along with responses to nutrient stress, implying a biosynthesis-centered, stress-associated functional group.","confidence":"Medium","size":19,"edges":35,"triangles":6,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0017000","count":3},{"id":"GO:0016126","count":2},{"id":"GO:0008209","count":2},{"id":"GO:0097171","count":2}]},{"hash":"1167894041991985345","title":"Hormone signaling and stress responses","description":"Top GO terms indicate involvement in diverse hormone signaling and development processes across organisms (male sex differentiation; steroid hormone receptor complex assembly; prostate gland development; cytokinin and gibberellin signaling). The presence of stress- and protein-assembly related terms (response to unfolded protein, cellular response to type I interferon, protein heterooligomerization, histone methylation) suggests the cluster also includes proteins linked to stress responses and chromatin dynamics. Overall, the common thread appears to be signaling-associated proteins with roles in hormone pathways, with some cross-talk to stress responses.","confidence":"Medium","size":19,"edges":15,"triangles":2,"max_degree":12,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0046661","count":8},{"id":"GO:0006463","count":8},{"id":"GO:0071357","count":8},{"id":"GO:0009938","count":8},{"id":"GO:0009736","count":8}]},{"hash":"427271196490292464","title":"Mitochondrial respiration and oxidative phosphorylation","description":"The cluster\u2019s top terms cluster around mitochondrial energy production and redox handling: mitochondrial electron transport chains, oxidative phosphorylation, proton and iron ion transport, and hydrogen peroxide metabolism. While a few terms are obsolete or outliers (e.g., photosynthesis), the dominant signal is mitochondrial respiration and associated redox processes.","confidence":"Medium","size":19,"edges":31,"triangles":9,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0008635","count":2},{"id":"GO:0042743","count":2},{"id":"GO:0006827","count":2},{"id":"GO:0015992","count":2}]},{"hash":"1238850342062723805","title":"Cell Cycle and Division Machinery","description":"The strongest GO terms cluster around cell division, cell cycle, and mitotic cell cycle, suggesting this group comprises proteins involved in cell cycle progression and mitosis; additional terms likely reflect broader cellular maintenance but do not override the core theme.","confidence":"High","size":19,"edges":25,"triangles":0,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":8},{"id":"GO:0007049","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0051291","count":6},{"id":"GO:0000055","count":5}]},{"hash":"700905296798803022","title":"Ubiquitin-Proteasome Regulation and Chromatin Dynamics","description":"The terms cluster around ubiquitin-mediated proteolysis (SCF-dependent processes and SCF complex assembly) and chromatin-related functions (nucleosome assembly, chromosome condensation), with a genome maintenance note (global genome nucleotide-excision repair). Together this suggests a theme of regulated proteolysis shaping chromatin structure and DNA repair, with translation regulation and differentiation terms as supportive signals.","confidence":"Medium","size":19,"edges":26,"triangles":0,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:2000766","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0045657","count":2},{"id":"GO:0030261","count":1},{"id":"GO:0006334","count":1}]},{"hash":"2050806765924295041","title":"TLR signaling and cytokine-mediated immune activation","description":"The GO terms cluster around Toll-like receptor signaling (TLR8 and Toll pathways), inflammatory response regulation, dendritic cell cytokine production, interferon production, and B cell proliferation\u2014together pointing to innate immune sensing and cytokine-driven activation of immune responses. A noisy obsolete term is present but does not alter the overall theme.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090116","count":2},{"id":"GO:0034158","count":1},{"id":"GO:0050729","count":1},{"id":"GO:0002730","count":1},{"id":"GO:0008063","count":1}]},{"hash":"1645178609403822879","title":"RNA Metabolism and Transcription Regulation","description":"The cluster shows enrichment for DNA-templated transcription and its regulation, along with mRNA processing and nuclear poly(A) tail shortening, which together point to RNA metabolism and transcription control as a core theme. The remaining terms (chlorophyll/chloroplast processes, immunity, ion transport, behavior) are sporadic and likely reflect annotation noise or context-specific roles, making a single cohesive function less certain beyond RNA-related processes.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0010028","count":1},{"id":"GO:0015994","count":1},{"id":"GO:0002377","count":1}]},{"hash":"442673753806574330","title":"Genome maintenance and chromatin regulation","description":"The top GO terms point to DNA repair, DNA replication, and the SOS response, with additional chromatin-related processes such as histone H2B ubiquitination and DNA methylation. There are also RNA-focused terms (regulatory ncRNA-mediated gene silencing and rRNA maturation), suggesting nuclear genome regulation and RNA-based control. Taken together, the cluster appears to group proteins involved in preserving genome integrity and modulating chromatin state, with some RNA-mediated regulatory activities.","confidence":"Medium","size":19,"edges":16,"triangles":0,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0000462","count":1},{"id":"GO:0031047","count":1},{"id":"GO:0006605","count":1},{"id":"GO:0006311","count":1}]},{"hash":"962460331777366460","title":"Developmental signaling and cell fate specification","description":"The top GO terms point to signaling pathways (G protein-coupled receptor signaling, EGFR ligand maturation) and diverse cell fate decisions (wing cell fate, cone cell fate, spermatid differentiation). While there are also stress-related terms, the dominant theme is regulators of developmental signaling and differentiation across tissues, suggesting a cohesive cluster of signaling\u2013fate determinants rather than a single specific function. ","confidence":"Medium","size":19,"edges":18,"triangles":0,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0007186","count":1},{"id":"GO:0019236","count":1},{"id":"GO:0032815","count":1},{"id":"GO:0035311","count":1},{"id":"GO:1904211","count":1}]},{"hash":"1823093366679840763","title":"Vitamins and Xenobiotics Transmembrane Transporters","description":"All top GO terms point to transmembrane transport across membranes, covering vitamins, xenobiotics, ions, glycerophosphodiesters, and fatty acids, suggesting a set of broad-specificity membrane transporters. A single SOS response term is present but does not change the overall transport-centric theme.","confidence":"High","size":19,"edges":35,"triangles":19,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":19},{"id":"GO:0006855","count":19},{"id":"GO:0042908","count":12},{"id":"GO:0071805","count":12},{"id":"GO:0001407","count":11}]},{"hash":"314869992795899598","title":"Protein quality control across organelles","description":"Based on the GO terms, there is a theme of cellular stress responses touching multiple organelles: unfolded protein response and ER stress, mitochondrial protein import, and detoxification of oxidants, with additional signals of transcriptional/nuclear regulation and nucleolar activities that can be affected under stress. This suggests a cross-organellar protein homeostasis and quality-control program rather than a single organelle-specific function, hence a label focusing on protein quality control across organelles. ","confidence":"Medium","size":19,"edges":106,"triangles":218,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0030150","count":2},{"id":"GO:0000122","count":1},{"id":"GO:0098869","count":1},{"id":"GO:0046826","count":1}]},{"hash":"305966697384112308","title":"Developmental Signaling and Actin Dynamics","description":"The top GO terms point to developmental processes (brain development, multicellular organism growth, Wnt signaling) along with actin cytoskeleton remodeling (Arp2/3 complex\u2013mediated nucleation, actin filament bundle assembly). While other terms touch on transcription regulation and histone acetylation, the strongest shared theme is coordination of development signaling with changes in the actin cytoskeleton, suggesting a cluster of proteins involved in morphogenesis and cellular movement. Some terms like phototaxis and defense response are less central but present, likely reflecting broader functional overlaps in the protein set.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034314","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0035264","count":2},{"id":"GO:0043982","count":2},{"id":"GO:0050830","count":2}]},{"hash":"469428106433663652","title":"Cardiac calcium signaling and excitability","description":"The top GO terms cluster around calcium handling (import and release of Ca2+), regulation of action potentials in SA node cells, and related signaling pathways (including GPCR signaling) with additional links to mechanotransduction and synaptic signaling. Together these terms point to calcium-driven electrical excitability in cardiac tissue, particularly pacemaker function, and calcium-dependent signaling that can influence mechanical responses and synaptic-like plasticity. The label emphasizes a cohesive theme of calcium signaling governing excitability in heart (and related signaling contexts). ","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0098907","count":7},{"id":"GO:0007205","count":7},{"id":"GO:0007253","count":6},{"id":"GO:0071260","count":5},{"id":"GO:0098703","count":5}]},{"hash":"1164713707143932178","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000961","count":2},{"id":"GO:0080156","count":2},{"id":"GO:0031426","count":2},{"id":"GO:1905639","count":2},{"id":"GO:0031425","count":2}]},{"hash":"2233588676727454794","title":"Plant Cell Cycle and Chloroplast Import","description":"Dominated by spindle assembly and cell cycle terms (6 each) and chloroplast thylakoid membrane protein import (6), this cluster centers on plant cell division linked with chloroplast protein trafficking. The co-occurrence of these GO terms suggests proteins involved in mitotic machinery and the import of proteins into chloroplasts, potentially coordinating cell division with chloroplast biogenesis. The other terms (mechanical response, calcium transport, cold response) likely reflect broader plant signaling contexts that accompany growth but are less central to the core theme.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0051225","count":6},{"id":"GO:0007049","count":6},{"id":"GO:0045038","count":6},{"id":"GO:0071260","count":5},{"id":"GO:0098703","count":5}]},{"hash":"2108973969687450625","title":"Mitotic Chromosome Dynamics and Calcium Signaling","description":"The top GO terms point to mitosis-related processes (spindle assembly, spindle regulation, chromosome condensation, nucleosome assembly, segregation) and calcium signaling (calcium import and release), suggesting a cluster centered on mitotic chromosome dynamics with accompanying calcium signaling. However, the lack of interactions (edges) and single-term annotations indicate the connections are weak and the cluster is heterogeneous, warranting a cautious, moderate label.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":1},{"id":"GO:0060236","count":1},{"id":"GO:0030261","count":1},{"id":"GO:0032147","count":1},{"id":"GO:0006334","count":1}]},{"hash":"2128814685068137356","title":"Neural development and synaptic signaling with drug responses","description":"This cluster centers on neural development and synaptic activity, with GO terms like cerebellar granule cell differentiation, regulation of glutamatergic transmission, and long-term potentiation, plus behavioral/drug-response terms (ethanol, amphetamine). While some metabolism/transport terms appear, the dominant theme is neural development and synaptic signaling linked to substance responses.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021707","count":2},{"id":"GO:1990569","count":2},{"id":"GO:0051967","count":1},{"id":"GO:0018964","count":1},{"id":"GO:1900273","count":1}]},{"hash":"1357663057437134566","title":"Telomere maintenance and cell cycle regulation","description":"The cluster is dominated by GO terms centered on telomere maintenance/capping and cell cycle control (telomerase-regulated maintenance, telomere capping, and CDK activity regulation), with additional diverse terms such as mRNA processing and differentiation that indicate broader regulatory roles rather than a single pathway.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":3},{"id":"GO:1904355","count":3},{"id":"GO:0035994","count":3},{"id":"GO:0045736","count":3},{"id":"GO:0006397","count":3}]},{"hash":"575647485169076025","title":"ER protein folding and quality control","description":"Most GO terms center on proteostasis and ER-associated handling of proteins: response to unfolded protein, protein folding in endoplasmic reticulum, ER targeting/translocation, and ubiquitin-proteasome\u2013mediated quality control. A few terms pertain to development or RNA transport, which appear unrelated to the core proteostasis theme, but the dominant signal supports ER folding and quality control.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006986","count":1},{"id":"GO:0071630","count":1},{"id":"GO:0070389","count":1},{"id":"GO:0031204","count":1},{"id":"GO:0001707","count":1}]},{"hash":"1691720900500205709","title":"Immune-Neuroendocrine Signaling and Exocytosis","description":"The proteins are linked to immune signaling (IL-18 pathway, B cell homeostasis), neuroendocrine secretion (dense core granule exocytosis, synaptic vesicle priming), and general signal transduction (Rho/Rac, GPCR internalization, insulin signaling, vasoconstriction). Although there are no direct interactions, the shared theme is signaling and regulated secretion across immune, neural, and endocrine systems, justifying this label.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":2},{"id":"GO:0032094","count":1},{"id":"GO:0035655","count":1},{"id":"GO:0016082","count":1},{"id":"GO:0002031","count":1}]},{"hash":"720289458900980962","title":"Mitochondrial Lipid Biosynthesis and Dynamics","description":"The leading GO terms center on mitochondrial lipids (cardiolipin and phosphatidic acid biosynthesis), lipid catabolism, and processes that regulate mitochondrial fusion, plus peroxisome inheritance, pointing to a theme of mitochondrial lipid metabolism and organelle maintenance. A couple of low-frequency, unrelated terms appear, likely noise. Confidence: High.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007512","count":2},{"id":"GO:0032196","count":1},{"id":"GO:0030719","count":1},{"id":"GO:0048017","count":1},{"id":"GO:0006654","count":1}]},{"hash":"2230385079843620708","title":"Mitotic spindle dynamics and microtubule-based transport","description":"The top GO terms center on mitotic spindle organization and microtubule dynamics (centrosome separation, metaphase chromosome alignment, plus/minus-end microtubule sliding, spindle\u2013kinetochore attachments, and cytokinesis via the actomyosin contractile ring). The presence of dendritic transport of receptor complexes indicates motor-driven microtubule transport in cells, aligning with plus- and minus-end directed sliding. Altogether, this cluster reflects proteins involved in spindle formation, microtubule dynamics, and motor-based cargo transport. ","confidence":"High","size":18,"edges":136,"triangles":590,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0007100","count":13},{"id":"GO:0007080","count":13},{"id":"GO:0070462","count":12},{"id":"GO:0000915","count":12},{"id":"GO:0098971","count":12}]},{"hash":"935665155701825591","title":"Neural and Organ Development Signaling","description":"This cluster is dominated by developmental signaling terms (Smoothened/Hedgehog, Roundabout/ROBO), nervous system development, and organogenesis (kidney development), with supporting terms in axonogenesis and signaling pathways, suggesting a cohesive theme of developmental signaling guiding neural and organ development. Some items like T cell signaling and ubiquitination are broader context signals, so the label is representative but not exclusive.","confidence":"Medium","size":18,"edges":25,"triangles":11,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0007224","count":3},{"id":"GO:0050852","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0035385","count":3},{"id":"GO:0001822","count":3}]},{"hash":"941660565899376561","title":"Terpenoid and Sterol Biosynthesis","description":"The cluster is dominated by terms tied to isoprenoid/terpenoid pathways, including cholesterol, monoterpene, quinone, and geranyl/farnesyl/geranylgeranyl diphosphate biosynthesis. These converge on terpenoid and sterol production, with a few minor terms related to other biosynthetic processes that do not override the main theme. ","confidence":"High","size":18,"edges":37,"triangles":25,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0006695","count":1},{"id":"GO:0043693","count":1},{"id":"GO:0015031","count":1},{"id":"GO:0051290","count":1},{"id":"GO:1901663","count":1}]},{"hash":"1527865647233613039","title":"Vitamin and pigment biosynthesis with xenobiotic response","description":"The cluster is dominated by biosynthetic GO terms: biotin biosynthetic process, cobalamin biosynthetic process, light-independent chlorophyll biosynthetic process, and antibiotic biosynthetic process, pointing to metabolic synthesis of vitamins and pigments (and related secondary metabolites). The presence of cellular response to xenobiotic stimulus and response to cocaine adds a xenobiotic handling dimension, suggesting a broader detox/response role alongside biosynthesis. Additional terms for tRNA wobble uridine modification and arginine methylation hint at supporting RNA/ protein modification activities within this metabolic context. Overall, the proteins appear linked to biosynthetic metabolism with xenobiotic response. ","confidence":"Medium","size":18,"edges":16,"triangles":1,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":8},{"id":"GO:0009102","count":7},{"id":"GO:0017000","count":7},{"id":"GO:0042220","count":7},{"id":"GO:0002098","count":6}]},{"hash":"910853853550686440","title":"DNA Replication and Transcription Regulation During the Cell Cycle","description":"This cluster is enriched for DNA replication, mitotic cell cycle, and transcription regulation, with supporting terms on mRNA transport and kinase signaling. The common theme is coordinated control of genome duplication and gene expression during cell-cycle progression, with additional signaling components.","confidence":"High","size":18,"edges":10,"triangles":2,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0000742","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0045944","count":3},{"id":"GO:0000278","count":3}]},{"hash":"507754018678622777","title":"Unknown","description":"This cluster shows a highly diverse mix of GO terms\u2014ranging from protein ubiquitination and cell division to neuron development and neurotransmitter loading, plus several metabolism and transport processes\u2014indicating no single cohesive function or pathway tying all proteins together.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0033574","count":2},{"id":"GO:0031175","count":2},{"id":"GO:0042128","count":2}]},{"hash":"2091003526347022656","title":"Wnt-Driven Cell Proliferation","description":"This cluster is enriched for terms related to canonical Wnt signaling activation and mitotic cell cycle processes (cell division), pointing to a shared role in promoting cell growth and proliferation; auxiliary terms like ribosomal export and mitochondrial fission likely reflect general cellular growth accompanying division.","confidence":"Medium","size":18,"edges":77,"triangles":144,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043525","count":6},{"id":"GO:0010738","count":6},{"id":"GO:0000278","count":5},{"id":"GO:0090263","count":5},{"id":"GO:0051301","count":5}]},{"hash":"1035150694888684658","title":"Unknown","description":"The terms span diverse domains (immune antigen processing, systemic resistance, antimicrobial peptide regulation, endocrine renin\u2013angiotensin signaling, skin and neurobehavioral processes, plus plant xylan metabolism), with no clear single function tying the proteins together, so a cohesive label isn\u2019t discernible.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0010838","count":2},{"id":"GO:0002803","count":2},{"id":"GO:0045493","count":2},{"id":"GO:0019886","count":2}]},{"hash":"1196412458369126321","title":"Chromatin methylation and heterochromatin formation","description":"The cluster centers on methylation activities (peptidyl-lysine, N-terminal glycine, rRNA) and heterochromatin-related processes, including rDNA heterochromatin formation and negative regulation of transcription by RNA Pol II, pointing to an epigenetic regulation module governing chromatin state and transcription. ","confidence":"High","size":18,"edges":150,"triangles":771,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0018023","count":6},{"id":"GO:0031167","count":6},{"id":"GO:0018013","count":6},{"id":"GO:0018027","count":6},{"id":"GO:0000183","count":6}]},{"hash":"2197011454649545628","title":"Unknown","description":"The top GO terms span diverse processes (cell morphogenesis, membrane targeting, mating/conjugation, ER stress response, protein quality control, iron-sulfur cluster assembly, and DNA replication), with some terms marked obsolete, indicating no single cohesive function for the cluster. Therefore, a specific, intuitive label is not justifiable.","confidence":"","size":18,"edges":35,"triangles":25,"max_degree":16,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000902","count":4},{"id":"GO:1902037","count":4},{"id":"GO:0031204","count":4},{"id":"GO:0000742","count":4},{"id":"GO:1903382","count":4}]},{"hash":"565996895418073625","title":"RNA Processing and Ribosome Biogenesis","description":"Dominated by spliceosome-mediated RNA splicing, mRNA stability regulation, Pol II transcription termination, and rRNA maturation with ribosome assembly, indicating a coherent RNA maturation/gene-expression theme.","confidence":"High","size":18,"edges":89,"triangles":276,"max_degree":14,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000398","count":7},{"id":"GO:0031047","count":7},{"id":"GO:0048026","count":7},{"id":"GO:1901407","count":5},{"id":"GO:0010610","count":5}]},{"hash":"1741998301812765606","title":"Spliceosome-Mediated mRNA Processing","description":"This cluster is dominated by splicing and mRNA maturation terms (mRNA splicing via spliceosome, cis splicing, small-subunit processome assembly, mRNA modification, polyadenylation) plus regulatory and stress-related ties to mRNA stability and splicing regulation, indicating a cohesive RNA-processing function centered on the spliceosome.","confidence":"High","size":18,"edges":121,"triangles":434,"max_degree":17,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":9},{"id":"GO:0006378","count":7},{"id":"GO:0031047","count":7},{"id":"GO:0048026","count":7},{"id":"GO:0010610","count":7}]},{"hash":"1666643536241610310","title":"Chromatin silencing and transcription regulation","description":"The top terms are dominated by heterochromatin formation and negative regulation of transcription by RNA polymerase II, indicating a core function in chromatin-mediated transcriptional repression. Other terms touch on chromatin-related processes and development, with additional immune/migration-related annotations likely reflecting broader roles; overall, the dominant theme is chromatin silencing and transcription control.","confidence":"High","size":18,"edges":39,"triangles":45,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":9},{"id":"GO:0030466","count":8},{"id":"GO:0071674","count":7},{"id":"GO:2000973","count":7},{"id":"GO:0007286","count":7}]},{"hash":"472256480404251242","title":"Neural development and signaling pathways","description":"The cluster shows strong enrichment for nervous system development, dendrite development, axon guidance (Roundabout), and synaptic plasticity, pointing to roles in neural connectivity and signaling. It also includes hedgehog signaling and cochlea morphogenesis, plus kidney development, suggesting broader developmental signaling and organogenesis. Ubiquitination and Golgi localization terms hint at protein processing and trafficking that support these developmental processes. Overall, a cohesive theme around neural development and signaling with related organogenesis is favored.","confidence":"High","size":18,"edges":68,"triangles":103,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0050852","count":13},{"id":"GO:0007399","count":13},{"id":"GO:0035385","count":13},{"id":"GO:0007224","count":12},{"id":"GO:0051835","count":12}]},{"hash":"456479239993019980","title":"Ribosome Biogenesis and Translation","description":"The top GO terms cluster around translation, tRNA modification, and prolyl-tRNA aminoacylation, plus export of the ribosomal large subunit from the nucleus, indicating involvement in ribosome assembly and protein synthesis. Secondary terms related to cell division may reflect growth, but the central theme is translation machinery.","confidence":"High","size":18,"edges":32,"triangles":25,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0051301","count":2},{"id":"GO:0006400","count":2},{"id":"GO:0006433","count":2},{"id":"GO:0000055","count":1}]},{"hash":"1870817711551318631","title":"Presynaptic Vesicle Release and Plasticity","description":"This cluster is dominated by terms related to presynaptic function and synaptic regulation, including vesicle priming, dense core vesicle exocytosis, and regulation of synaptic plasticity. The presence of brain development and retrograde/neuropeptide signaling terms supports a neuronal context, while lipid and eicosanoid biosynthesis align with membrane signaling at synapses; a few immune-related terms may be peripheral. ","confidence":"Medium","size":18,"edges":17,"triangles":0,"max_degree":4,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0007420","count":4},{"id":"GO:0099526","count":3},{"id":"GO:0016082","count":3},{"id":"GO:1902479","count":3},{"id":"GO:0043065","count":3}]},{"hash":"1237056497534380266","title":"Isoprenoid and sterol biosynthesis","description":"Based on GO terms including cholesterol biosynthetic process, monoterpene biosynthetic process, quinone biosynthetic process, and geranylgeranyl diphosphate biosynthetic process, this cluster appears enriched for isoprenoid/terpenoid and sterol metabolism; translation and developmental terms are present but less cohesive with the central biosynthesis theme.","confidence":"High","size":18,"edges":24,"triangles":0,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":4},{"id":"GO:0006412","count":3},{"id":"GO:0042594","count":2},{"id":"GO:0001701","count":2},{"id":"GO:0006695","count":2}]},{"hash":"2135574753358488669","title":"N-terminal Acetylation Enzymes","description":"This cluster is dominated by GO terms related to N-terminal and peptidyl acetylation (e.g., N-terminal protein amino acid acetylation, N-terminal peptidyl-methionine acetylation, peptidyl-lysine N6-acetylation, and related propionylation) and includes supporting terms like melatonin biosynthetic process and spermidine acetylation. The strongest signal is acetylation/modification of proteins and peptides, indicating a common theme of N-terminal acetyltransferase activity and related acetylation pathways. Some terms (angiogenesis, sporulation) appear tangential but do not override the prevailing acetylation theme.","confidence":"High","size":18,"edges":15,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0061606","count":5},{"id":"GO:0030187","count":5},{"id":"GO:0017196","count":5},{"id":"GO:0001525","count":5},{"id":"GO:0018003","count":5}]},{"hash":"1936483656301648163","title":"Ubiquitin-Dependent Regulation","description":"The cluster centers on ubiquitination-related processes (ubiquitin-dependent protein catabolic process, protein polyubiquitination, and negative regulation of ubiquitination) and includes regulation of circadian rhythm, suggesting a shared role in proteostasis timing; additional immune and developmental terms (B cell receptor signaling, germinal center formation, skeletal muscle development) imply broader ubiquitin-regulated signaling across tissues.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":9},{"id":"GO:0042752","count":8},{"id":"GO:0051260","count":7},{"id":"GO:0000209","count":6},{"id":"GO:2000312","count":6}]},{"hash":"1844869414801325433","title":"Adipogenesis and mechanotransduction","description":"The cluster is driven by adipocyte differentiation and mechanosensing signals, shown by fat cell differentiation, cellular response to mechanical stimulus, and response to muscle stretch, along with cell migration related to tissue remodeling. Immune and telomere terms appear but are less central to the main theme. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":6},{"id":"GO:0070431","count":6},{"id":"GO:2001275","count":5},{"id":"GO:1904355","count":5},{"id":"GO:0035994","count":5}]},{"hash":"387148987136868257","title":"Reproductive Hormone Signaling and Innate Immunity","description":"The top GO terms strongly point to reproductive signaling (luteinizing hormone and follicle-stimulating hormone pathways, uterus development, sperm DNA condensation), while also highlighting innate immune defenses (innate immune response, defense against virus, interferon-alpha production) and PLC/IP3 signaling. This suggests a cluster where GPCR-PLC\u2013IP3 mediated signaling participates in both reproductive biology and antiviral responses, making the combined theme a concise label. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0009992","count":16},{"id":"GO:0042700","count":16},{"id":"GO:0060065","count":16},{"id":"GO:0042699","count":16},{"id":"GO:0051607","count":16}]},{"hash":"766409922933996602","title":"Cytoskeleton remodeling and cell adhesion signaling","description":"This cluster is driven by GO terms related to actin-based structures and dynamics (filopodium assembly, regulation of filopodium assembly, positive regulation of substrate adhesion-dependent spreading), small GTPase signaling (Rho-like pathways), and genes involved in cell shape changes and morphogenesis (hair follicle placode formation). Mitochondrial fission and cell cycle terms appear but are supportive or secondary to the central theme of cytoskeletal remodeling governing cell adhesion, spreading, and movement during development. Overall, the common thread is cytoskeletal dynamics coordinating adhesion, signaling, and morphogenesis.","confidence":"Medium","size":18,"edges":14,"triangles":3,"max_degree":7,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0007049","count":7},{"id":"GO:1900026","count":7},{"id":"GO:0000266","count":7},{"id":"GO:0051489","count":7},{"id":"GO:0045792","count":7}]},{"hash":"1057642632056609456","title":"mRNA splicing and translation initiation","description":"The cluster shows strong signals for spliceosome-mediated mRNA processing (splicing, small-subunit processome assembly, alternative splicing) and for translation initiation complex formation (translation preinitiation complex, eIF4F complex assembly, IRES-dependent initiation). This suggests these proteins function together in RNA processing and the initiation of translation, justifying a combined label that captures both themes.","confidence":"High","size":18,"edges":43,"triangles":49,"max_degree":13,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006376","count":5},{"id":"GO:0006378","count":5},{"id":"GO:0045292","count":5},{"id":"GO:0031047","count":4},{"id":"GO:0016556","count":4}]},{"hash":"395088259601958028","title":"Ribosome Biogenesis and Translation","description":"Dominant signals are ribosome biogenesis (including small subunit), translation, and maturation of SSU-rRNA, with tRNA pseudouridine synthesis also present. Together these points suggest a cluster of proteins involved in ribosome assembly and protein synthesis, with secondary links to cell cycle and vesicle trafficking that may reflect broader growth coordination.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0007049","count":4},{"id":"GO:0006412","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0042274","count":3},{"id":"GO:0051301","count":3}]},{"hash":"831869947596235377","title":"Organelle Inheritance and Vesicle Transport","description":"The top GO terms cluster around inheritance of organelles (mitochondrion, peroxisome, vacuole) and processes linked to cell division and cytokinesis (spindle orientation, membrane addition at the division site), with supporting terms for vesicle transport along actin and related cell growth/migration cues. This suggests a theme of intracellular trafficking and organelle inheritance during division, with some involvement in cell migration pathways.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045033","count":2},{"id":"GO:0006930","count":2},{"id":"GO:0007107","count":2},{"id":"GO:0000011","count":2},{"id":"GO:0000132","count":2}]},{"hash":"708110303506806586","title":"Developmental gene regulation and differentiation","description":"The terms point to roles in development and differentiation across tissues (brain, uterus, Sertoli and myocardial precursors) and in transcriptional control (including ncRNA-mediated silencing). Coupled with growth regulation and extracellular signaling, this supports a theme of developmental gene regulation and cell fate specification.","confidence":"Medium","size":18,"edges":10,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0031047","count":1},{"id":"GO:0010735","count":1},{"id":"GO:0003257","count":1},{"id":"GO:0016049","count":1}]},{"hash":"1885728562806389576","title":"Ubiquitin-Mediated Regulation of Signaling","description":"The dominant signal is ubiquitination (polyubiquitination, K48-linked, autoubiquitination) paired with regulation of signaling and apoptosis, suggesting a cluster of ubiquitin-related regulators modulating pathway activity and cell fate. A few outliers (synaptic potentiation, peroxisome import) exist, but the core theme is ubiquitin-dependent control of signaling and survival.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060291","count":2},{"id":"GO:1900095","count":1},{"id":"GO:0000209","count":1},{"id":"GO:0023051","count":1},{"id":"GO:0016558","count":1}]},{"hash":"2144365403445955833","title":"Plant endomembrane trafficking and plastid organization","description":"The top GO terms cluster around endosome transport/organization and actin cytoskeleton dynamics, pointing to intracellular trafficking; additional terms like amyloplast organization, chloroplast stroma import, and gravitropism strongly tie the function to plastids and plant gravity sensing. Together they suggest a program coordinating vesicle trafficking with plastid dynamics in plant cells.","confidence":"Medium","size":18,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0060313","count":2},{"id":"GO:0002692","count":2},{"id":"GO:0043314","count":2},{"id":"GO:0009660","count":2},{"id":"GO:0045037","count":2}]},{"hash":"1358668054958994119","title":"Genome Stability and Telomere Maintenance","description":"The cluster is characterized by strong signals for DNA repair, DNA recombination, DNA-templated transcription, and telomere maintenance/localization to telomeres, pointing to a shared involvement in genome integrity and chromosome end maintenance. The presence of translation-related terms may reflect multifunctional nuclear proteins or annotation overlaps, but they do not outweigh the genome-maintenance theme. Overall, the proteins seem tied to nuclear genome processing and telomere biology.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0071915","count":1}]},{"hash":"597884367030797564","title":"Mitochondrial energy metabolism and proteostasis","description":"This cluster is enriched for terms tied to mitochondrial energy production (mitochondrial electron transport, aerobic respiration) and proteostasis pathways (ubiquitin recycling, negative regulation of proteolysis, bradykinin catabolic process). Additional terms point to signaling and protein interactions (insulin receptor signaling, protein heterooligomerization). The combination suggests a group whose core function relates to cellular energy metabolism with modulation by protein turnover and signaling.","confidence":"Medium","size":18,"edges":44,"triangles":38,"max_degree":16,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0010815","count":5},{"id":"GO:0010992","count":4},{"id":"GO:0045861","count":4},{"id":"GO:0006122","count":4},{"id":"GO:0008286","count":4}]},{"hash":"2122427424040923945","title":"Mitochondrial tRNA aminoacylation and translation","description":"This cluster is dominated by GO terms for mitochondrial tRNA aminoacylation across several amino acids (threonine, histidine, proline, glycine) and for translation, pointing to a core role in mitochondrial protein synthesis. The presence of mitochondrial DNA metabolic process and DNA biosynthetic process terms suggests a broader link to mtDNA maintenance. Overall, the data support a theme around mitochondrial translation machinery and its connection to genome upkeep.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070159","count":1},{"id":"GO:0000105","count":1},{"id":"GO:0006450","count":1},{"id":"GO:0032042","count":1},{"id":"GO:0006433","count":1}]},{"hash":"478028571177743065","title":"Ion Transport and Cardiac Electrophysiology","description":"The GO terms show strong signals for ion transport across membranes (sodium/potassium), membrane depolarization, and regulation of ventricular/AV nodal action potentials, pointing to ion movement and cardiac electrical activity. Signaling terms (cAMP/cGMP) add context, while a few terms like aerotaxis and touch sensing appear peripheral noise; overall the theme fits ion transport linked to cardiac excitability.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009454","count":10},{"id":"GO:0010754","count":10},{"id":"GO:0071320","count":10},{"id":"GO:0071321","count":10},{"id":"GO:0098719","count":10}]},{"hash":"1550275331314099941","title":"Mechanosensitive Calcium Signaling and Neuroendocrine Secretion","description":"This cluster centers on calcium dynamics in response to mechanical stimuli and neuroendocrine processes, with terms for calcium import, release from stores, and synaptic regulation, as well as related secretion (e.g., vasopressin). While some terms are related to unrelated pathways, the dominant theme is calcium-driven signaling in mechanosensory and neural contexts.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":8},{"id":"GO:0098703","count":8},{"id":"GO:0009409","count":8},{"id":"GO:0051209","count":8},{"id":"GO:1900383","count":8}]},{"hash":"615307263043455762","title":"RNA Modification and Cofactor Biosynthesis","description":"The cluster centers on RNA-related modifications (tRNA wobble uridine modification, tRNA methylation, mRNA capping, and arginine methylation) and biosynthetic pathways for cofactors such as cobalamin and biotin, with an additional note of antibiotic biosynthesis. This combination suggests a functional theme around RNA processing/modification intertwined with biosynthesis of small molecules and cofactors, rather than a single signaling or response pathway.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":10},{"id":"GO:0009236","count":7},{"id":"GO:0009102","count":6},{"id":"GO:0019919","count":5},{"id":"GO:0002098","count":5}]},{"hash":"1333515344330395065","title":"RNA decay and translation regulation","description":"This cluster's top GO terms center on mRNA turnover and translation control, including deadenylation-dependent decapping and decay, poly(A) tail shortening, and negative regulation of translation, plus transcription elongation by RNA polymerase II. Together these suggest a group of proteins involved in post-transcriptional mRNA processing and transcriptional elongation; other terms (apoptotic process and glycosylation) are less defining for the cluster.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":2},{"id":"GO:0006486","count":2},{"id":"GO:0001829","count":1},{"id":"GO:0000290","count":1},{"id":"GO:0000289","count":1}]},{"hash":"1332258879822280314","title":"Polysaccharide and Capsule Biosynthesis","description":"The cluster is dominated by GO terms related to UDP-sugar metabolism (UDP-glucose/galactose/GlcNAc), polysaccharide and capsule biosynthesis, and cell wall organization, pointing to a coherent glycan biosynthesis/capsule formation theme. Some terms (e.g., glycogen, globoside, sphingolipid-related) further support broader glycan or glycolipid biosynthetic activity; overall, these proteins appear to function in building polysaccharide-based structures such as capsules and cell walls.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006011","count":3},{"id":"GO:0071555","count":2},{"id":"GO:0045227","count":2},{"id":"GO:0052573","count":2},{"id":"GO:0006048","count":2}]},{"hash":"165592582014093702","title":"Epidermal sphingolipid metabolism and keratinocyte differentiation","description":"The terms point to sphingolipid biosynthesis (sphingosine, phytosphingosine) and ceramide catabolism, plus keratinocyte differentiation and adhesion regulation. This suggests a cohesive theme around epidermal lipid metabolism and keratinocyte maturation, with supporting signals from calcium response and xenobiotic/pH responses common in skin biology.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090285","count":1},{"id":"GO:0046512","count":1},{"id":"GO:0046514","count":1},{"id":"GO:0001953","count":1},{"id":"GO:0071277","count":1}]},{"hash":"1530016141941914707","title":"Endosome Trafficking and Synaptic Transport","description":"This cluster centers on membrane trafficking, especially endocytosis and receptor recycling, with neuronal context suggested by glutamatergic synaptic transmission and related signaling (Rho) that drives cytoskeletal remodeling; including xenobiotic transport hints at membrane transporter activity as well. Some terms are regulatory or obsolete, indicating annotation noise but not a conflicting theme.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":2},{"id":"GO:0051036","count":1},{"id":"GO:0035249","count":1},{"id":"GO:0035023","count":1},{"id":"GO:0034968","count":1}]},{"hash":"1302265383554366594","title":"Calcium signaling and mechanotransduction","description":"Based on the top GO terms, this cluster centers on calcium dynamics (calcium import and release) and signaling pathways activated by GPCRs and mechanical stimuli. Terms like cellular response to mechanical stimulus, calcium ion import, and calcium release indicate calcium\u2011dependent signaling and mechanotransduction as a unifying theme, with supporting components in migration and synaptic plasticity regulation.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":7},{"id":"GO:0007205","count":7},{"id":"GO:0016477","count":7},{"id":"GO:0071260","count":6},{"id":"GO:0098703","count":6}]},{"hash":"1138816195613297626","title":"Metabolic Biosynthesis and Ion Transport","description":"GO terms span biosynthesis (antibiotic, LPS, L-serine) and catabolism (stilbene), as well as phosphatase activity and ion homeostasis/transport (calcium, zinc, cadmium). This suggests a broad metabolic/transport theme rather than a single precise function, hence the label Metabolic Biosynthesis and Ion Transport.","confidence":"Medium","size":17,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0046272","count":3},{"id":"GO:0046839","count":3},{"id":"GO:0016311","count":3},{"id":"GO:0006874","count":3}]},{"hash":"1611009518384018415","title":"GPI anchor biosynthesis and protein glycosylation","description":"Top terms cluster around glycosylation and GPI-anchor biosynthesis, notably GPI anchor biosynthetic process and protein glycosylation, suggesting a module of proteins involved in post-translational modification of proteins in the ER. Some terms are obsolete or more general metabolic processes, likely annotation noise, but the central theme remains glycosylation-related biogenesis.","confidence":"High","size":17,"edges":114,"triangles":414,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0002526","count":3},{"id":"GO:0006486","count":3},{"id":"GO:0044209","count":2},{"id":"GO:0046939","count":2},{"id":"GO:0046940","count":2}]},{"hash":"1927890809741360200","title":"Epigenetic transcriptional regulation and chromatin remodeling","description":"This cluster shows a strong enrichment for epigenetic-related terms: negative regulation of transcription by RNA polymerase II, chromatin remodeling, histone modifications (H2B ubiquitination, H3-K27 trimethylation), and DNA methylation, plus nucleosome density regulation. While a few terms pertain to heart development, the dominant signal is epigenetic control of transcription and chromatin state.","confidence":"High","size":17,"edges":95,"triangles":279,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":9},{"id":"GO:0060303","count":8},{"id":"GO:0036091","count":8},{"id":"GO:0043044","count":7},{"id":"GO:0033697","count":6}]},{"hash":"473889303087358301","title":"Plant AGP glycosylation and cell wall biosynthesis","description":"Most terms point to arabinogalactan protein metabolism, AGP glycosylation, and plant cell wall processes (root hair development, seed coat mucilage, cell wall organization), suggesting a cluster of glycoproteins involved in cell wall assembly and tissue morphogenesis in plants. Some outliers reference insect development, likely cross-species annotations, but the dominant theme is plant cell wall\u2013associated glycoprotein biosynthesis.","confidence":"High","size":17,"edges":62,"triangles":67,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0080147","count":4},{"id":"GO:0071555","count":3},{"id":"GO:0030311","count":2},{"id":"GO:0007299","count":2},{"id":"GO:0010493","count":2}]},{"hash":"531101923717484804","title":"Membrane lipid metabolism and metal ion transport","description":"The cluster\u2019s terms cluster around lipid-related processes (lipopolysaccharide biosynthetic process; phospholipid dephosphorylation) and metal ion transport/homeostasis (zinc, cadmium, copper transmembrane transport; intracellular calcium ion homeostasis), suggesting a common theme of membrane lipid metabolism linked to ion transport. Some terms (L-serine biosynthesis; stilbene catabolic process) appear peripheral, but do not outweigh the dominant lipid/metal transport signal.","confidence":"Medium","size":17,"edges":103,"triangles":359,"max_degree":15,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0009103","count":8},{"id":"GO:0016311","count":8},{"id":"GO:0097755","count":7},{"id":"GO:0046839","count":7},{"id":"GO:0006564","count":7}]},{"hash":"1279066752941193684","title":"Bacterial Secondary Metabolism and Vitamin Biosynthesis","description":"The top GO terms cluster around biosynthetic processes common in microbes, notably biotin biosynthesis, menaquinone biosynthesis, and antibiotic biosynthetic processes, suggesting a microbial/metabolic focus. RNA guanine-N7-methylation may relate to gene expression regulation in bacteria, while some immune signaling terms (e.g., T cell receptor signaling) likely reflect cross-species annotation noise. Overall, a theme of microbial secondary metabolism and vitamin biosynthesis best fits the cluster.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0035690","count":5},{"id":"GO:0071560","count":5},{"id":"GO:0009102","count":5},{"id":"GO:0097011","count":4},{"id":"GO:0036265","count":4}]},{"hash":"1358023361955632596","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000398","count":7},{"id":"GO:0001731","count":5},{"id":"GO:0002188","count":5},{"id":"GO:0034729","count":4},{"id":"GO:0048026","count":4}]},{"hash":"578570297316531076","title":"Carbohydrate metabolism and sugar catabolism","description":"Top GO terms indicate broad carbohydrate metabolism and sugar catabolic pathways (glycolysis; glucose-6-phosphate; N-acetylglucosamine; N-acetylmannosamine; N-acetylneuraminate; D-allose), plus peptidoglycan turnover and cobalamin biosynthesis, suggesting a cohesive theme of sugar processing. A few transcription regulation terms are present but appear secondary to the dominant carbohydrate metabolism signals.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":4},{"id":"GO:0006096","count":3},{"id":"GO:0009236","count":3},{"id":"GO:0006051","count":2},{"id":"GO:0009254","count":2}]},{"hash":"1660189198132739702","title":"Cardiovascular Development Signaling","description":"These terms cluster around heart development and the signaling networks that control cardiac growth and vascular responses (hippo, Wnt, VEGF, JNK regulation) plus related metabolic signaling. Although a skin differentiation term appears, the dominant theme is cardiovascular development and its key pathway regulators, so Cardiovascular Development Signaling is an intuitive, representative label.","confidence":"High","size":17,"edges":24,"triangles":4,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030216","count":11},{"id":"GO:0006915","count":11},{"id":"GO:0035329","count":11},{"id":"GO:0060044","count":11},{"id":"GO:0090263","count":10}]},{"hash":"163623576509773077","title":"Virus Entry and Replication Activation","description":"These GO terms cluster around viral infection processes: entry of viral particles (fusion of virus membrane with host plasma membrane), RNA-templated DNA biosynthesis (reverse transcription) and host-mediated activation of viral genome replication, as well as lipid droplet organization that can support viral replication. Some other terms reflect general host cell processes hijacked during infection (e.g., ribosome biogenesis and protein isomerization). Overall, the dominant theme is virus entry and replication with associated host responses.","confidence":"Medium","size":17,"edges":74,"triangles":113,"max_degree":13,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0006278","count":3},{"id":"GO:0010849","count":3},{"id":"GO:0044829","count":3},{"id":"GO:2000276","count":3}]},{"hash":"253041942427113957","title":"Ubiquitin-mediated proteostasis and ER stress","description":"These proteins cluster around protein quality control, with strong signals for ubiquitination/deubiquitination, ER-associated degradation, autophagy (aggrephagy), and responses to ER stress, plus related nuclear repair processes. The presence of transcription regulation and a brain-specific developmental term appears ancillary to the core theme of maintaining proteome integrity via ubiquitin pathways and stress responses.","confidence":"High","size":17,"edges":131,"triangles":615,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0006357","count":7},{"id":"GO:0030433","count":7},{"id":"GO:1902236","count":6},{"id":"GO:0014070","count":6},{"id":"GO:0034140","count":6}]},{"hash":"448398999178138160","title":"Developmental morphogenesis and neural signaling","description":"The terms point to broad developmental processes (heart and retina formation, angiogenesis, cell budding) and neural signaling components (synaptic vesicle endocytosis, potassium channel clustering), with proteolysis suggesting remodeling. This pattern fits a cluster centered on developmental morphogenesis with associated neural signaling activities.","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":4},{"id":"GO:0045163","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0008284","count":2},{"id":"GO:1900242","count":2}]},{"hash":"1287350564571124525","title":"Developmental Translation and Gene Regulation","description":"The top term is translation, but the cluster also includes brain development and other tissue differentiation terms, along with regulation-related processes such as protein sumoylation and ncRNA-mediated gene silencing. This suggests a theme of gene-expression control during development, with protein synthesis at the core and regulatory layers shaping neural and reproductive tissue differentiation.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0007420","count":4},{"id":"GO:0016925","count":4},{"id":"GO:0031047","count":3},{"id":"GO:0010735","count":3}]},{"hash":"2057056175137153459","title":"Neural development and synaptic plasticity","description":"The proteins are enriched for brain development, subpallium development, and long-term potentiation, indicating a neural development and synaptic plasticity theme. The presence of cellular response to insulin stimulus and regulation of phosphatidylinositol dephosphorylation suggests metabolic signaling roles that support neuronal activity, with pentose phosphate pathway terms reflecting neuronal metabolism as a supporting factor.","confidence":"High","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0032869","count":2},{"id":"GO:0060291","count":2},{"id":"GO:0060304","count":2}]},{"hash":"644228617887522691","title":"Fungal biofilm and cell wall polysaccharide metabolism","description":"The cluster is dominated by GO terms for biofilm formation (single-species on host or inanimate substrate) and for catabolic processes of fungal cell wall polysaccharides (xylan, cellulose, mannan, beta-glucan), plus related ergosteryl glycoside metabolism. This points to a cohesive theme of fungal biofilm development with remodeling/degradation of cell wall carbohydrates, justifying a label centered on fungal biofilm and cell wall metabolism.","confidence":"High","size":17,"edges":16,"triangles":0,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0044407","count":4},{"id":"GO:0045493","count":4},{"id":"GO:1904462","count":4},{"id":"GO:0070879","count":4},{"id":"GO:0030245","count":4}]},{"hash":"362177479189156495","title":"Nuclear transcription and chromatin remodeling","description":"Based on GO terms, the cluster is enriched for DNA-templated transcription, RNA Pol II regulation, and nucleosome assembly with chromatin remodeling, indicating a nuclear gene-expression module. Additional terms for RNA methylation and related modifications align with RNA processing in the nucleus, reinforcing a theme of transcription control and chromatin dynamics rather than cytosolic metabolism. The presence of a few plant signaling terms is peripheral to the dominant pattern.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0036265","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0043044","count":3},{"id":"GO:0051301","count":3}]},{"hash":"944920937650023471","title":"ER Stress and Protein Folding","description":"This cluster is dominated by GO terms related to unfolded protein response and ER stress (e.g., response to unfolded protein; positive regulation of translation initiation in response to ER stress), together with protein folding and isomerization (peptidyl-prolyl isomerization), indicating a cohesive theme of ER stress\u2013driven protein homeostasis. Cadmium ion response and chlorophyll biosynthesis regulation also align with stress-related cellular adjustments, supporting a general stress-activated protein-folding/translation control role, despite some plant-specific terms.","confidence":"High","size":17,"edges":19,"triangles":3,"max_degree":16,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0006986","count":6},{"id":"GO:0071276","count":5},{"id":"GO:0036494","count":5},{"id":"GO:0051291","count":4}]},{"hash":"1234847793829285614","title":"Mitochondrial metabolite transport and redox homeostasis","description":"The cluster is dominated by GO terms for transport of various metabolites into or across the mitochondrial membranes (e.g., alpha-ketoglutarate, citrate, ornithine, glycine, pyrimidine nucleotides) and for redox-related processes (cell redox homeostasis, response to superoxide, malate-aspartate shuttle), suggesting proteins that coordinate mitochondrial metabolite exchange with oxidative balance.","confidence":"High","size":17,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0045454","count":4},{"id":"GO:1990544","count":4},{"id":"GO:0000303","count":4},{"id":"GO:1990519","count":4},{"id":"GO:0015742","count":4}]},{"hash":"814270982623142290","title":"tRNA charging and translation","description":"This cluster is dominated by multiple tRNA aminoacylation activities (methionyl-, isoleucyl-, leucyl-, valyl-) and core translation terms (translation, translational fidelity), pointing to a cohesive role in tRNA charging and protein synthesis. A few other terms (transcription regulation and chromatin-related edits) appear ancillary or represent annotation noise rather than core function.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006431","count":4},{"id":"GO:0006450","count":4},{"id":"GO:0006428","count":4},{"id":"GO:0006412","count":4},{"id":"GO:0006438","count":4}]},{"hash":"1161406203759436147","title":"Redox Metabolism and Detoxification","description":"This cluster centers on redox-related processes: NAD+ biosynthesis, sulfur assimilation, and oxidation-reduction activity, plus cellular oxidant detoxification and xenobiotic response (including menadione-related stress). The inclusion of proton transmembrane transport and tRNA wobble modification hints at metabolic and translational adjustments linked to redox state and sulfur metabolism. Together, these terms suggest a cohesive theme of redox balance, metabolism supporting detox pathways, and stress response.","confidence":"Medium","size":17,"edges":9,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009435","count":2},{"id":"GO:1902600","count":2},{"id":"GO:0000103","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0055114","count":2}]},{"hash":"1390586063383862128","title":"Arabinogalactan protein glycosylation and cell wall development","description":"The cluster centers on glycosylation of extracellular glycoproteins, especially arabinogalactan proteins (AGPs), with GO terms referring to AGP biosynthesis/metabolism, poly-N-acetyllactosamine, Lewis A epitopes, and related glycosylation processes. Supporting terms include mucilage biosynthesis, root hair development, and cell adhesion/polarity maintenance, all pointing to plant cell wall assembly and extracellular matrix functions driven by AGPs and related glycoproteins.","confidence":"Medium","size":17,"edges":97,"triangles":251,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0030311","count":3},{"id":"GO:0007299","count":3},{"id":"GO:0010493","count":3},{"id":"GO:0075015","count":3},{"id":"GO:0018258","count":3}]},{"hash":"594625605537418095","title":"Ubiquitin-Dependent Protein Degradation","description":"The cluster is dominated by GO terms tied to ubiquitination and proteasomal catabolism (e.g., ubiquitin-dependent proteolysis, K48-linked ubiquitination, SCF-dependent proteasomal degradation) and includes autoubiquitination, all pointing to ubiquitin\u2013proteasome\u2013mediated protein turnover. Additional terms like Wnt receptor catabolic process and peroxisomal protein import reflect broader connections to receptor turnover and quality control via ubiquitination, supporting a cohesive degradation-focused theme.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":8},{"id":"GO:0070936","count":6},{"id":"GO:0031146","count":6},{"id":"GO:1900095","count":5},{"id":"GO:0016558","count":5}]},{"hash":"449441047998414280","title":"NF-kappaB-mediated immune signaling via ubiquitination","description":"The top terms cluster around NF-kappaB signaling and its regulation (including non-canonical NF-kappaB), NOD2 signaling, and ubiquitin-proteasome\u2013dependent protein degradation, plus IL-1 production and transcriptional regulation; these together point to a theme of NF-kappaB\u2013driven immune signaling modulated by ubiquitination. A few peripheral terms relate to broader transcription/cell-cycle regulation and dopamine signaling, but the core pattern supports this immune-ubiquitin NF-kappaB axis.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0032088","count":5},{"id":"GO:0070431","count":5},{"id":"GO:0031146","count":4},{"id":"GO:0016567","count":3},{"id":"GO:0000083","count":3}]},{"hash":"1870172025043831721","title":"Ribosome Biogenesis and Translation","description":"The cluster is strongly enriched for ribosome-related processes: ribosome biogenesis (GO:0042254), ribosomal subunit biogenesis (GO:0042274), ribosomal large subunit export from nucleus (GO:0000055), cytoplasmic translation (GO:0002181), translation (GO:0006412), and tRNA modification (GO:0006400). Together these point to a cohesive set of proteins involved in assembling ribosomes, exporting ribosomal subunits, and carrying out protein synthesis, with only a few peripheral terms (e.g., cell cycle, septum assembly) contributing relatively little to the main signal.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0000055","count":2},{"id":"GO:1901001","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0006400","count":2}]},{"hash":"2147990333041934952","title":"Bacterial translation and cell wall biosynthesis","description":"The cluster is characterized by strong representation of ribosome biogenesis and cytoplasmic translation terms (and ribosomal large subunit assembly), alongside cell wall biosynthesis processes (cell wall organization and peptidoglycan biosynthetic pathway, including D-alanine). This combination points to a core bacterial housekeeping module coordinating protein synthesis with cell wall construction, rather than a specialized signaling or catabolic pathway. Minor terms like interleukin-4 response or halogenated hydrocarbon metabolism are likely incidental. ","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0030632","count":1},{"id":"GO:0008360","count":1}]},{"hash":"1736984536073948353","title":"Unknown","description":"The Top Terms are highly heterogeneous, spanning nucleic acid metabolism (nuclease, DNA rewinding, telomerase assembly), defense, nematode and plant development terms, and hormone signaling, with no clear shared process. Edges and triangles are zero, suggesting no coherent functional cluster. Because there is no single dominant function linking the proteins, the safe label is Unknown with no confidence in a representative function.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090305","count":1},{"id":"GO:0036292","count":1},{"id":"GO:0051607","count":1},{"id":"GO:0061321","count":1},{"id":"GO:0018996","count":1}]},{"hash":"644444929399604897","title":"Neuronal development and synaptic signaling","description":"This cluster prominently features neural-related processes: long-term synaptic potentiation, excitatory postsynaptic potential, axonogenesis, and mRNA transport, all pointing to neuronal differentiation and synaptic function. Additional terms like cellular response to hypoxia can occur in neurons, while others (mitotic cell cycle, branching in blood vessel morphogenesis) reflect broader developmental processes. Overall, the strongest signal centers on neuronal development and synaptic activity.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0043065","count":2},{"id":"GO:0060291","count":2}]},{"hash":"111924371747465759","title":"RNA processing and translation initiation","description":"The top GO terms cluster around RNA processing and translation machinery: alternative splicing via the spliceosome, small-subunit processome assembly, formation of the translation preinitiation complex, and mRNA modification, with additional nuclear maintenance functions. This points to a cohesive group of proteins involved in RNA processing and initiation of protein synthesis, rather than signaling or metabolism. ","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":1},{"id":"GO:0045598","count":1},{"id":"GO:0043966","count":1},{"id":"GO:0001833","count":1},{"id":"GO:0051457","count":1}]},{"hash":"781598915169183273","title":"Ribosome Biogenesis and Nuclear Transport","description":"This cluster centers on nuclear processes involved in assembling and exporting ribosomes, including ribosome biogenesis, maturation of LSU rRNA, andexport of the large subunit from the nucleus, along with guidance of proteins to the nucleus. These terms together point to a cohesive theme of ribosome assembly and nuclear-cytoplasmic transport. Some remaining terms refer to other signaling or cell-cycle processes, but they appear less connected to the core ribosome/nuclear theme. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042517","count":1},{"id":"GO:0051457","count":1},{"id":"GO:0000055","count":1},{"id":"GO:1901857","count":1},{"id":"GO:0042254","count":1}]},{"hash":"64040343663169369","title":"ER-Golgi vesicle trafficking","description":"The top terms are dominated by vesicle transport within the secretory pathway (ER\u2013Golgi and Golgi\u2013ER traffic, endocytic recycling, exocytosis, Golgi to vacuole, and endosome-to-Golgi retrograde), with a couple of mitotic and development terms that may reflect broader cellular roles. Overall, the shared function appears to be vesicle trafficking through the ER-Golgi network.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0090307","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0032456","count":3},{"id":"GO:0006887","count":3}]},{"hash":"2259632603564311275","title":"Chromatin modification and transcriptional regulation","description":"The top GO terms point to histone demethylation and transcriptional control (e.g., histone H3 demethylation and DNA-templated transcription) with accompanying developmental roles (myoblast differentiation, vasculogenesis) and signaling regulation (Notch, hypoxia response). This pattern suggests proteins involved in regulating gene expression through chromatin modification and associated developmental pathways, even though several terms are obsolete and there are no observed edges in the network. Confidence: Medium","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0070544","count":7},{"id":"GO:0034720","count":7},{"id":"GO:0042264","count":6},{"id":"GO:0042265","count":6},{"id":"GO:0045663","count":6}]},{"hash":"265262382847120829","title":"Mitochondrial Metabolite Transport","description":"The top GO terms cluster around transport of various metabolites into and out of mitochondria (ATP, \u03b1-ketoglutarate, citrate, pyrimidine nucleotides, ornithine, glycine) and related metabolic/shuttle processes (malate-aspartate). A related signaling term (IGF stimulus response) may reflect metabolic regulation, but the dominant signal is mitochondrial metabolite transport and exchange. ","confidence":"High","size":17,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1990544","count":16},{"id":"GO:0000303","count":16},{"id":"GO:1990519","count":16},{"id":"GO:0015742","count":16},{"id":"GO:0097274","count":16}]},{"hash":"210631938832161842","title":"N-terminal acetylation and polyamine metabolism","description":"This cluster centers on acetylation-related GO terms (N-terminal acetylation, propionylation, various peptidyl acetylations) and polyamine metabolism (putrescine catabolic process, spermidine acetylation, arginine biosynthesis feeding polyamine pathways). The melatonin biosynthetic term also connects to N-acetyltransferase activity, while angiogenesis and glucosamine metabolism appear as downstream or supportive processes. Together, the dominant theme is protein acetylation together with polyamine turnover, pointing to a combined role in acetylation machinery and polyamine biosynthesis/degradation.","confidence":"High","size":17,"edges":57,"triangles":139,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0061606","count":8},{"id":"GO:0030187","count":8},{"id":"GO:0017196","count":8},{"id":"GO:0001525","count":8},{"id":"GO:0018003","count":8}]},{"hash":"1851068449193818901","title":"Membrane Transport and Vesicle Loading","description":"The GO terms point to transport across membranes (xenobiotic transport, transmembrane transport, glucose import, selenite transport, phosphate ion transport) and a vesicle-related process (neurotransmitter loading into synaptic vesicles), suggesting a cohesive theme of membrane transport and vesicle packaging rather than a single specific substrate. Some terms are obsolete, so interpretation is cautious but centers on transport functions.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090116","count":2},{"id":"GO:0009405","count":1},{"id":"GO:0098700","count":1},{"id":"GO:0042908","count":1},{"id":"GO:0071486","count":1}]},{"hash":"2021904606651576273","title":"Cell Polarity and Cytoskeleton Remodeling","description":"The cluster centers on processes like endocytic recycling, lamellipodium morphogenesis, ECM disassembly, and centrosome localization, all of which tie to cell polarity and actin-driven migration. PI signaling and lipid biosynthesis further connect membrane dynamics to polarity establishment, suggesting a cohesive group of proteins coordinating cytoskeletal remodeling, membrane trafficking, and extracellular interactions.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990126","count":2},{"id":"GO:0018023","count":1},{"id":"GO:0006654","count":1},{"id":"GO:2000769","count":1},{"id":"GO:0022617","count":1}]},{"hash":"1680074064327356089","title":"Cytoskeletal dynamics in muscle and neural development","description":"This cluster centers on actin-related processes (actin filament polymerization, cell shape/polarity regulation) and muscle fiber development, with neural contexts (substantia nigra development, retina homeostasis) suggesting a common theme of cytoskeleton-driven tissue development and associated organelle transport/inheritance (mitochondrion, vacuole). The mix of muscle and neural terms alongside cytoskeletal ideas supports this cohesive interpretation, though some terms (e.g., ascospore wall assembly) are more peripheral, hence a Medium confidence.","confidence":"Medium","size":16,"edges":25,"triangles":16,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0048741","count":3},{"id":"GO:0021762","count":3},{"id":"GO:0071963","count":2},{"id":"GO:0001895","count":2},{"id":"GO:0000011","count":2}]},{"hash":"1088311989844616455","title":"Wnt and Hippo signaling in keratinocytes","description":"This cluster is dominated by GO terms linking canonical Wnt signaling, Hippo signaling, and keratinocyte differentiation, all pointing to regulation of epithelial cell growth and maturation. Additional terms on apoptosis, transcription, and cell cycle-related processes (centrosome cycle, DNA-templated transcription) fit a broader theme of proliferation versus differentiation control in epidermal cells, with keratinocytes as a central component. The convergence on keratinocyte differentiation and key signaling pathways suggests a cohesive functional module focused on epithelial growth control and maturation, hence a specific label around keratinocyte biology and signaling.","confidence":"High","size":16,"edges":10,"triangles":2,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0090263","count":13},{"id":"GO:0030216","count":13},{"id":"GO:0006915","count":13},{"id":"GO:0035329","count":13},{"id":"GO:0060044","count":13}]},{"hash":"1532335622802693580","title":"Telomere Chromatin Remodeling and Cell Cycle Control","description":"Top terms cluster around chromatin remodeling and cell cycle regulation, with telomere maintenance signals (telomere loop formation, rDNA heterochromatin) and replication-associated DNA repair suggesting a genome-stability theme. The presence of negative regulation of CDK activity and ERK cascade aligns with controlled cell cycle progression tied to chromatin state, though a couple plant-specific terms appear. ","confidence":"High","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0043044","count":3},{"id":"GO:0070373","count":2},{"id":"GO:0045736","count":2},{"id":"GO:1904850","count":2}]},{"hash":"308566446073078137","title":"Ribosome Biogenesis and DNA Replication","description":"The top GO terms are dominated by rRNA maturation (SSU and LSU from tricistronic transcript) and DNA replication, with an additional replication-associated repair term, pointing to nucleolar ribosome assembly and genome maintenance/cell-cycle roles. A few developmental terms appear but are not central to the cluster\u2019s core function.","confidence":"High","size":16,"edges":4,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0060303","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0048701","count":3},{"id":"GO:0000462","count":3},{"id":"GO:0006260","count":3}]},{"hash":"2236447594136489804","title":"Olfactory Signaling and cGMP/cAMP Responses","description":"The top GO terms overwhelmingly point to olfactory signaling (sensory perception of smell) and second messenger pathways (cellular responses to cGMP and cAMP), including negative regulation of receptor guanylyl cyclase signaling. This suggests a cohesive theme around odor-driven signal transduction and nucleotide-mediated signaling, with a few additional terms (aerotaxis, ion transport, heart rate regulation) likely reflecting broader signaling or transport roles within the cluster. Overall, the main theme is olfactory signaling coupled to cyclic nucleotide responses.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0010754","count":9},{"id":"GO:0007608","count":9},{"id":"GO:0071321","count":9},{"id":"GO:0009454","count":7},{"id":"GO:0071320","count":7}]},{"hash":"266476353471871433","title":"Biomolecule biosynthesis and RNA processing","description":"The GO terms show a mix of biosynthetic pathways (antibiotic, biotin, cobalamin, chlorophyll) alongside RNA maturation/modification processes (tRNA wobble uridine modification, 7-methylguanosine mRNA capping, ribosomal small subunit export). This suggests the cluster centers on broader biosynthesis and RNA processing/biogenesis rather than a single, cohesive pathway.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":4},{"id":"GO:0002098","count":3},{"id":"GO:0019919","count":3},{"id":"GO:1901052","count":3},{"id":"GO:0009102","count":3}]},{"hash":"2030366969480513549","title":"RNA Methylation and Vitamin Cofactor Biosynthesis","description":"The cluster shows enrichment for RNA modification (tRNA methylation, rRNA methylation, mRNA capping, and arginine methylation) alongside biosynthetic processes for vitamins/cofactors (cobalamin, biotin, ubiquinone). This points to a group of enzymes involved in RNA modification and metabolic cofactor biosynthesis, suggesting methyltransferase activity linked to RNA processing and vitamin pathway functions. The lack of edges means the connection is based on GO term associations rather than network structure.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":6},{"id":"GO:0019919","count":4},{"id":"GO:0009102","count":4},{"id":"GO:0002098","count":4},{"id":"GO:0016049","count":4}]},{"hash":"1559400228204559992","title":"Unknown","description":"The GO terms are highly diverse, spanning animal signaling regulation (TGF-beta/SMAD, NF-kappaB) and unrelated plant and cellular processes (vacuole fusion, meristem identity, photosystem adjustments), with several obsolete terms. There isn\u2019t a single coherent function that ties all entries together, so a precise cluster label isn\u2019t supported.","confidence":"","size":16,"edges":24,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0030512","count":4},{"id":"GO:0042347","count":4},{"id":"GO:0035970","count":4},{"id":"GO:0061191","count":4},{"id":"GO:0010991","count":4}]},{"hash":"1097867603111251422","title":"Unknown","description":"The terms span several unrelated areas (cobalamin and lignin biosynthesis, catecholamine metabolism, neurotransmitter transport, and various protein modifications), with no single cohesive function tying the proteins together. This cluster appears functionally heterogeneous, so a specific label cannot be reliably assigned.","confidence":"","size":16,"edges":18,"triangles":1,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":2},{"id":"GO:0009809","count":1},{"id":"GO:0042135","count":1},{"id":"GO:0006479","count":1},{"id":"GO:0006584","count":1}]},{"hash":"172682608419593138","title":"Telomere maintenance and shelterin assembly","description":"Most terms point to telomere biology, including establishment/maintenance of telomeres, shelterin complex assembly, G-quadruplex DNA formation, and telomeric loop formation. A replication-associated double-strand break repair term further ties into telomere maintenance, with a few hormone-response terms appearing less central. Overall, the cluster is best described by telomere maintenance and shelterin dynamics.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904850","count":1},{"id":"GO:1904792","count":1},{"id":"GO:0071919","count":1},{"id":"GO:0031627","count":1},{"id":"GO:0009723","count":1}]},{"hash":"1378697536673967339","title":"Methylation and Immune-Tolerance Regulators","description":"The cluster highlights several methylation-related processes (peptidyl-lysine trimethylation, dimethylation, N-terminal methylation, rRNA methylation) and chromatin-associated activity (rDNA heterochromatin formation), alongside GO terms for negative regulation of innate immune signaling (TLR5, IL-1\u03b2, NOD2 pathways) and K29-linked deubiquitination. This pattern suggests a group of proteins that modulate post-translational modifications and chromatin state, with a connected role in dampening or tuning immune responses. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018023","count":1},{"id":"GO:0031167","count":1},{"id":"GO:0018013","count":1},{"id":"GO:0018027","count":1},{"id":"GO:0000183","count":1}]},{"hash":"105740953854078416","title":"Carbohydrate metabolism and cell wall remodeling","description":"Top GO terms point to carbohydrate metabolism and polysaccharide processes (starch, alpha-glucan, sucrose, trehalose) and to cell wall organization, suggesting the proteins cluster around carbohydrate biosynthesis/degradation and cell wall remodeling. A small number of outlier terms (e.g., neuronal synaptic plasticity) may reflect annotation noise rather than core function.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":4},{"id":"GO:0048170","count":2},{"id":"GO:0044245","count":2},{"id":"GO:0051692","count":2},{"id":"GO:0019252","count":2}]},{"hash":"1873138969078799574","title":"Ubiquitin-dependent chromatin regulation","description":"The top terms cluster around nuclear processes that govern chromatin state, including ubiquitin-dependent proteolysis, histone catabolic/modification regulation, and dosage compensation via X inactivation, with V(D)J recombination reinforcing a chromatin remodeling context. A few terms touch on signaling and viral transport, which are less central to the core theme, suggesting a cohesive but somewhat mixed set of functions centered on chromatin regulation mediated by ubiquitin and histone modifications.","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":8},{"id":"GO:0036205","count":4},{"id":"GO:2000620","count":4},{"id":"GO:0070512","count":4},{"id":"GO:0009048","count":4}]},{"hash":"566876393338947126","title":"Neural development and synaptic plasticity","description":"Top terms are dominated by neural development and plasticity (multicellular organism development, cerebral cortex development, long-term synaptic potentiation, sensory perception of pain), with additional muscle development terms (mesoderm formation, myoblast fusion) reflecting broader developmental context. The cluster appears centered on neural development and synaptic function, with ancillary developmental processes, making this label a reasonable summary.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":6},{"id":"GO:0060291","count":6},{"id":"GO:0019233","count":6},{"id":"GO:0048240","count":5},{"id":"GO:0001707","count":5}]},{"hash":"2014716978553196451","title":"Stress-Associated Translational Regulation","description":"The GO terms center on translation regulation (regulation of translational termination) and stress granule assembly, indicating a core theme of translation control under cellular stress. Additional terms on proline hydroxylation and redox/oxygen homeostasis may reflect stress-linked post-translational modifications, but the strongest signal is stress-related control of protein synthesis.","confidence":"Medium","size":16,"edges":9,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006449","count":1},{"id":"GO:0018401","count":1},{"id":"GO:1901874","count":1},{"id":"GO:0019511","count":1},{"id":"GO:0032364","count":1}]},{"hash":"720461842999847903","title":"Extracellular Matrix Remodeling and Mechanotransduction","description":"This cluster centers on GO terms for extracellular matrix organization and skin development, with additional links to cellular response to mechanical stimulus and calcium signaling, suggesting a module involved in ECM interactions and force-responsive signaling. The calcium flux terms further connect mechanical cues to intracellular activity, while a neuronal plasticity term hints at broader signaling roles. Overall, the proteins likely participate in ECM remodeling and mechanotransduction pathways, with calcium signaling as a key mediator.","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0010745","count":5},{"id":"GO:0043588","count":5},{"id":"GO:0007613","count":4},{"id":"GO:0032516","count":4},{"id":"GO:0030198","count":4}]},{"hash":"1843578548259859569","title":"Nucleotide catabolism and RNA turnover","description":"The top GO terms are dominated by nucleotide and nucleobase catabolic processes (diadenosine polyphosphates, dGDP/dADP, diphosphoinositol polyphosphates, nucleobase-containing small molecules) and RNA-related activities (snoRNA catabolic process, adenosine to inosine editing), suggesting a functional cluster centered on nucleotide metabolism and RNA turnover rather than a single lipid or biosynthetic pathway. Some biosynthetic terms are present but less representative. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050992","count":2},{"id":"GO:0006656","count":1},{"id":"GO:1901907","count":1},{"id":"GO:0046067","count":1},{"id":"GO:0016077","count":1}]},{"hash":"1062506020036891246","title":"Negative Regulators of Inflammatory Signaling","description":"The top GO terms point to dampening of inflammatory and innate immune pathways (negative regulation of NF-kappaB activity, IL-8 production, and TLR5 signaling) and involvement in ubiquitin-related protein modification, suggesting these proteins act as brakes on immune signaling. Some terms (glial proliferation, osteoblast differentiation, estrogen signaling) hint at broader regulatory roles, but the common theme is negative regulation of inflammatory signaling via post-translational modification and transcriptional control.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":3},{"id":"GO:0032717","count":2},{"id":"GO:0060252","count":1},{"id":"GO:1902065","count":1},{"id":"GO:0001649","count":1}]},{"hash":"1333743151386651667","title":"Translation initiation complex assembly","description":"The top GO terms cluster around translation initiation: eukaryotic translation initiation factor 3 complex assembly, formation of translation preinitiation complex, and IRES-dependent viral translational initiation. These consistently point to proteins involved in assembling the translation initiation machinery, suggesting the cluster represents translation initiation factors or related components. A few other terms (uracil/allantoin transport, meiosis, deneddylation, transcription regulation) are present but are less coherent with the main theme, likely representing multifunctional proteins or annotation noise. Overall, a translation initiation focus best explains the observed terms.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015857","count":1},{"id":"GO:0015720","count":1},{"id":"GO:0048140","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0034260","count":1}]},{"hash":"613611440365941071","title":"Unknown","description":"The GO terms span cytoskeleton remodeling, signaling, development, and neuronal memory, but there is no single dominant theme or shared pathway, and the cluster has no interactions (edges/triangles), so a cohesive, representative label cannot be assigned with confidence.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008360","count":1},{"id":"GO:0006470","count":1},{"id":"GO:0060990","count":1},{"id":"GO:0043065","count":1},{"id":"GO:0035502","count":1}]},{"hash":"1724907783754417883","title":"Unknown","description":"The top GO terms spread across RNA turnover (deadenylation and decapping), metabolism (adenosine and lipid catabolism), stress and death pathways (cellular response to menadione, apoptotic process), and signaling (calcium-mediated signaling), with several entries marked obsolete and no edges linking the proteins. This lack of a cohesive shared function or pathway suggests there isn\u2019t a clear, interpretable cluster theme, so the safe label is Unknown.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006154","count":1},{"id":"GO:1901919","count":1},{"id":"GO:0043928","count":1},{"id":"GO:0031086","count":1},{"id":"GO:0000290","count":1}]},{"hash":"821957868130965998","title":"Ribosome Biogenesis and tRNA Processing","description":"The top GO terms point to RNA synthesis/processing: several entries for ribosome biogenesis and rRNA processing, plus tRNA queuosine biosynthesis and tRNA-guanine transglycosylation. A few chloroplast-related terms (plastoquinone biosynthesis, nonphotochemical quenching) and ubiquitin-dependent protein turnover appear but are less central. This makes a cohesive label around ribosome assembly and tRNA modification processes.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008616","count":1},{"id":"GO:0101030","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0042274","count":1},{"id":"GO:0006364","count":1}]},{"hash":"1218650221129994395","title":"Hypoxia-Responsive 2-OG Dioxygenases","description":"The top GO terms cluster around oxygen-dependent hydroxylation of peptides (aspartate, arginine, histidine) and transcriptional regulation under hypoxia, with links to vasculogenesis and myoblast differentiation; these are characteristic of 2-oxoglutarate-dependent dioxygenases that regulate gene expression and differentiation in response to oxygen levels, tying metabolism (gluconeogenesis) to hypoxic signaling.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006094","count":2},{"id":"GO:0045663","count":1},{"id":"GO:0042264","count":1},{"id":"GO:0042265","count":1},{"id":"GO:2001214","count":1}]},{"hash":"932395565621482120","title":"Lipid catabolism and cell wall remodeling with methylation","description":"The cluster is enriched for lipid catabolic processes (phosphatidylserine, triglyceride, monoacylglycerol) and cell wall-related terms (cell wall organization, cellulose catabolic), suggesting turnover/remodeling of membranes and cell wall components. It also includes several methylation-related terms (peptidyl-lysine methylation/dimethylation, N-terminal methylation, rRNA methylation), indicating involvement in post-translational and RNA modification. The combination points to a broader theme of biomolecule turnover alongside modification rather than a single cohesive pathway, leading to a moderate level of confidence in the label.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":3},{"id":"GO:0006660","count":2},{"id":"GO:0019433","count":2},{"id":"GO:0052651","count":2},{"id":"GO:0030245","count":2}]},{"hash":"1272252415934989850","title":"Mitotic Cell Division and Chromatin Methylation","description":"The cluster is dominated by mitosis-related terms (mitotic cell cycle, cell division, APC/C-dependent catabolic process) and chromatin modification via histone methylation (H3-K79 and H3-K27), pointing to roles in chromosome segregation and epigenetic regulation during cell division. Other terms touch on translation initiation, ER-Golgi transport, and actin nucleation, suggesting broader cellular coordination but the core signal is mitosis and chromatin regulation.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001162","count":2},{"id":"GO:0061087","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0031145","count":2},{"id":"GO:0071276","count":2}]},{"hash":"2067313783801982642","title":"Strigolactone biosynthesis and signaling","description":"The presence of GO terms for strigolactone biosynthesis and cellular response to strigolactone, along with secondary shoot formation, strongly suggests involvement in the strigolactone hormone pathway that regulates shoot architecture and development. Other terms are less cohesive, making the strigolactone theme the best-fit explanation for this cluster.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":1},{"id":"GO:0046272","count":1},{"id":"GO:0098869","count":1},{"id":"GO:0009820","count":1},{"id":"GO:0010223","count":1}]},{"hash":"404679874703613710","title":"Unknown","description":"The top terms cover nucleotide biosynthesis (UTP, CTP, GTP), chromatin-related regulation (dosage compensation, heterochromatin formation, histone methylation), and developmental processes (ventricular system development, spermatid differentiation, cilium movement). This mix suggests no single dominant theme linking all proteins, indicating a heterogeneous or potentially noisy cluster rather than a coherent functional module.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006228","count":1},{"id":"GO:0051568","count":1},{"id":"GO:0006241","count":1},{"id":"GO:0042464","count":1},{"id":"GO:0006183","count":1}]},{"hash":"2038084088268688740","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045694","count":1},{"id":"GO:0051533","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0000395","count":1},{"id":"GO:0032088","count":1}]},{"hash":"1100217330413558029","title":"Neuronal development and cytoskeletal remodeling","description":"The cluster centers on neuronal development, neuron projection development, and actin cytoskeleton regulation (Arp2/3-mediated actin nucleation), suggesting a theme of neurite outgrowth and neuronal differentiation, with supporting roles in translation initiation and vesicle transport that accompany growth and protein turnover. While some terms touch on general cellular processes, the predominant signals point to neuronal development and cytoskeletal dynamics.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0031175","count":3},{"id":"GO:0001731","count":2},{"id":"GO:2000601","count":2}]},{"hash":"113183739106133491","title":"Ribosome Biogenesis and rRNA Processing","description":"The cluster is dominated by GO terms for maturation of SSU/LSU rRNA, ribosome biogenesis, and formation of the translation preinitiation complex, with supporting terms like rRNA methylation. These collectively point to a core theme of ribosome assembly and initiation of translation, making the name appropriate. Peripheral terms such as seed coat development or growth hormone response are present but less representative.","confidence":"High","size":15,"edges":48,"triangles":114,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":4},{"id":"GO:0060416","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0036265","count":2}]},{"hash":"333523158013322648","title":"Chromatin Regulation and Transcription","description":"The dominant GO terms point to chromatin-level control of gene expression: DNA-templated transcription, rDNA heterochromatin formation and maintenance, regulation of nucleosome density, and peptidyl-lysine deacetylation, indicating chromatin remodeling and histone modification as a core theme. A few items (e.g., aggresome assembly, cobalamin biosynthesis) are less related and may reflect secondary associations or annotation noise, but the overall cluster clearly centers on transcription regulation via chromatin state.","confidence":"High","size":15,"edges":74,"triangles":178,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0000183","count":8},{"id":"GO:0060303","count":8},{"id":"GO:0006344","count":7},{"id":"GO:0045820","count":7}]},{"hash":"1678130233953513077","title":"Lipid catabolism and endocannabinoid signaling","description":"This cluster is dominated by lipid-related catabolic processes (triglyceride, diacylglycerol, monoacylglycerol catabolism; phospholipid remodeling and phosphatidylserine catabolism) and includes regulation of endocannabinoid signaling, indicating a core theme of lipid breakdown coupled to lipid-mediated signaling. Some outlier terms (stilbene/cellulose catabolism) exist, but the lipid catabolism signal is strong.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":5},{"id":"GO:2000124","count":5},{"id":"GO:0046272","count":4},{"id":"GO:0006660","count":4},{"id":"GO:0046839","count":4}]},{"hash":"1566824664785717925","title":"Broad Signaling and Cellular Response Proteins","description":"This cluster maps to a range of signaling and stimulus-response processes, including immune cytokine regulation, FGFR and insulin receptor signaling, trans-synaptic signaling in neural contexts, and stress-related responses (PMA and sorbitol), plus cell-cycle related spindle organization. The common thread is modulators of signaling and cellular response across diverse contexts rather than a single unified pathway, suggesting a multifunctional signaling cluster.","confidence":"Medium","size":15,"edges":75,"triangles":177,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0002741","count":15},{"id":"GO:0035607","count":15},{"id":"GO:0008286","count":15},{"id":"GO:0048679","count":15},{"id":"GO:1904628","count":15}]},{"hash":"238909126242975951","title":"RNA modification and protein methylation","description":"The cluster centers on translation and diverse methylation-related processes: tRNA wobble uridine modification, rRNA methylation, and various protein methylations (arginine, N-terminal). This points to a cohesive theme of RNA modification and methylation acting in conjunction with the translational machinery; a few biosynthetic terms are present but appear less central. Confidence: High","confidence":"","size":15,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0002098","count":1},{"id":"GO:0019919","count":1},{"id":"GO:1901052","count":1},{"id":"GO:0009102","count":1}]},{"hash":"1243112592353671688","title":"Developmental signaling and organogenesis","description":"This cluster combines terms tied to nervous system, heart, and skeletal development, indicating a role in developmental processes across tissues. It also includes signaling-related terms (Rho signaling, exocytosis regulation) and neural-associated responses (learning, forskolin response), suggesting broader developmental signaling and cellular communication roles. Some terms like aging or pseudohyphal growth are less consistent but may reflect cross-species or regulatory connections within signaling pathways.","confidence":"Medium","size":15,"edges":75,"triangles":186,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001302","count":4},{"id":"GO:0007124","count":4},{"id":"GO:0045956","count":4},{"id":"GO:0007266","count":4},{"id":"GO:0007399","count":4}]},{"hash":"1349902166691207327","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by translation- and ribosome-related GO terms: translation, initiation, termination, cytoplasmic translation, ribosome biogenesis, and selenocysteine incorporation. Deadenylation-dependent mRNA decay links mRNA turnover to translation, reinforcing a focus on protein synthesis. Minor terms like glial cell proliferation or response to antibiotic are present but do not define the group.","confidence":"High","size":15,"edges":89,"triangles":330,"max_degree":14,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0046677","count":6},{"id":"GO:0014009","count":5},{"id":"GO:0001514","count":5},{"id":"GO:0006415","count":5}]},{"hash":"2092557583933562706","title":"Transmembrane transport of nutrients and xenobiotics","description":"The top GO terms are overwhelmingly about transmembrane transport across membranes for a variety of substrates (vitamins, xenobiotics, glycerophosphodiesters, amino acids, cysteine, thiamine) and related import into peroxisomes, with one SOS response term as a potential secondary signal. This points to a core function of transporting diverse molecules across membranes, justifying a label centered on transmembrane transport of nutrients and xenobiotics.","confidence":"High","size":15,"edges":18,"triangles":1,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0035461","count":11},{"id":"GO:0006855","count":11},{"id":"GO:0001407","count":9},{"id":"GO:0015910","count":9},{"id":"GO:0043213","count":9}]},{"hash":"2303749975135771583","title":"DNA Repair and Cell Cycle Regulation","description":"The cluster centers on genome maintenance: base-excision repair and DNA recombination dominate the GO terms, with a notable signal for cell cycle control (positive regulation of G1/S transition). Other terms reflect diverse stress responses and peripheral processes, but the DNA repair and cell-cycle theme best captures the core of the cluster.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006284","count":4},{"id":"GO:0042493","count":3},{"id":"GO:0046856","count":3},{"id":"GO:2001153","count":3},{"id":"GO:1900087","count":3}]},{"hash":"1719257323220771622","title":"Plant telomere maintenance and chromatin dynamics","description":"Top GO terms indicate chromatin organization (nucleosome assembly, transcription regulation) and telomere biology (shelterin assembly, telomeric loop formation, G-quadruplex DNA). The concomitant hormone-response terms (cytokinin, ethylene, ABA) suggest a plant-specific regulatory context. Together, these point to a theme of chromatin dynamics intertwined with telomere maintenance in plants, influenced by hormone signaling.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009736","count":3},{"id":"GO:0006334","count":3},{"id":"GO:0000122","count":2},{"id":"GO:1904850","count":2},{"id":"GO:1904792","count":2}]},{"hash":"410084363237270371","title":"Cardiac morphogenesis and Ca2+ signaling with trafficking","description":"The top GO terms indicate heart-specific development (ventricular cardiac muscle morphogenesis, regulation of cardiac conduction) and calcium handling (negative regulation of ryanodine receptor activity), while terms about Golgi retention, endosome organization, and receptor recycling point to intracellular trafficking. Together, these features suggest a cohesive theme of cardiac development and Ca2+ signaling intertwined with membrane trafficking.","confidence":"Medium","size":15,"edges":11,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0055010","count":2},{"id":"GO:1903779","count":2},{"id":"GO:0060315","count":2}]},{"hash":"90362705427272125","title":"Diverse Small-Molecule Biosynthesis","description":"The top GO terms point to a variety of biosynthetic processes across different metabolites, including amino acids (methionine, threonine), isoprenoids/lipids (IPP/MEP pathway, farnesyl diphosphate, cholesterol, menaquinone), and related metabolic activities, with a few redox-associated processes. This suggests the cluster represents a broad collection of biosynthetic pathways rather than a single, cohesive pathway, hence a broad metabolic biosynthesis label.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009086","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0098869","count":3},{"id":"GO:1902987","count":3},{"id":"GO:0009234","count":3}]},{"hash":"2228977076459713755","title":"Gene Expression and Cytoskeletal Dynamics","description":"This cluster is driven by core gene expression processes\u2014mRNA splicing, transcription, ribosome biogenesis, and translation initiation\u2014along with cytoskeletal remodeling signals like microtubule-based movement and Arp2/3-mediated actin nucleation. The presence of a spinal cord development term and histone methylation hints suggests broader regulatory links to development and chromatin-level control of gene expression. Overall, the combination points to coordination between RNA processing/translation and cytoskeleton dynamics.","confidence":"Medium","size":15,"edges":15,"triangles":1,"max_degree":14,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000398","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0007018","count":4},{"id":"GO:0021510","count":4}]},{"hash":"1685759191778276267","title":"Neural and Vascular Development","description":"This cluster\u2019s top GO terms cover both vascular development (labyrinthine layer blood vessel development, angiogenesis, heart development) and nervous system development and function (Schwann cell development, axonogenesis, excitatory postsynaptic potential, long-term potentiation, visual perception). The overlap implies proteins involved in coordinated neurovascular development and neural signaling/plasticity rather than a single narrow pathway.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060716","count":7},{"id":"GO:0000278","count":7},{"id":"GO:0007507","count":7},{"id":"GO:0001525","count":7},{"id":"GO:0014044","count":7}]},{"hash":"1979844373572613751","title":"Plant AGP glycosylation and cell wall biosynthesis","description":"This cluster is dominated by GO terms tied to plant cell wall formation and glycoprotein modification\u2014especially arabinogalactan proteins (AGPs), RG-II pectin biosynthesis, and general cell wall organization. While a few terms refer to insect development, the strongest signals point to plant cell wall biosynthesis and AGP glycosylation as the shared theme.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080147","count":3},{"id":"GO:0010306","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0030311","count":1},{"id":"GO:0007299","count":1}]},{"hash":"554979884471255244","title":"Root hair cell development and cell wall biosynthesis","description":"This cluster is enriched for plant-specific processes: root hair cell development (GO:0080147), cell wall organization, and rhamnogalacturonan II biosynthesis, pointing to proteins involved in root hair formation and cell wall biosynthesis. The remaining terms are more general or ancillary, but the plant cell wall/root hair theme is the most coherent explanation for the set.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006449","count":1},{"id":"GO:0018401","count":1},{"id":"GO:1901874","count":1},{"id":"GO:0019511","count":1},{"id":"GO:0032364","count":1}]},{"hash":"395124264624537394","title":"Organellar Protein Import and Quality Control","description":"This cluster links proteins involved in importing and targeting proteins into organelles (mitochondrial matrix, chloroplast stroma, membranes) and in proteostasis mechanisms (unfolded protein response, ubiquitin-proteasome quality control). The mix of mitochondrial and chloroplast import terms together suggests a shared role in organellar protein trafficking and maintenance, despite a few unrelated terms that may reflect broader annotations; overall, the theme is organellar protein import/quality control.","confidence":"High","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030150","count":3},{"id":"GO:0032094","count":2},{"id":"GO:0045037","count":2},{"id":"GO:0045039","count":2},{"id":"GO:0000002","count":2}]},{"hash":"1285259378735711116","title":"Stress-Response and Cytoskeleton Remodeling","description":"The top terms show actin filament severing (cytoskeleton remodeling) alongside multiple stress-response terms (responses to xenobiotic stimulus, cold, ethanol, and lipopolysaccharide). Other terms are less connected (chromatin binding regulation, megakaryocyte differentiation, thiamine biosynthesis), so the most coherent theme is stress-induced cytoskeletal dynamics.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051014","count":2},{"id":"GO:0042493","count":1},{"id":"GO:0019835","count":1},{"id":"GO:0009409","count":1},{"id":"GO:0035563","count":1}]},{"hash":"1481715330940993712","title":"Muscle differentiation and calcium signaling","description":"The cluster includes terms tied to skeletal muscle cell differentiation, calcium signaling (import and release of Ca2+), and mechanical stimulus response, with supporting terms for transcriptional regulation and ubiquitin-mediated protein turnover. This suggests a cohesive module coordinating muscle development and calcium-dependent signaling, alongside chromatin remodeling and proteostasis linked to differentiation. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":4},{"id":"GO:0006511","count":3},{"id":"GO:0035914","count":3},{"id":"GO:0006334","count":3},{"id":"GO:0071260","count":2}]},{"hash":"855100833568662857","title":"SRP-Dependent ER Targeting and ER Stress","description":"Most terms point to SRP-dependent cotranslational targeting of proteins to the ER membrane (signal recognition, translocation), with additional links to ER stress and ufmylation, suggesting a consolidating theme around ER protein targeting and quality control. The cannabinoid biosynthesis terms are isolated and likely incidental. Overall, the cluster appears to center on co-translational targeting to the ER and associated stress responses.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990592","count":1},{"id":"GO:0046331","count":1},{"id":"GO:0031987","count":1},{"id":"GO:0034976","count":1},{"id":"GO:0006617","count":1}]},{"hash":"1015538030820942279","title":"Actin cytoskeleton remodeling and polymerization","description":"This cluster is dominated by actin-related processes\u2014nucleation, polymerization, filament movement, and network formation (e.g., Arp2/3-mediated nucleation and ruffle assembly)\u2014indicating actin dynamics as the central theme. The megakaryocyte and oligodendrocyte development terms reflect morphogenesis shaped by actin remodeling, reinforcing the shared function.","confidence":"High","size":15,"edges":103,"triangles":430,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0007121","count":3},{"id":"GO:0035855","count":3},{"id":"GO:0030048","count":3},{"id":"GO:0014003","count":3},{"id":"GO:0045010","count":3}]},{"hash":"1792270979650096668","title":"Lipid Biosynthesis and Membrane Maintenance","description":"The top GO terms are dominated by lipid-related processes: unsaturated fatty acid biosynthesis, ergosterol biosynthesis, and sphingolipid/metabolic pathways (mannosyl-inositol phosphorylceramide metabolism), as well as membrane-associated functions like myelin maintenance and sebaceous gland differentiation. This suggests the cluster centers on lipid metabolism and membrane biology, with secondary terms (nitric oxide, nitrate assimilation, development) adding metabolic and organismal context but not overturning the lipid-focused theme.","confidence":"Medium","size":15,"edges":14,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":2},{"id":"GO:0000001","count":2},{"id":"GO:0001949","count":2},{"id":"GO:0006809","count":2},{"id":"GO:0032443","count":2}]},{"hash":"1538586189673353685","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070911","count":1},{"id":"GO:0006361","count":1},{"id":"GO:0006362","count":1},{"id":"GO:0006296","count":1},{"id":"GO:0070816","count":1}]},{"hash":"644172331764890597","title":"RNA and protein methylation","description":"This cluster is dominated by GO terms for methylation and RNA modification (mRNA capping, rRNA methylation, tRNA wobble uridine modification, and arginine methylation), with a few related biosynthetic terms. The common thread is methyltransferase- or modification-related functions acting on RNA and proteins, suggesting a methylation-centric role for these proteins.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006370","count":2},{"id":"GO:0090116","count":1},{"id":"GO:0019919","count":1},{"id":"GO:0009102","count":1},{"id":"GO:0002098","count":1}]},{"hash":"1809723498818074980","title":"ER Protein Folding and Quality Control","description":"The cluster centers on unfolded protein response, ER-specific chaperone-assisted refolding, ER-associated protein folding/maturation, and ubiquitin-proteasome\u2013mediated quality control, indicating a proteostasis/quality-control theme in the secretory pathway; other terms like heat response support stress-related folding.","confidence":"High","size":15,"edges":15,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006986","count":2},{"id":"GO:0071630","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0031204","count":2},{"id":"GO:0001707","count":2}]},{"hash":"519117245880605525","title":"Multivesicular body sorting and Golgi-ER trafficking","description":"The proteins are connected by endomembrane trafficking functions: multivesicular body sorting/assembly, Golgi to ER retrograde transport, vesicle docking and fusion with the Golgi, and intracellular protein transport. The presence of an autophagy-related term (negative regulation of autophagosome assembly) reinforces a trafficking/autophagy nexus, suggesting this cluster centers on vesicle trafficking through the endomembrane system rather than cytoskeletal or metabolic roles.","confidence":"High","size":15,"edges":20,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0071985","count":3},{"id":"GO:0010458","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0036258","count":3},{"id":"GO:0048280","count":3}]},{"hash":"2100954629718501975","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007014","count":2},{"id":"GO:0018032","count":2},{"id":"GO:0072089","count":2},{"id":"GO:1902187","count":2},{"id":"GO:2000637","count":2}]},{"hash":"986499647360530995","title":"Mitosis and Nuclear Transport Regulators","description":"Top GO terms indicate strong association with mitosis (chromatid segregation, spindle assembly, APC-dependent proteolysis) and nuclear transport (nuclear pore localization, viral mRNA export). Ubiquitin-dependent degradation aligns with cell-cycle control, supporting a cohesive theme around regulation of division and nuclear trafficking. Some outliers (pancreatic secretion, dendrite development) appear incidental. ","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000070","count":3},{"id":"GO:2000060","count":3},{"id":"GO:0040020","count":3},{"id":"GO:0030157","count":3},{"id":"GO:1905705","count":3}]},{"hash":"1357220304274219325","title":"Stress Response and Development","description":"This cluster centers on cellular stress responses (heat, ER stress, apoptosis) and developmental processes (multicellular growth and forebrain development), suggesting a theme of stress-activated signaling influencing development, despite some obsolete terms and diverse functions.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009408","count":4},{"id":"GO:0030433","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0035264","count":3},{"id":"GO:0007275","count":3}]},{"hash":"1191548259873713026","title":"Nuclear proteostasis and stress response","description":"The GO terms point mainly to nuclear protein quality control and stress-related processes: ubiquitin-proteasome\u2013mediated quality control, response to unfolded proteins and heat, and chaperone/refolding-related activity, alongside related nuclear transport and protein targeting activities. Although there are broader nuclear processes like DNA replication and mesoderm formation represented, the strongest signal is nuclear proteostasis and stress response, making this a coherent, specific label for the cluster.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006469","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0006986","count":4},{"id":"GO:0071630","count":4},{"id":"GO:0070389","count":4}]},{"hash":"1750369621917977673","title":"Golgi SNARE Vesicle Trafficking and Postsynaptic Delivery","description":"The top GO terms cluster around Golgi-related trafficking (ER-to-Golgi, intra-Golgi, Golgi-to-vacuole, vesicle fusion with Golgi, retrograde transport, Golgi ribbon formation) and SNARE complex assembly, plus exocytic insertion of neurotransmitter receptors into the postsynaptic membrane and related synaptic potentiation. This points to a cohesive theme of Golgi- and SNARE-mediated vesicle trafficking that delivers receptors to the synapse and modulates synaptic vesicle recycling.","confidence":"High","size":15,"edges":26,"triangles":12,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0090161","count":9},{"id":"GO:0006888","count":8},{"id":"GO:0006891","count":8},{"id":"GO:0048280","count":8},{"id":"GO:0006896","count":7}]},{"hash":"1010216181780166116","title":"Cardiac Stress Signaling and Development","description":"The terms point to heart development and cardiac hypertrophy in response to stress, coupled with regulation of kinase signaling (autophosphorylation, serine/threonine kinases, GTPase activity). The hypoxia response further supports a stress-related signaling context, suggesting this cluster centers on cardiac signaling and developmental processes. ","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071456","count":5},{"id":"GO:0000278","count":4},{"id":"GO:0006469","count":4},{"id":"GO:0051028","count":4},{"id":"GO:0031954","count":4}]},{"hash":"1779115163732421349","title":"Plant secondary metabolite biosynthesis and lipid metabolism","description":"The top GO terms cluster around production of plant secondary metabolites (alkaloids, stilbenes, antibiotic-like compounds) and lipid-related processes (triglyceride catabolism, phospholipid dephosphorylation), with a hint of detoxification. This suggests a cohesive theme of secondary metabolism paired with lipid turnover in plants.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0009102","count":2},{"id":"GO:0046272","count":2},{"id":"GO:0009820","count":2}]},{"hash":"1303966416760380667","title":"Drosophila epithelial morphogenesis and Golgi trafficking","description":"The top GO terms point to epithelial morphogenesis (wing disc morphogenesis and morphogenesis of follicular epithelium) coupled with Golgi organization and a set of membrane transport processes, suggesting a cluster of proteins involved in developmental morphogenesis and intracellular trafficking. The presence of mitotic cell cycle and GTPase regulation hints at coordinated cell division and signaling during development, supporting a role in epithelial morphogenesis with trafficking components.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0007472","count":1},{"id":"GO:0016333","count":1},{"id":"GO:0007030","count":1}]},{"hash":"904054131163735161","title":"Multitissue Development","description":"The top GO terms cluster around broad developmental processes across multiple tissues (brain/forebrain, skin, pigmentation) and general multicellular development, with a few terms tied to cell cycle and cytoskeletal remodeling. This suggests a general developmental/differentiation program rather than a single, cohesive pathway, hence the label Multitissue Development with Medium confidence. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0098907","count":3},{"id":"GO:0007205","count":3},{"id":"GO:2000601","count":2},{"id":"GO:0043473","count":2}]},{"hash":"1975780552990904929","title":"Development and Vesicle Trafficking","description":"These terms point to broad developmental programs (eye morphogenesis, smooth muscle and nervous system development) together with vesicle trafficking processes (Golgi-to-lysosome/endosome transport and clathrin-coated vesicle loading). The mix of developmental and intracellular transport/regulatory terms suggests the cluster reflects proteins involved in coordinating development with vesicle trafficking and 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:0043046","count":2},{"id":"GO:0034587","count":2},{"id":"GO:0048593","count":2},{"id":"GO:0048745","count":2},{"id":"GO:0035021","count":2}]},{"hash":"1580798936511930089","title":"TGF-\u03b2 signaling regulation cluster","description":"This cluster's top GO terms center on transforming growth factor beta (TGF-\u03b2) signaling, including negative regulation of TGF-\u03b2 receptor signaling, cellular response to TGF-\u03b2 stimulus, and SMAD-related regulation, plus peptidyl-threonine dephosphorylation, which is a common regulatory step in this pathway. A few terms (NF-\u03baB signaling, vacuole fusion, photosystem stoichiometry, meristem maintenance) appear as outliers or cross-species noise but do not override the main theme. Therefore, the label TGF-\u03b2 signaling regulation best captures the predominant function of this cluster.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030512","count":1},{"id":"GO:0042347","count":1},{"id":"GO:0035970","count":1},{"id":"GO:0061191","count":1},{"id":"GO:0010991","count":1}]},{"hash":"136325362570800816","title":"RNA and protein methyltransferases","description":"RNA and protein methyltransferases. The top GO terms are dominated by methylation activities (rRNA methylation; arginine and lysine methylation; histone methylation), indicating a cluster of enzymes that modify RNA or proteins via methyl groups and potentially influence transcription and chromatin state. Other terms like senescence, growth, xenobiotic response, and cobalamin biosynthesis reflect broader cellular contexts but do not override the core methylation theme.","confidence":"High","size":14,"edges":69,"triangles":177,"max_degree":13,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0031167","count":7},{"id":"GO:0019919","count":6},{"id":"GO:0090398","count":6},{"id":"GO:0016049","count":6},{"id":"GO:0000122","count":6}]},{"hash":"409214160770654353","title":"Unknown","description":"The terms are highly heterogeneous, including RNA base modification (rRNA and tRNA methylation), antibiotic biosynthesis, plant cell wall biosynthesis, and various signaling and developmental processes from both plant and animal contexts, with no single cohesive function tying them all together.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070476","count":3},{"id":"GO:0030488","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0035118","count":2},{"id":"GO:0010417","count":2}]},{"hash":"584524811417719752","title":"Bacterial Cell Wall Synthesis and Division","description":"The top GO terms cluster around peptidoglycan biosynthesis and turnover, cell wall organization, and cell division/cell cycle, pointing to bacterial cell wall biogenesis and division as the core function. Additional terms like cellulose catabolic process and antibiotic biosynthetic process hint metabolic versatility but do not override the central theme.","confidence":"High","size":14,"edges":14,"triangles":1,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":4},{"id":"GO:0008360","count":3},{"id":"GO:0030245","count":3},{"id":"GO:0009252","count":3},{"id":"GO:0009254","count":3}]},{"hash":"1355022857423940908","title":"Mitochondrial Metabolite Transport and Stress Response","description":"The cluster centers on transport of mitochondrial metabolites (alpha-ketoglutarate, malate-aspartate shuttle, citrate, pyrimidine nucleotides) and ATP across mitochondrial membranes, coupled with stress-related functions such as response to fatty acids, superoxide, and apoptotic mitochondrial changes, indicating a cohesive mitochondrial metabolism and stress-signaling theme.","confidence":"High","size":14,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070542","count":5},{"id":"GO:0008637","count":5},{"id":"GO:0097274","count":5},{"id":"GO:0006469","count":4},{"id":"GO:1990544","count":4}]},{"hash":"1083276304263980880","title":"Nuclear Transcription and RNA Processing","description":"This cluster centers on nuclear gene expression machinery: DNA-templated transcription and its regulation, chromatin-associated localization, cell cycle and DNA replication processes, snoRNP assembly, and RNA surveillance/decay (rRNA). The peroxisome import term appears as a potential annotation outlier. ","confidence":"High","size":14,"edges":13,"triangles":0,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0000492","count":2},{"id":"GO:0071169","count":2},{"id":"GO:0070651","count":2}]},{"hash":"1650095912657496751","title":"Mitochondrial Transport and Metabolism","description":"The GO terms cluster around mitochondrial function: membrane fission, various metabolite transports (alpha-ketoglutarate, citrate, glycine, pyrimidines), the malate-aspartate shuttle, and ATP transmembrane transport. There is also a link to oxidative stress response (superoxide) and mitochondrial maintenance. Even though one term is labeled obsolete, the core theme is mitochondrial transport and metabolism, suggesting proteins functioning in mitochondrial metabolite movement and related redox balance. ","confidence":"High","size":14,"edges":14,"triangles":1,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0090149","count":5},{"id":"GO:0000002","count":5},{"id":"GO:1990544","count":4},{"id":"GO:0000303","count":4},{"id":"GO:1990519","count":4}]},{"hash":"1787652900906702668","title":"Mitochondrial Metabolite Transport","description":"The top GO terms point to transport of multiple metabolites across mitochondrial membranes (e.g., alpha-ketoglutarate, citrate, malate-aspartate shuttle, glycine, ornithine, pyrimidine nucleotides) and ATP transmembrane transport, plus a cellular response to superoxide. This strongly suggests a cluster of mitochondrial carrier proteins/modulators coordinating energy metabolism and redox homeostasis, making \u201cmitochondrial metabolite transport\u201d a concise, representative label.","confidence":"High","size":14,"edges":14,"triangles":0,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1990544","count":7},{"id":"GO:0000303","count":7},{"id":"GO:1990519","count":7},{"id":"GO:0015742","count":7},{"id":"GO:0097274","count":7}]},{"hash":"228004317225364408","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001782","count":2},{"id":"GO:0002635","count":2},{"id":"GO:0051661","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0048535","count":2}]},{"hash":"326706641944215051","title":"RNA splicing and translation initiation machinery","description":"The GO terms cluster around RNA processing and splicing regulation (spliceosome, alternative splicing, small-subunit processome) as well as translation initiation complex assembly (preinitiation complex, eIF4F, IRES-dependent initiation). Additional terms for mRNA modification and stress-related mRNA stability support a cohesive theme of RNA metabolism linked to translation control. Together these indicate a core RNA-processing and translation-initiation module.","confidence":"High","size":14,"edges":66,"triangles":220,"max_degree":11,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":9},{"id":"GO:0031047","count":7},{"id":"GO:0048026","count":7},{"id":"GO:0016556","count":6},{"id":"GO:0034462","count":6}]},{"hash":"711996029600544388","title":"Vacuolar amino acid transporters","description":"This cluster is dominated by GO terms for import and transmembrane transport of amino acids into the vacuole (glutamate, histidine, tyrosine, lysine, asparagine), suggesting a core set of vacuolar amino acid transporters; the translation term is present but likely secondary.","confidence":"Medium","size":14,"edges":42,"triangles":85,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0090515","count":2},{"id":"GO:2000487","count":2},{"id":"GO:0090513","count":2},{"id":"GO:0090514","count":2}]},{"hash":"1587354051029219392","title":"Glucose-starvation response and transmembrane transport","description":"The cluster combines GO terms tied to glucose limitation responses (cellular response to glucose starvation; invasive growth in response to glucose limitation; pseudohyphal growth) with multiple transmembrane transport processes (nitrate, phosphate, xenobiotic, xenobiotic transmembrane, selenite transport). This pattern suggests proteins that coordinate nutrient uptake and stress-driven growth changes under low-glucose conditions, rather than a single narrow function. The presence of vesicle-related terms like neurotransmitter loading also aligns with membrane trafficking roles that support transporter activity under nutrient stress.","confidence":"Medium","size":14,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015706","count":3},{"id":"GO:0042149","count":3},{"id":"GO:0007124","count":2},{"id":"GO:0001403","count":2},{"id":"GO:0098700","count":2}]},{"hash":"329815033565398625","title":"Lipid and retinoid/steroid biosynthesis","description":"The top GO terms are dominated by lipid and retinoid/steroid metabolic processes (very long-chain fatty acid biosynthesis, retinal and retinol/retinoic acid metabolism, and testosterone biosynthesis), suggesting a cohesive function in lipid-derived metabolite production. While a few terms (e.g., transcription regulation, sporulation, antibiotic response) are present, they are outnumbered by the lipid/steroid-related biosynthetic processes, supporting a main theme around lipid and retinoid/steroid metabolism.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0042761","count":3},{"id":"GO:0042574","count":3},{"id":"GO:0002138","count":3}]},{"hash":"358515862348305309","title":"Valine and isoleucine/threonine biosynthesis","description":"The top GO terms cluster around amino acid biosynthesis: valine and isoleucine biosynthesis, threonine biosynthesis, and related metabolic processes (including folic acid biosynthesis). This points to a cohesive set of enzymes involved in amino acid production with supporting one-carbon metabolism, rather than signaling or transport roles. Some annotations are marked obsolete, but the core theme remains amino acid biosynthesis.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019509","count":2},{"id":"GO:0016310","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0009088","count":2},{"id":"GO:0019284","count":2}]},{"hash":"79445078923520811","title":"Cholesterol Transport and Lipid Metabolism","description":"Dominant GO terms point to lipoprotein processing (lipoprotein transport/catabolic process/efflux) and cholesterol handling (biosynthesis regulation, storage, import), suggesting a lipid homeostasis module; a single outlier term (flagellated sperm motility) does not negate the overall theme.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000272","count":2},{"id":"GO:0042953","count":1},{"id":"GO:1904807","count":1},{"id":"GO:0006642","count":1},{"id":"GO:0010886","count":1}]},{"hash":"61791939192295510","title":"Nucleoside Salvage Pathways","description":"The proteins cluster around salvage and interconversion of nucleosides and nucleotides (inosine, guanosine, uridine, cytidine), with broader purine/pyrimidine metabolism and NAD salvage terms highlighted, indicating a cohesive nucleotide salvage function.","confidence":"High","size":14,"edges":14,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0019358","count":1},{"id":"GO:0015949","count":1},{"id":"GO:0006218","count":1},{"id":"GO:0006190","count":1},{"id":"GO:0006216","count":1}]},{"hash":"198119986726368616","title":"Neuronal synaptic plasticity and memory signaling","description":"The strongest signals are regulation of neuronal synaptic plasticity and short-term memory, along with calcium-dependent signaling via calcineurin-NFAT and protein dephosphorylation, pointing to activity-dependent synaptic remodeling. Additional terms about cell shape regulation and cytokinesis fit with structural changes underlying synapses. Some annotations (N-glycan processing, kidney development) may be peripheral or reflect multi-function proteins. Overall, the cluster most coherently maps to neuronal signaling and plasticity.","confidence":"Medium","size":14,"edges":12,"triangles":0,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0048168","count":8},{"id":"GO:0006491","count":8},{"id":"GO:0008360","count":7},{"id":"GO:0006470","count":7},{"id":"GO:0043065","count":7}]},{"hash":"344193607508521978","title":"Mitochondrial Metabolite Transport","description":"This cluster is enriched for mitochondrial transmembrane transport processes, including ATP, citrate, alpha-ketoglutarate, and malate-aspartate shuttle activities, pointing to a core theme of mitochondrial metabolite exchange and energy metabolism. Some non-transport terms appear but are less central to the main function.","confidence":"High","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1990544","count":11},{"id":"GO:0000303","count":11},{"id":"GO:1990519","count":11},{"id":"GO:0015742","count":11},{"id":"GO:0097274","count":11}]},{"hash":"900975401907025732","title":"Neural and cardiac development signaling","description":"The top GO terms cluster around neural development (spinal cord development, regulation of myelination) and cardiac development/contraction, suggesting roles in nervous and cardiovascular development with shared signaling pathways (PI3K/AKT and Rho). Some terms (e.g., germ cell development) are outliers, but the dominant theme is neural and cardiac development with related signaling. ","confidence":"Medium","size":14,"edges":13,"triangles":0,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0021510","count":3},{"id":"GO:0070493","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0055013","count":2},{"id":"GO:0031641","count":2}]},{"hash":"183647147269850338","title":"Cell Cycle Checkpoints and Signaling","description":"This cluster prominently features terms related to mitotic control (mitotic spindle assembly checkpoint signaling, transcription regulation during G2/M) and major signaling pathways (canonical NF-kappaB signaling), suggesting a group of proteins involved in regulating cell division and intracellular signaling. Other terms touch on RNA localization and adhesion-related signaling, which are supportive of broader regulatory roles but less cohesive. Overall, the most representative theme is regulation of cell cycle progression and signaling, giving a Medium confidence.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0019878","count":2},{"id":"GO:0033624","count":1},{"id":"GO:0051237","count":1},{"id":"GO:0090282","count":1}]},{"hash":"248873483138343630","title":"Osteogenesis and epidermal development","description":"This cluster centers on development and regeneration in bone and epithelial tissues: enrichment for osteoblast proliferation, wound healing of epidermis, and amelogenesis; plus EGFR ligand maturation and endodermal differentiation hint at epithelial\u2013mesenchymal interactions. A few terms (NK cell regulation, unfolded protein response) may reflect ancillary processes or pleiotropy. Overall, the dominant themes link bone formation and epidermal development.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033690","count":2},{"id":"GO:0006507","count":2},{"id":"GO:0035313","count":2},{"id":"GO:0097186","count":2},{"id":"GO:0035987","count":2}]},{"hash":"827502128854776740","title":"RNA Methylation and rRNA Processing","description":"The Top Terms are dominated by RNA methylation and capping processes (rRNA modification, rRNA methylation, guanine-N7 methylation, 7-methylguanosine capping, and related activities) with a nucleolar emphasis (nucleologenesis), indicating a cohesive set of methyltransferases involved in RNA maturation. Minor terms about antibiotic biosynthesis/response are present but do not define the main theme. ","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000154","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0036261","count":1},{"id":"GO:0017126","count":1},{"id":"GO:0036265","count":1}]},{"hash":"716685919845303946","title":"Unknown","description":"No shared functional terms or connectivity are evident for this cluster\u2014there are no edges or top GO terms, and only four proteins were re-added by ReCIPE without linking evidence. This prevents a confident, representative label.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2300918927758044523","title":"Neural signaling and drug response","description":"This cluster features terms tied to neural communication and behavioral responses, including regulation of synaptic transmission, long-term potentiation, and responses to ethanol/amphetamine, as well as modulation of pain perception and sensory processing. While a few terms like protein repair or metabolism appear incidental, the dominant pattern centers on neuronal signaling and stimulus-driven behavior, supporting a Medium confidence in this label.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030091","count":1},{"id":"GO:0015671","count":1},{"id":"GO:0051967","count":1},{"id":"GO:0018964","count":1},{"id":"GO:1900273","count":1}]},{"hash":"589368510640228875","title":"Synaptic Receptor Trafficking and Vesicle Transport","description":"The terms repeatedly point to delivery and recycling of neurotransmitter receptors at synapses (exocytic insertion, receptor recycling, Golgi-to-plasma membrane transport, ER-to-Golgi transport) and to related vesicle and vacuolar processes, which together suggest a cohesive theme of neuronal receptor trafficking and vesicle transport underlying synaptic function and plasticity.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098967","count":1},{"id":"GO:0042144","count":1},{"id":"GO:1902259","count":1},{"id":"GO:1900483","count":1},{"id":"GO:0006888","count":1}]},{"hash":"1817778708871483355","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032196","count":1},{"id":"GO:0009863","count":1},{"id":"GO:1900150","count":1},{"id":"GO:0000961","count":1},{"id":"GO:0080156","count":1}]},{"hash":"566747744741308245","title":"Diverse Substrate Membrane Transporters","description":"The GO terms point to transmembrane transport of many substrates (nitrate, galactose, sodium, arabinose, phosphate, fucose, 4-hydroxyphenylacetate) and include a vesicular transport step (neurotransmitter loading into synaptic vesicle), suggesting the cluster represents transporter proteins with broad substrate ranges rather than a single pathway. The absence of edges does not contradict this interpretation, as transporters can be functionally diverse yet share membrane transport activity.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":2},{"id":"GO:0015757","count":2},{"id":"GO:0098700","count":2},{"id":"GO:0015706","count":2},{"id":"GO:0006004","count":2}]},{"hash":"1381565719322872078","title":"Fungal polysaccharide catabolism and cell wall remodeling","description":"Most top GO terms point to degradation and metabolism of fungal cell wall polysaccharides (xylan, cellulose, mannan, beta-glucan) and related cell wall remodeling/disassembly, plus biofilm formation. A few terms are less related (cell cycle, morphogenesis, differentiation), but the dominant theme is fungal carbohydrate catabolism and cell wall dynamics.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045493","count":2},{"id":"GO:0030245","count":2},{"id":"GO:0007050","count":1},{"id":"GO:2000495","count":1},{"id":"GO:0002318","count":1}]},{"hash":"1212034740830913614","title":"Epigenetic regulation: DNA methylation and heterochromatin","description":"Top terms are dominated by DNA methylation and heterochromatin regulation (e.g., cytosine methylation and heterochromatin formation), with a few development-related terms; the core signal points to epigenetic regulation of chromatin rather than a single pathway. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090309","count":2},{"id":"GO:0010424","count":2},{"id":"GO:0021766","count":1},{"id":"GO:0060669","count":1},{"id":"GO:2001040","count":1}]},{"hash":"307022258934663901","title":"Neuronal Mitochondrial-Peroxisomal Dynamics and Synaptic Function","description":"The cluster combines organelle dynamics terms (mitochondrial membrane organization, mitochondrial and peroxisome fission), apoptotic signaling, and synaptic processes (GABAergic transmission, synaptic vesicle budding, GPCR internalization), suggesting a coherent theme of how organelle dynamics intersect with synaptic vesicle trafficking and receptor regulation in neurons.","confidence":"High","size":13,"edges":10,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":6},{"id":"GO:0007006","count":5},{"id":"GO:0000266","count":5},{"id":"GO:0006915","count":5},{"id":"GO:0051932","count":4}]},{"hash":"2018292061339250871","title":"Signaling Regulators and Synaptic Organization","description":"The top GO terms cluster around regulation of signaling pathways (tyrosine dephosphorylation, ERK and PI3K/AKT pathways, T cell receptor signaling) and synaptic architecture (postsynaptic density assembly, synaptic vesicle clustering), with one outlier on kinetochore localization. This points to proteins that modulate signaling and influence synaptic organization, hence the chosen label.","confidence":"Medium","size":13,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0035335","count":9},{"id":"GO:1903984","count":8},{"id":"GO:0050860","count":8},{"id":"GO:0070373","count":8},{"id":"GO:2000808","count":8}]},{"hash":"1293538936776336921","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by GO terms related to ribosome biogenesis (ribosome biogenesis, ribosomal subunit biogenesis, ribosomal large/small subunit export from nucleus), cytoplasmic translation, and tRNA modification, pointing to a cohesive group of proteins involved in assembling and operating the ribosome and in translation. The presence of cell cycle and cell division terms suggests a broader link to growth and proliferation, but the core signal remains ribosome production and function. ","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":10},{"id":"GO:0000055","count":7},{"id":"GO:1901001","count":6},{"id":"GO:0002181","count":6},{"id":"GO:0006400","count":6}]},{"hash":"2266345338043344899","title":"Neurodevelopment and synaptic signaling","description":"The cluster centers on neural-related processes: Schwann cell development, excitatory postsynaptic potential, and visual perception suggest nervous system development and function, complemented by transcription-related GO terms (DNA-templated transcription, positive regulation of DNA binding) indicating coordinated gene expression control. While there are outliers (heart development and ABA signaling), the dominant theme is neural development and synaptic signaling with transcriptional regulation as a common mechanism.","confidence":"Medium","size":13,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0014044","count":8},{"id":"GO:0007507","count":7},{"id":"GO:0006351","count":7},{"id":"GO:0060079","count":7},{"id":"GO:0007601","count":7}]},{"hash":"1964979595899782849","title":"Epithelial Differentiation and Proliferation Regulation","description":"The cluster centers on epithelial differentiation signals (keratinocyte and intestinal epithelial differentiation) and growth-control pathways (canonical Wnt signaling and Hippo signaling), plus cell cycle and apoptosis terms, suggesting a module that coordinates epithelial cell fate with controlled proliferation. The presence of negative regulation of motility and tissue-specific differentiation reinforces a cohesive epithelial development/proliferation theme.","confidence":"High","size":13,"edges":41,"triangles":61,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0090263","count":6},{"id":"GO:0030216","count":6},{"id":"GO:0006915","count":6},{"id":"GO:0035329","count":6},{"id":"GO:0060044","count":6}]},{"hash":"592907639485913673","title":"Amino Acid and Vitamin Biosynthesis","description":"The top GO terms are dominated by biosynthetic processes for amino acids and vitamins (biotin, cobalamin, L-tyrosine, L-lysine, protoporphyrinogen IX) and related metabolic pathways, with one term for DNA-templated transcription. This points to a cluster of proteins involved in various biosynthetic pathways rather than a single unified function, hence a label centered on biosynthesis is most representative. ","confidence":"Medium","size":13,"edges":13,"triangles":1,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0009102","count":5},{"id":"GO:0006782","count":5},{"id":"GO:0019878","count":5},{"id":"GO:0009103","count":5}]},{"hash":"976727629573741198","title":"Biosynthesis of vitamins, cofactors, and nucleic acids","description":"The proteins cluster around biosynthetic pathways for vitamins and cofactors (biotin, thiamine, menaquinone, protoporphyrin/heme) and essential nucleotide modifications (tRNA queuosine, rRNA base methylation), indicating a shared theme of metabolic biosynthesis and modification. A few terms like antibiotic response and fermentation appear as peripheral context but don\u2019t override the main theme.","confidence":"Medium","size":13,"edges":9,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006782","count":4},{"id":"GO:0009234","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0009102","count":3},{"id":"GO:0046677","count":3}]},{"hash":"2056700301872713445","title":"Synapse Organization and Vesicle Trafficking","description":"The cluster centers on synapse organization and vesicle transport between the ER/Golgi and synaptic compartments (anterograde and retrograde transport), indicating a module involved in assembling/maintaining synapses and handling synaptic protein trafficking. Additional terms point to transcriptional and mRNA regulation and signaling pathway modulation (Wnt, JNK), suggesting coordinated gene expression control related to neuronal connectivity. Overall, it reflects a synapse-focused trafficking and regulatory program.","confidence":"Medium","size":13,"edges":17,"triangles":3,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0090263","count":3},{"id":"GO:0043488","count":3},{"id":"GO:0045944","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0050808","count":2}]},{"hash":"2081129740838098259","title":"Chaperone-Mediated Folding and ER Quality Control","description":"The top GO terms cluster around unfolded protein response and chaperone-driven refolding, plus ER-associated degradation, indicating a module focused on protein quality control under stress. Additional terms related to ciliary/photoreceptor localization and cell-cycle processes suggest broader roles in trafficking and assembly of complex protein systems relying on chaperones.","confidence":"Medium","size":13,"edges":12,"triangles":0,"max_degree":12,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0090526","count":7},{"id":"GO:0006986","count":7},{"id":"GO:0070389","count":6},{"id":"GO:0045842","count":6},{"id":"GO:1903546","count":6}]},{"hash":"89463507133272995","title":"Unknown","description":"The top terms span transcription regulation, DNA replication, protein homeostasis, and organelle import, with no single unifying process. This heterogeneity suggests the cluster does not reflect one coherent function, hence Unknown.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032968","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0006272","count":1},{"id":"GO:0070682","count":1},{"id":"GO:1903007","count":1}]},{"hash":"760536638391051744","title":"Telomere maintenance and chromatin remodeling","description":"The top GO terms emphasize chromatin state and telomere biology (rDNA heterochromatin formation, chromatin remodeling, G-quadruplex DNA formation, telomeric loop formation, shelterin assembly), pointing to coordinated regulation of chromatin structure at repetitive regions and telomeres. The occasional stress-related terms (ethylene, ABA, LPS response) suggest chromatin dynamics during stress that can impact telomere regulation. Together, these terms define a cohesive function centered on telomere maintenance through chromatin remodeling.","confidence":"High","size":13,"edges":16,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":3},{"id":"GO:0043044","count":3},{"id":"GO:0032496","count":3},{"id":"GO:1904850","count":2},{"id":"GO:1904792","count":2}]},{"hash":"1613370707515993855","title":"Antibiotic and small-molecule metabolism","description":"This cluster shows a notable presence of antibiotic-related terms (antibiotic biosynthetic process, clavulanic acid biosynthetic process) along with diverse small-molecule metabolism and catabolic processes (xanthine catabolism, fatty acid alpha-oxidation, ectoine catabolism), suggesting a broader theme of secondary and primary metabolism for various compounds. However, the terms span unrelated pathways, so the connection is not fully cohesive.","confidence":"Medium","size":13,"edges":26,"triangles":17,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0046300","count":4},{"id":"GO:0033050","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0045329","count":4},{"id":"GO:0006151","count":4}]},{"hash":"469694618952162770","title":"Root Hair Cell Wall Biosynthesis","description":"Based on GO terms dominated by plant cell wall biosynthesis and root hair development (rhamnogalacturonan II, homogalacturonan, glucuronoxylan, mucilage biosynthesis, and plant-type secondary cell wall biogenesis), this cluster likely represents proteins involved in root hair cell wall assembly and related polysaccharide biosynthesis. The emphasis on wall organization and multiple polysaccharide biosynthetic processes supports a cohesive function in constructing root hair cell walls.","confidence":"High","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":5},{"id":"GO:0080147","count":5},{"id":"GO:0010306","count":4},{"id":"GO:0010192","count":2},{"id":"GO:0007114","count":2}]},{"hash":"201537236768941688","title":"Unknown","description":"The set of GO terms is highly heterogeneous, including cell wall/mannoprotein biosynthesis and mucilage biosynthesis (glycosylation-related processes) alongside neural development (Schwann cell development, excitatory postsynaptic potential) and cell cycle/DNA replication terms. This lack of a single cohesive biological theme makes a specific, representative label untenable.","confidence":"","size":13,"edges":31,"triangles":17,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006487","count":2},{"id":"GO:0000032","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0005978","count":2},{"id":"GO:0010192","count":2}]},{"hash":"411427895578477867","title":"Ubiquitin-dependent proteolysis and antiviral defense","description":"The top GO terms cluster around ubiquitination-related processes (protein polyubiquitination, autoubiquitination, ubiquitin-dependent protein catabolic process) and peroxisome matrix import, with accompanying immune-related terms (defense response to virus, B cell homeostasis, germinal center regulation). This suggests a functional module where ubiquitin-regulated protein turnover intersects with antiviral signaling and immune regulation, possibly via peroxisomal pathways. ","confidence":"Medium","size":13,"edges":11,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0016558","count":2},{"id":"GO:0060816","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0001782","count":2},{"id":"GO:0000209","count":2}]},{"hash":"2008064071786902772","title":"Chromatin remodeling during differentiation","description":"The top GO terms cluster around chromatin organization and modification (nucleosome assembly/disassembly, histone acetylation, sperm DNA decondensation) together with differentiation and stem cell regulation (oligodendrocyte differentiation, regulation of stem cell division). This points to a cohesive theme where chromatin dynamics influence developmental differentiation and cell-cycle control, with a few peripheral terms related to cell division mechanics. ","confidence":"Medium","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048709","count":2},{"id":"GO:2000617","count":1},{"id":"GO:0015031","count":1},{"id":"GO:0007117","count":1},{"id":"GO:0031116","count":1}]},{"hash":"2096190840296965529","title":"Nuclear RNA processing and ER stress response","description":"The GO terms cluster around nuclear gene expression: mRNA splicing via the spliceosome and negative regulation of transcription by RNA Pol II, suggesting RNA processing and transcription control. Additional terms point to cellular stress handling, including ER stress response and regulation of protein refolding, indicating a broader role in protein quality control during stress. While some terms are obsolete, the core theme centers on nuclear RNA processing and stress-related protein handling.","confidence":"Medium","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":1},{"id":"GO:0007329","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0098869","count":1},{"id":"GO:0046826","count":1}]},{"hash":"841241840056178784","title":"Mitotic stress response and protein folding","description":"This cluster centers on mitosis (mitotic cell cycle) and links to cellular stress responses (oxidative stress, dsRNA response) and protein quality control (unfolded protein response, chaperone-assisted refolding, and protein complex assembly). The presence of several obsolete histone modification terms suggests chromatin regulation during cell cycle as a secondary association, but the dominant theme is coordination of cell division with stress management and protein folding.","confidence":"Medium","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0070301","count":5},{"id":"GO:0071360","count":4},{"id":"GO:0006986","count":4},{"id":"GO:0070389","count":4}]},{"hash":"483265015984274177","title":"Membrane Ion Transport and Phosphoregulation","description":"The cluster is enriched for transmembrane and ion transport GO terms (potassium, sodium, arsenite transport, and general transmembrane transport) and for phosphorylation/dephosphorylation processes, pointing to a theme of regulated membrane transport. While some terms (DNA replication, viral process) are less clearly connected, the strongest signal is membrane transport with phosphorylation regulation.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0016310","count":2},{"id":"GO:0006813","count":2},{"id":"GO:2000185","count":2},{"id":"GO:0015700","count":2}]},{"hash":"845938134798355083","title":"Unknown","description":"The terms span ribosome biogenesis (maturation of SSU-rRNA), transcriptional and chromatin regulation (negative regulation of Pol II, heterochromatin formation, histone methylation marks), and immune/developmental processes (chemokine production, central tolerance, placenta morphogenesis) with no single coherent theme tying them together. Thus there isn\u2019t a clear, specific function label for this cluster.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030490","count":1},{"id":"GO:0060669","count":1},{"id":"GO:0000122","count":1},{"id":"GO:2001040","count":1},{"id":"GO:0061188","count":1}]},{"hash":"2102587296276915941","title":"Unknown","description":"The top GO terms span disparate themes (pheromone-regulated transcription, tRNA biosynthesis, endothelial proliferation, visual perception, G-protein assembly, ubiquitin-dependent protein degradation, protein refolding, NOS activity, photomorphogenesis, and DNA replication termination), with no clear shared function tying the proteins together. Therefore, no specific, representative label can be assigned.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007329","count":1},{"id":"GO:0008616","count":1},{"id":"GO:0001938","count":1},{"id":"GO:0007601","count":1},{"id":"GO:1902605","count":1}]},{"hash":"318762495248955544","title":"Developmental signaling and organogenesis","description":"This cluster's GO terms cluster around developmental processes and signaling pathways with organ formation contexts, including kidney/metanephros development, pharyngeal system development, and dorsal/ventral neural tube patterning (via Smoothened). Other terms touch on estrogen receptor signaling regulation and ciliary localization, which can intersect developmental signaling. Overall, the shared theme is involvement in developmental signaling and organogenesis, though individual terms vary in specificity.","confidence":"Medium","size":13,"edges":12,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0007000","count":1},{"id":"GO:0006935","count":1},{"id":"GO:0033146","count":1},{"id":"GO:0097499","count":1},{"id":"GO:0060831","count":1}]},{"hash":"962782090571106282","title":"Microbial energy metabolism pathways","description":"The top GO terms point to energy generation and carbon processing in microbes, including electron transport chain, TCA cycle, sulfate reduction, and methanogenesis, with additional signals from photosynthesis and various catabolic processes. A few terms (like flagellum assembly) are more structural, but the shared theme is microbial metabolism focused on energy production. Confidence: Medium","confidence":"","size":13,"edges":13,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0019684","count":2},{"id":"GO:0044780","count":1},{"id":"GO:0019483","count":1},{"id":"GO:0022900","count":1}]},{"hash":"2190732324685053378","title":"Epigenetic Regulators of Transcription","description":"The top GO terms point to histone demethylation (H3-K36/K4) and DNA-templated transcription, indicating chromatin modification and transcriptional control as the core theme. Auxiliary terms involving post-translational hydroxylation and differentiation/vasculogenesis further support a broader role in epigenetic regulation affecting development. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0070544","count":5},{"id":"GO:0034720","count":5},{"id":"GO:0030961","count":4},{"id":"GO:0045668","count":4},{"id":"GO:0045663","count":3}]},{"hash":"1081417840959891277","title":"ER-Golgi Transport and ER Network Organization","description":"This cluster centers on endoplasmic reticulum to Golgi vesicle transport, protein secretion, and ER tubular network formation/maintenance, with these ER-related processes dominating the top terms. A few neuronal EMT-related terms are present but less representative, so the cohesive theme is ER trafficking and organization in the secretory pathway.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0009306","count":1},{"id":"GO:2000269","count":1},{"id":"GO:0071787","count":1},{"id":"GO:1990809","count":1}]},{"hash":"159158327609913490","title":"Neuromuscular development and motor function","description":"The top terms center on motor neuron differentiation, neuromuscular control of posture, and muscle movement, with a supporting emphasis on neurofilament cytoskeleton organization, all pointing to neuromuscular development and nerve\u2013muscle connectivity. Collagen biosynthesis may reflect extracellular matrix roles in muscle/nerve environments, reinforcing this theme. Overall, the cluster appears to group proteins involved in neuromuscular development and function.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021523","count":1},{"id":"GO:0044257","count":1},{"id":"GO:0050881","count":1},{"id":"GO:0050884","count":1},{"id":"GO:0032964","count":1}]},{"hash":"1555344206132842725","title":"RNA and protein methylation enzymes","description":"The top GO terms are dominated by methylation-related processes, including tRNA methylation and wobble uridine modification, 7-methylguanosine mRNA capping, and several protein methylations (arginine, N-terminal, and glycine). The presence of chlorophyll and cobalamin biosynthesis methyltransferase-related terms suggests a broader role for methyltransferases across metabolism. Together, these points indicate a cohesive theme around methylation enzymes acting on RNA and proteins.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002098","count":3},{"id":"GO:0019919","count":3},{"id":"GO:1901052","count":3},{"id":"GO:0036068","count":3},{"id":"GO:0016049","count":3}]},{"hash":"649169890738403132","title":"RNA Processing and Translation Initiation","description":"This cluster centers on RNA metabolism, featuring multiple terms tied to translation initiation (formation of the translation preinitiation complex, translation reinitiation, IRES-dependent translation) and mRNA processing/splicing (spliceosome-mediated splicing, small-subunit processome assembly, alternative splicing, and general mRNA modification). The shared theme appears to be RNA processing and regulation of translation, suggesting the proteins function in coordinating RNA maturation with translational control.","confidence":"High","size":12,"edges":14,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0030433","count":2}]},{"hash":"910100620689205617","title":"Epigenetic Chromatin Regulation","description":"Top GO terms cluster around various methylation processes (histone, rRNA, tRNA, peptide-arginine) and chromatin-related activities (chromatin remodeling, heterochromatin formation), with some association to androgen receptor signaling. This coherent theme points to regulation of gene expression via chromatin state, despite a few metabolic terms that may be incidental. Therefore, the label reflects the core function of the cluster as epigenetic/chromatin regulation.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019919","count":3},{"id":"GO:0002098","count":3},{"id":"GO:0006744","count":3},{"id":"GO:0043985","count":3},{"id":"GO:0031167","count":2}]},{"hash":"257196742708885959","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0042619","count":4},{"id":"GO:0009103","count":4},{"id":"GO:0045226","count":3},{"id":"GO:0019673","count":3}]},{"hash":"1775255940513569432","title":"Developmental regulation and gene expression","description":"This cluster centers on processes related to development (multicellular development, fat cell differentiation, cell migration) and regulation of gene expression (DNA-templated transcription, mRNA processing, nuclear export regulation, and cell cycle control), suggesting a cohesive theme of coordinating differentiation and transcriptional programs across tissues. While some terms are broad, the combination points to a developmental/gene-expression\u2013regulatory module rather than a single functional category.","confidence":"Medium","size":12,"edges":9,"triangles":2,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":10},{"id":"GO:0019233","count":10},{"id":"GO:0006351","count":9},{"id":"GO:0046827","count":9},{"id":"GO:1904355","count":8}]},{"hash":"721203245532190556","title":"Trafficking-Linked Immune Signaling","description":"The cluster combines GO terms for Golgi organization and endocytic recycling (trafficking) with immune defense processes (defense response to protozoan/virus and NLRP3 inflammasome assembly), suggesting proteins that coordinate intracellular trafficking with immune signaling. A few terms hint at neural context (glial differentiation, neuromuscular junction assembly), but the overarching theme appears to be trafficking-related modulation of immune responses.","confidence":"Medium","size":12,"edges":10,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0042832","count":2},{"id":"GO:0007030","count":2},{"id":"GO:0032456","count":2},{"id":"GO:1900025","count":1},{"id":"GO:0051124","count":1}]},{"hash":"2144699816860408981","title":"DNA replication and chromatin maintenance","description":"The cluster is enriched for DNA replication terms and chromatin-related processes, suggesting a coordinated role in genome replication and chromatin state regulation; some entries use obsolete terms but reflect the same themes.","confidence":"High","size":12,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0006311","count":5},{"id":"GO:0071894","count":5},{"id":"GO:0042766","count":5},{"id":"GO:0070870","count":5}]},{"hash":"480227048515693736","title":"Neuronal transcription and signaling","description":"The top GO terms cluster around neuronal function, including sensory perception of sound, GABAergic synaptic transmission, and receptor guanylyl cyclase signaling, alongside transcription-related processes. Several terms also appear as outliers (lysine biosynthesis, vacuole targeting, peroxisome regulation), but the dominant theme centers on neuronal signaling and gene regulation, justifying a label focused on these aspects.","confidence":"Medium","size":12,"edges":11,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0007605","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0019878","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0007168","count":2}]},{"hash":"1963732232274875917","title":"Bacterial LPS and polysaccharide biosynthesis","description":"The top GO terms point to lipopolysaccharide and exopolysaccharide biosynthesis (O antigen, colanic acid, LPS core) and sugar-nucleotide precursor pathways (dTDP-rhamnose, galactose, ADP-L-glycero-beta-D-manno-heptose). This indicates proteins in the cluster mainly contribute to assembly of the bacterial cell envelope polysaccharides, especially LPS and related surface components. Other biosynthetic terms (PHB, vitamin K) appear ancillary. ","confidence":"High","size":12,"edges":16,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0009243","count":2},{"id":"GO:0042619","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0019305","count":2}]},{"hash":"1410312000491445821","title":"Viral replication and RNA processing","description":"This cluster centers on RNA polymerase II transcription and RNA processing (terminations, splicing, CTD regulation, RNA-templated DNA biosynthesis) alongside viral lifecycle processes (uncoating, virion assembly, host-mediated activation of viral genome replication). The convergence of host transcription/RNA processing terms with virion-related terms suggests proteins that connect RNA processing with viral replication. Some terms are obsolete, which temper certainty, but the dominant theme is the intersection of RNA processing and viral lifecycle.","confidence":"Medium","size":12,"edges":47,"triangles":115,"max_degree":10,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1901407","count":5},{"id":"GO:0031047","count":5},{"id":"GO:0048026","count":5},{"id":"GO:0006369","count":5},{"id":"GO:0006457","count":4}]},{"hash":"2008339063029387985","title":"Calcium signaling in excitable cells","description":"The top GO terms point to calcium handling and excitability, including calcium import across the plasma membrane and release of sequestered calcium into the cytosol, plus regulation of SA node action potentials. There are related signals for mechanical stimulus response and synaptic plasticity via receptor localization, all consistent with calcium-dependent signaling in neurons and cardiac/excitable tissues. Overall, this cluster reflects calcium signaling pathways governing cellular excitability.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098907","count":4},{"id":"GO:0007205","count":4},{"id":"GO:0071260","count":3},{"id":"GO:0098703","count":3},{"id":"GO:0009409","count":3}]},{"hash":"803442158307290792","title":"Heart Development and Blood Circulation","description":"This cluster shows clear signals for cardiovascular biology, with non-obsolete terms like right ventricular compact myocardium morphogenesis and blood circulation indicating heart development and functional circulation. There are also hints of transcriptional regulation and endocrine regulation (growth hormone secretion), but the strongest theme centers on cardiac formation and blood flow. Note that several GO terms are obsolete, which reduces confidence in broader functional inference.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033697","count":1},{"id":"GO:0036091","count":1},{"id":"GO:0071894","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0060123","count":1}]},{"hash":"406565626988754930","title":"Unknown","description":"The top GO terms span immune cytokine regulation, neural development signaling, insulin signaling, axon regeneration, PKC-related responses, osmotic stress, trans-synaptic signaling, mitotic spindle organization, sperm capacitation, and nuclear migration during mitosis. This wide mix of processes suggests there isn\u2019t a single coherent biological function tying the cluster together, making an informative, specific label difficult. It may reflect heterogeneous roles or a mixture of proteins from different pathways.","confidence":"","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0002741","count":12},{"id":"GO:0035607","count":12},{"id":"GO:0008286","count":12},{"id":"GO:0048679","count":12},{"id":"GO:1904628","count":12}]},{"hash":"1392204386111242270","title":"Unknown","description":"Top GO terms include responses to xenobiotic stimulus, lipopolysaccharide, cold, herbicide, cytolysis, megakaryocyte differentiation, thiamine biosynthesis, and neuronal development. The terms are extremely diverse with no clear unifying function or pathway, suggesting this is a heterogeneous set rather than a cohesive functional cluster.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":5},{"id":"GO:0032496","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0019835","count":4},{"id":"GO:0009409","count":4}]},{"hash":"159629533100603302","title":"Ubiquitin-Dependent Protein Degradation","description":"Based on the enriched GO terms, the cluster centers on ubiquitin-mediated proteolysis and turnover, including ubiquitin-dependent protein catabolic processes, autoubiquitination, K48-linked ubiquitination, ERAD, and degradation of receptors like the Wnt receptor; a peroxisome import term seems incidental. Overall, the proteins appear to function in ubiquitin-dependent protein degradation pathways.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0051865","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0016558","count":3},{"id":"GO:0060816","count":3}]},{"hash":"1207586419635257941","title":"Viral entry, replication, and release","description":"Most top GO terms describe steps in the viral life cycle: uncoating, membrane fusion, virion assembly, host-mediated activation of viral genome replication, viral release, and the overall viral life cycle. A term for RNA-templated DNA biosynthesis (reverse transcription) also aligns with retroviral replication. Together these indicate a viral infection/replication theme.","confidence":"High","size":12,"edges":12,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006457","count":1},{"id":"GO:0019061","count":1},{"id":"GO:0006278","count":1},{"id":"GO:0010849","count":1},{"id":"GO:0044829","count":1}]},{"hash":"1133940207690689425","title":"Proteostasis and ER-associated degradation","description":"Predominant themes are proteostasis and protein turnover: ribosome-associated ubiquitin-dependent degradation, cytoplasmic protein quality control by the proteasome, ER-to-cytosol retrograde transport, ER-associated misfolded protein catabolic process, and nonfunctional rRNA decay related to ribosome quality control. A few terms about synaptic vesicle endocytosis and plasma membrane tubulation seem less connected to this core, possibly annotation noise.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070651","count":1},{"id":"GO:1900182","count":1},{"id":"GO:1990116","count":1},{"id":"GO:0051974","count":1},{"id":"GO:0071629","count":1}]},{"hash":"2080029420490224101","title":"Transcription regulation and genome maintenance","description":"This cluster centers on nuclear processes: transcription control and chromatin-related activities (DNA-templated transcription, SAGA complex localization, histone deubiquitination, translation preinitiation complex formation, mRNA export) alongside genome maintenance (homologous recombination repair, trinucleotide repeat maintenance) and protein turnover (proteasome assembly). A couple of developmental terms are present, but the overarching theme is gene expression regulation and genome stability in the nucleus.","confidence":"Medium","size":12,"edges":9,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0000724","count":2},{"id":"GO:0016578","count":1},{"id":"GO:0072742","count":1},{"id":"GO:0030447","count":1}]},{"hash":"1086817020673171353","title":"Unknown","description":"The protein set shows no coherent functional signal: GO terms span mitochondrial processing, conjugation, ubiquinone biosynthesis, environmental catabolic processes, plant growth regulation, aerotaxis, epithelial adhesion, and mechanical stimulus response, with no edges or clusters linking them. This lack of a unifying function or pathway prevents a meaningful label beyond Unknown.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006627","count":1},{"id":"GO:0000746","count":1},{"id":"GO:1901006","count":1},{"id":"GO:0050899","count":1},{"id":"GO:0046265","count":1}]},{"hash":"1061228386800004456","title":"Cell-cycle Regulation and Translation Initiation","description":"The Top Terms point to mitotic cell cycle activity and the formation of translation preinitiation complexes, along with mRNA transport and kinase signaling. The presence of actin nucleation and chromatin methylation hints at broader cellular regulation coordinating division, gene expression, and cytoskeletal dynamics. While the set spans multiple processes, the clearest theme is regulatory control linking cell cycle progression with translation initiation, justifying this label. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0051028","count":5},{"id":"GO:0071456","count":5},{"id":"GO:0031954","count":5},{"id":"GO:0043547","count":5}]},{"hash":"948978805128440445","title":"Ubiquitin-Mediated Regulation of Mitosis and Neural Development","description":"The top GO terms point to ubiquitin-related processes (K11-linked ubiquitination and ubiquitin-dependent protein catabolic process) and cell-cycle activities (mitotic cell cycle, metaphase/anaphase transition), alongside neural development and neurite growth (nervous system development, dendrite/axon morphogenesis, synaptic plasticity). This suggests a coherent theme where ubiquitination modulates both cell division and neural morphogenesis, forming a functional cluster rather than unrelated processes.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070979","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0000278","count":1},{"id":"GO:0031915","count":1},{"id":"GO:0050775","count":1}]},{"hash":"1757520569991203027","title":"Unknown","description":"No GO terms or network connections to link these proteins into a shared function; cannot determine a representative theme for this cluster.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1883597514003353107","title":"Excitable Membrane Ion Transport and Action Potential Regulation","description":"The cluster is dominated by GO terms describing ion transport across the plasma membrane (sodium import and potassium export) and electrical activity in cardiac tissue (membrane depolarization and regulation of ventricular and AV nodal action potentials). This points to a shared function in maintaining membrane excitability in excitable cells. Some terms (cAMP/cGMP signaling, aerotaxis, optic nerve structure, touch perception) are more distant but do not override the primary theme. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0098719","count":8},{"id":"GO:0010754","count":7},{"id":"GO:0071320","count":7},{"id":"GO:0071321","count":7},{"id":"GO:0097623","count":7}]},{"hash":"362173861326861396","title":"Signaling and vesicle trafficking across systems","description":"This cluster combines GO terms from nervous, endocrine, and immune signaling, including synaptic vesicle priming, dense core granule exocytosis, GPCR internalization, Rac signaling, insulin signaling, and IL-18 signaling; it also touches on B cell homeostasis and myelin maintenance, suggesting a broad theme of signaling and vesicle trafficking across diverse biological contexts.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032094","count":1},{"id":"GO:0035655","count":1},{"id":"GO:0016082","count":1},{"id":"GO:0002031","count":1},{"id":"GO:0008286","count":1}]},{"hash":"2216463203898336467","title":"Unknown","description":"The terms include embryonic morphogenesis (germ-band extension, apical constriction in gastrulation) and a mix of unrelated processes (glycosylation, protein folding, hypoxia signaling, plant ethylene signaling, and heterocyst development). This broad, non-cohesive set provides no single unifying function for the cluster, so a specific, representative label cannot be assigned.","confidence":"","size":12,"edges":11,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0007377","count":1},{"id":"GO:0006490","count":1},{"id":"GO:0003384","count":1},{"id":"GO:0006487","count":1},{"id":"GO:0006457","count":1}]},{"hash":"2107562457496014500","title":"Unknown","description":"The terms span kidney development, memory, calcium signaling/cardiac function, and oxidative processes with no clear shared theme; there are no connections between terms to tie the proteins to a single cohesive function, so a specific label isn\u2019t justifiable.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035502","count":1},{"id":"GO:0007614","count":1},{"id":"GO:1901844","count":1},{"id":"GO:1901841","count":1},{"id":"GO:0007616","count":1}]},{"hash":"1841300397083716954","title":"Calcium-Driven Signaling and Synaptic Plasticity","description":"This cluster centers on signaling pathways and calcium dynamics, with several terms pointing to calcium import and release, GPCR- and Wnt-mediated signaling, and regulation of synaptic plasticity, suggesting a core theme of calcium-dependent signaling governing synaptic function. Some additional terms (e.g., dsRNA response, mechanical stimulus, cold) reflect broader stress or environmental responses but do not override the central calcium/synaptic signaling pattern.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016055","count":4},{"id":"GO:2001275","count":4},{"id":"GO:0007205","count":4},{"id":"GO:0016477","count":4},{"id":"GO:0071360","count":3}]},{"hash":"1231415785300679023","title":"Synaptic development and vesicle trafficking","description":"The top GO terms cluster around dendrite development, exocytosis, and receptor localization to the synapse, plus signaling and Golgi localization-related trafficking. This suggests the proteins are involved in neuronal growth and the delivery/localization of synaptic components, i.e., synaptic maturation and vesicle trafficking. ","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0016358","count":5},{"id":"GO:0006887","count":4},{"id":"GO:0097120","count":4},{"id":"GO:0019933","count":4},{"id":"GO:0006470","count":4}]},{"hash":"331305619491059341","title":"Calcium signaling and temperature stress response","description":"This cluster centers on calcium dynamics (calcium import and release) and temperature-related stress responses (heat and cold), suggesting calcium-mediated signaling under environmental stress. While there are other terms related to ubiquitination and synaptic plasticity, the core pattern ties calcium signaling to temperature stress.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":3},{"id":"GO:0000209","count":3},{"id":"GO:0071260","count":2},{"id":"GO:0098703","count":2},{"id":"GO:0009409","count":2}]},{"hash":"2100921433874414394","title":"GPCR Calcium Signaling and Vasopressin Secretion","description":"The terms show GPCR signaling (even an obsolete GPCR pathway term), calcium import and release, and vasopressin secretion, plus links to synaptic localization and mechanosensory responses. This suggests a cohesive theme of GPCR-driven Ca2+ signaling governing peptide release and synaptic modulation in neuronal or neuroendocrine contexts, with some additional stress-sensing terms. Some terms are obsolete, but the core pattern points to calcium-dependent GPCR signaling and secretion.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":3},{"id":"GO:0071260","count":2},{"id":"GO:0098703","count":2},{"id":"GO:0009409","count":2},{"id":"GO:0051209","count":2}]},{"hash":"232770796375423200","title":"Meiotic chromosome pairing and chromatin regulation","description":"The top terms strongly point to meiosis, with synaptonemal complex organization, chiasma assembly, and DNA double-strand break processing indicating meiotic recombination and chromosome pairing. Chromatin-related processes like histone ubiquitination and phosphorylation regulation further support a chromatin-level control of meiosis. Some terms (e.g., prolactin secretion, peroxisome import) appear less related and may reflect background signals, but the core pattern aligns with meiotic chromosome dynamics.","confidence":"High","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0070459","count":11},{"id":"GO:0016558","count":11},{"id":"GO:0071894","count":11},{"id":"GO:0051026","count":11},{"id":"GO:0071455","count":11}]},{"hash":"1748584419672671214","title":"Central carbon metabolism (glycolysis to TCA)","description":"The top GO terms center on glycolysis, pyruvate biosynthesis, acetyl-CoA formation, and the TCA cycle, with quinolinate biosynthesis (NAD) linked as part of energy metabolism. A few terms like response to cAMP and morphine are peripheral; overall the cluster appears to represent central carbon metabolism and energy production.","confidence":"High","size":11,"edges":47,"triangles":100,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0042866","count":4},{"id":"GO:0051591","count":3},{"id":"GO:0043278","count":3},{"id":"GO:0042853","count":3},{"id":"GO:0019805","count":3}]},{"hash":"785474229637815451","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0042273","count":2}]},{"hash":"1359806032158669650","title":"Protein and Metabolite Acetylation Cluster","description":"The top GO terms are centered on acetylation events (N-terminal acetylation, peptidyl-lysine N6-acetylation, lysine acetylation, spermidine acetylation), suggesting a cohesive theme of acetylation-modified proteins and metabolites. Some metabolic terms (mycothiol and glucosamine biosynthesis) may reflect acetyl-CoA\u2013linked processes, but the dominant signal is acetylation-related modification across proteins and related metabolites.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010125","count":4},{"id":"GO:0061606","count":3},{"id":"GO:0030187","count":3},{"id":"GO:0017196","count":3},{"id":"GO:0001525","count":3}]},{"hash":"2249724184420713185","title":"Root Hair Cell Wall Formation","description":"This cluster is enriched for plant-specific terms such as root hair cell development and rhamnogalacturonan II biosynthesis, plus cell wall organization and a cellular response to hydrogen peroxide, indicating a program of root hair\u2013associated wall remodeling and ROS signaling in plants. While a few terms are less directly tied (DNA recombination, aging, renal water transport), the dominant theme centers on plant cell wall construction and root hair growth.","confidence":"Medium","size":11,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0070301","count":2},{"id":"GO:0010306","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0080147","count":2},{"id":"GO:0042493","count":1}]},{"hash":"1787601917624452360","title":"Translation Machinery and Ribosome Biogenesis","description":"Most enriched GO terms are about translation and ribosome assembly (translation, cytoplasmic translation, translational initiation/termination, ribosome biogenesis, selenocysteine incorporation, translational fidelity). A couple of terms (JNK signaling, glial proliferation) may reflect broader regulatory links, but the dominant theme is the protein synthesis machinery. ","confidence":"High","size":11,"edges":24,"triangles":24,"max_degree":8,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0042254","count":5},{"id":"GO:0002181","count":4},{"id":"GO:0046677","count":4},{"id":"GO:0006415","count":4}]},{"hash":"949783056885060586","title":"Steroid and Retinoid Lipid Biosynthesis","description":"This cluster shows strong enrichment for retinoid metabolism (retinal, retinol, retinoic acid) and steroid biosynthesis (testosterone, glucocorticoid), along with very long-chain fatty acid biosynthesis, pointing to a core theme of lipid-based metabolic pathways and hormone-related biosynthesis. Some terms like antibiotic response or PHB biosynthesis appear less central, but the dominant signal is lipid metabolism involving steroids and retinoids. ","confidence":"Medium","size":11,"edges":46,"triangles":102,"max_degree":10,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":9},{"id":"GO:0006355","count":8},{"id":"GO:0042761","count":7},{"id":"GO:0042574","count":7},{"id":"GO:0002138","count":7}]},{"hash":"431406975426826528","title":"Diverse membrane transport","description":"This cluster is dominated by transmembrane transport terms for a variety of substrates (glycerophosphodiesters, amino acids, lipids, molybdate, teichoic acids, and even doxorubicin), plus phospholipid translocation and membrane-associated processes like cytochrome complex assembly. The common theme is transport across membranes and related membrane functions, making \u201cDiverse membrane transport\u201d a fitting, specific label.","confidence":"High","size":11,"edges":10,"triangles":0,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0001407","count":10},{"id":"GO:0015910","count":10},{"id":"GO:0003333","count":10},{"id":"GO:0015689","count":10},{"id":"GO:0000770","count":10}]},{"hash":"2210028550028689744","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000462","count":11},{"id":"GO:0031047","count":11},{"id":"GO:0006605","count":11},{"id":"GO:0006311","count":11},{"id":"GO:0071894","count":11}]},{"hash":"2026590874657520354","title":"Unknown","description":"The top GO terms span proteostasis, metabolism, and cell-cycle processes (proteasome assembly, peroxisome import, oxidative stress response, division/centriole elongation, DNA replication, ATP biosynthesis) with no single coherent functional theme; thus a definite label is not supported.","confidence":"","size":11,"edges":42,"triangles":72,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0070682","count":2},{"id":"GO:0016558","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0034599","count":2},{"id":"GO:0002027","count":2}]},{"hash":"2151070818416920731","title":"Capsule and cell-wall glycosylation biosynthesis","description":"These proteins show a cohesive theme around polysaccharide capsule and cell wall biosynthesis, including hyaluronan and capsule polysaccharide biosynthetic processes, various glycosylation pathways (O-linked, including GalNAc), and cell wall organization. UDP-glucose metabolism provides sugar substrates, and mycolate layer assembly ties to cell wall biosynthesis in custom contexts. Altogether, the cluster represents capsule and cell-wall glycosylation activities.","confidence":"High","size":11,"edges":10,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0030213","count":1},{"id":"GO:0018242","count":1},{"id":"GO:0070592","count":1},{"id":"GO:0016266","count":1},{"id":"GO:0036108","count":1}]},{"hash":"1871580816685141251","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":10,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":3},{"id":"GO:1902600","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0006189","count":1},{"id":"GO:0019404","count":1}]},{"hash":"2116060221195811004","title":"Mitochondrial Heme Synthesis and Metal Ion Homeostasis","description":"The terms cluster around heme biosynthesis and assembly of mitochondrial respiratory components, with a strong accompanying signal for metal ion handling and detoxification (iron, zinc, cobalt, cadmium). This suggests a functional module linking mitochondrial heme production to metal ion balance and detox pathways.","confidence":"Medium","size":11,"edges":7,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0033108","count":2},{"id":"GO:0006782","count":1},{"id":"GO:0018160","count":1},{"id":"GO:0006783","count":1},{"id":"GO:0010043","count":1}]},{"hash":"1824893425103517831","title":"Reproductive Hormone Signaling and Uterine Development","description":"The strongest terms point to reproductive biology\u2014LH and FSH signaling pathways and uterus development, with sperm DNA condensation reinforcing a reproductive context. While immune terms (innate immune response, interferon production) appear, they likely reflect shared signaling pathways (GPCR-PLC-IP3) rather than a cohesive immune function of the cluster. Overall, the dominant theme is reproductive signaling and development.","confidence":"Medium","size":11,"edges":44,"triangles":88,"max_degree":10,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0009992","count":8},{"id":"GO:0042700","count":8},{"id":"GO:0060065","count":8},{"id":"GO:0042699","count":8},{"id":"GO:0051607","count":8}]},{"hash":"801146460741535116","title":"Integrin signaling and cytoskeletal remodeling in skin","description":"The cluster centers on integrin-mediated signaling and cytoskeletal dynamics, as shown by terms like integrin signaling, regulation of actin depolymerization, and skin development, suggesting a coordinated adhesion-cytoskeleton program in skin/epithelial contexts. Other terms (calcium/manganese transport, phospholipid dephosphorylation, dephosphorylation) point to membrane signaling and ion homeostasis that often accompany adhesion and cytoskeletal remodeling. While there are some metabolic and transport processes present, the cohesive theme appears to be adhesion-driven signaling and cytoskeletal regulation in skin.","confidence":"Medium","size":11,"edges":9,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0007229","count":2},{"id":"GO:0098703","count":2},{"id":"GO:0006828","count":2},{"id":"GO:0043588","count":2},{"id":"GO:0046272","count":1}]},{"hash":"1646813997512795993","title":"Neural development and synaptogenesis","description":"This cluster is dominated by GO terms tied to neural development and synaptic formation, including axonogenesis, excitatory postsynaptic potentials, and positive regulation of synapse assembly, as well as dopamine response and Wnt signaling that frequently influence neural signaling and connectivity. Some terms like mitotic cell cycle and heart development appear as broader developmental processes, but the core pattern points to neural development and synaptic regulation.","confidence":"Medium","size":11,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0060079","count":3},{"id":"GO:0007409","count":3},{"id":"GO:1903351","count":3}]},{"hash":"1096667925818555416","title":"ER-Golgi trafficking and ER stress response","description":"The dominant terms point to ER-to-Golgi vesicle transport, Golgi organization, and ER stress response, with a notable ER-based prolyl hydroxylation step involved in protein maturation; these together suggest involvement in protein processing and quality control in the secretory pathway. While there are also transcription-related terms, the clear core theme is ER-Golgi trafficking and ER stress, possibly with some cross-talk to transcriptional regulation. Confidence in this labeling is Medium.","confidence":"Medium","size":11,"edges":4,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0006351","count":3},{"id":"GO:1903358","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0098869","count":2}]},{"hash":"1301417291599804868","title":"Calcineurin-NFAT signaling and morphogenesis","description":"The top terms cluster around regulation of the calcium-dependent calcineurin-NFAT pathway, with notes on tissue morphogenesis such as blood vessel branching, dendrite morphogenesis, and muscle fiber-type transitions. This suggests a theme of signaling-driven morphogenesis across multiple tissues, anchored by calcium/NFAT signaling.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051533","count":2},{"id":"GO:0060316","count":2},{"id":"GO:0050774","count":2},{"id":"GO:0014883","count":2},{"id":"GO:0001569","count":2}]},{"hash":"412257089300801393","title":"Neuronal synapse organization and survival regulation","description":"The Top Terms include clear neuronal-related processes, such as synapse organization and negative regulation of neuron apoptotic process, suggesting a theme around neuronal connectivity and survival. Additional terms point to broader signaling and protein-regulation mechanisms (e.g., TGF-beta/SMAD-related regulation and ubiquitin-protein transferase activity) that can influence neural development and maintenance. The mix indicates a plausible but not tightly constrained theme centered on neuronal signaling and survival, with some obsolescent terms and no edges tying the proteins together. ","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030512","count":1},{"id":"GO:0080182","count":1},{"id":"GO:0031064","count":1},{"id":"GO:0051443","count":1},{"id":"GO:2000146","count":1}]},{"hash":"378614535898320478","title":"ER protein folding and quality control","description":"The top GO terms cluster around ER proteostasis: response to unfolded proteins, ER-specific protein folding/refolding, and ubiquitin-proteasome\u2013mediated quality control, plus ER-targeting of nascent proteins. While a couple terms touch on development or nuclear transport, the dominant theme is ER-associated folding and quality control mechanisms.","confidence":"Medium","size":11,"edges":10,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006986","count":1},{"id":"GO:0071630","count":1},{"id":"GO:0070389","count":1},{"id":"GO:0031204","count":1},{"id":"GO:0001707","count":1}]},{"hash":"658035862512557574","title":"Meiosis spindle assembly and septin-mediated cell morphology","description":"The top terms point to meiotic processes (spindle assembly in female meiosis, meiotic chromosome alignment) and cytoskeletal regulation (septin ring assembly/disassembly and bud neck septin ring organization), together with embryonic development-related changes in cell shape and differentiation. This suggests the cluster centers on meiosis-related spindle dynamics alongside septin-driven cell morphology during development. A peripheral item like sperm mitochondrion organization may connect here through gamete-related processes but is less dominant. Confidence: Medium","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000921","count":1},{"id":"GO:0030382","count":1},{"id":"GO:0007224","count":1},{"id":"GO:0016476","count":1},{"id":"GO:0051311","count":1}]},{"hash":"1915955637197532509","title":"Cell stress response and apoptosis","description":"This cluster shows multiple stress-associated GO terms (cellular responses to cadmium ion, ethanol, exogenous dsRNA, and unfolded protein) together with innate immune response and apoptotic process, indicating a functional grouping around stress signaling leading to cell death and potential immune engagement. The mitotic cell cycle/division terms are present but appear less central than the stress and apoptosis signals, making the overall theme best described as cell stress response with apoptosis.","confidence":"Medium","size":11,"edges":7,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0071361","count":2}]},{"hash":"1460247122217928325","title":"Actin Cytoskeleton Remodeling and Membrane Trafficking","description":"The top terms point to actin-based structure formation and remodeling (lamellipodium morphogenesis, podosome assembly) along with membrane trafficking and signaling (endocytic recycling, phosphatidylinositol signaling, phosphatidic acid biosynthesis). These features together suggest a cohesive module of cytoskeleton dynamics coupled to membrane traffic and adhesion turnover, despite a few unrelated terms that may be noise. Overall, the cluster appears to represent actin-driven cell motility and adhesion processes.","confidence":"High","size":11,"edges":10,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006654","count":1},{"id":"GO:2000769","count":1},{"id":"GO:1990126","count":1},{"id":"GO:0022617","count":1},{"id":"GO:0010252","count":1}]},{"hash":"622273760275211153","title":"Magnesium Homeostasis and Proteostasis","description":"Top GO terms indicate magnesium ion transmembrane transport, intracellular magnesium ion homeostasis, and cellular response to magnesium ion, pointing to a magnesium handling theme. Additional terms reference oxidative stress response and oxidation-dependent protein catabolic processes, as well as protein quality control and peroxisomal protein import, suggesting a broader connection to proteostasis under oxidative stress. Taken together, the cluster seems to reflect coordinated metal ion management with stress-related protein turnover, though the link is not extremely tight, so I assign a Medium confidence label.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903830","count":1},{"id":"GO:0010961","count":1},{"id":"GO:0071286","count":1},{"id":"GO:0070407","count":1},{"id":"GO:0016558","count":1}]},{"hash":"1636249599847102597","title":"Metal/oxidative stress response with transcription","description":"This cluster is dominated by GO terms for cellular responses to multiple metals and oxidants (cadmium, diamide, copper, arsenite, nitroglycerin) and includes DNA-templated transcription, suggesting a set of proteins that sense or respond to environmental/chemical stress and coordinate transcriptional programs. A couple of terms relate to broader developmental or stress contexts, but the core theme centers on stress response and transcriptional regulation.","confidence":"Medium","size":11,"edges":28,"triangles":30,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0072738","count":2},{"id":"GO:0070207","count":2},{"id":"GO:2001033","count":2}]},{"hash":"1604019969376268765","title":"Calcium-Dependent Mechanosensory and Synaptic Signaling","description":"The cluster centers on calcium signaling events (calcium import, release from stores) and responses to mechanical stimuli, plus a note on synaptic plasticity via receptor localization to the synapse. This pattern suggests a coherent theme of calcium-driven mechanosensory signaling influencing neural/synaptic function, despite a few peripheral or obsolete GO terms.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":2},{"id":"GO:0098703","count":2},{"id":"GO:0009409","count":2},{"id":"GO:0051209","count":2},{"id":"GO:1900383","count":2}]},{"hash":"1138095267852971460","title":"Calcium signaling in heart and neurons","description":"The terms cluster around calcium handling (calcium import, release of sequestered calcium), regulation of cardiac action potential in the SA node, and signaling pathways (GPCR/PKC) linked to excitability and synaptic plasticity, with supporting notes on mechanical stimuli. This points to a shared theme of Ca2+-dependent signaling controlling heart and neural excitability and signaling.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098907","count":4},{"id":"GO:0007205","count":4},{"id":"GO:0071260","count":3},{"id":"GO:0098703","count":3},{"id":"GO:0009409","count":3}]},{"hash":"709576023236518148","title":"Diverse metabolic catabolic pathways","description":"This cluster shows enrichment for a variety of catabolic and metabolic processes, including lipid catabolism (triglycerides, monoacylglycerol, phosphatidylserine), glycolysis, cellulose catabolism, nitrate assimilation, and cholesterol biosynthesis, with regulatory signaling (endocannabinoid pathway) also present but not dominant. The terms collectively point to broad metabolic activity rather than a single specific function, so a general metabolic-catabolic label fits best.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006660","count":2},{"id":"GO:0019433","count":2},{"id":"GO:0052651","count":2}]},{"hash":"632506452684333921","title":"N-terminal and polyamine acetylation","description":"The cluster\u2019s top GO terms are dominated by acetylation-related processes: various forms of N-terminal acetylation and peptidyl acetylation (including methionine, glutamic acid, and lysine), as well as spermidine acetylation. This points to a coherent theme of acetyltransferase activity and acetylation-driven regulation, with some additional terms (melatonin biosynthesis, angiogenesis, sporulation, glucosamine metabolism) likely reflecting broader metabolic roles or annotation noise. Overall, the cluster appears centered on acetylation-modifying processes.","confidence":"High","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0061606","count":11},{"id":"GO:0030187","count":11},{"id":"GO:0017196","count":11},{"id":"GO:0001525","count":11},{"id":"GO:0018003","count":11}]},{"hash":"1141177140537579906","title":"Hedgehog signaling in eye development","description":"Dominant GO terms center on Smoothened/Hedgehog signaling and camera-type eye development, with links to neural tube patterning and left-right symmetry, suggesting a developmental role of Hedgehog signaling in eye and axis formation. Trafficking-related terms like endosome localization and ubiquitination support regulation of signaling rather than a purely structural function.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036010","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0023035","count":1},{"id":"GO:0006516","count":1},{"id":"GO:0060546","count":1}]},{"hash":"799590654608389531","title":"Xenobiotic Response and Cholesterol Biosynthesis with Inflammation","description":"This cluster shows enrichment for xenobiotic and toxic-substance responses, along with cholesterol biosynthesis, and inflammatory signaling such as IL-6 production and nitric oxide\u2013related pathways. The combination suggests proteins involved in detoxification and lipid metabolism that interface with inflammatory responses, with supporting terms like prostaglandin secretion and organofluorine metabolism. Hence, a label capturing xenobiotic response, lipid/cholesterol metabolism, and inflammation is appropriate.","confidence":"High","size":10,"edges":14,"triangles":3,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006695","count":8},{"id":"GO:0009636","count":8},{"id":"GO:0042493","count":8},{"id":"GO:0072604","count":7},{"id":"GO:0070988","count":7}]},{"hash":"1421817680861163874","title":"Unknown","description":"The GO terms span immune signaling (NF-\u03baB), xenobiotic/antibiotic response, detoxification, host-symbiont interaction, and even behavioral phenotypes, with no single cohesive process linking them. The cluster has no edges or triangles, suggesting no tightly connected pathway, so a specific, intuitive label cannot be assigned.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008284","count":3},{"id":"GO:0000122","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0043123","count":2}]},{"hash":"1553219727895053804","title":"Amino acid catabolism and redox stress response","description":"Cluster proteins are enriched for amino acid catabolic processes (L-alanine, L-valine) and related metabolism (beta-alanine biosynthesis, lipoate metabolism), along with redox-related processes (oxidation-reduction, NADPH oxidation, cellular oxidant detoxification) and hyperoxia response. A single outlier term (alternative mRNA splicing via spliceosome) appears but is not central. Overall, the cluster links amino-acid degradation with redox/oxidative stress management rather than a single tight pathway.","confidence":"Medium","size":10,"edges":38,"triangles":73,"max_degree":9,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0042853","count":8},{"id":"GO:0055114","count":7},{"id":"GO:0006574","count":7},{"id":"GO:0032496","count":6},{"id":"GO:0009106","count":6}]},{"hash":"393784303948533002","title":"Iron-Sulfur Metabolism and Stress Regulation","description":"The terms cluster around iron-sulfur cluster assembly and iron ion sequestration, as well as various negative/regulated responses to cellular stress and apoptosis (oxidative and ER stress contexts). This suggests a theme centered on metal handling (iron/Fe-S) linked to stress response pathways, with some peripheral terms related to basic processes like DNA replication and protein targeting. Confidence in a tight, single-function label is moderate to low due to heterogeneity across the terms.","confidence":"Low","size":10,"edges":10,"triangles":1,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1902037","count":3},{"id":"GO:0031204","count":3},{"id":"GO:0000742","count":3},{"id":"GO:1903382","count":3},{"id":"GO:0090084","count":3}]},{"hash":"1035661898332215152","title":"Glycolysis and energy metabolism with nutrient signaling","description":"The top GO terms highlight central carbon metabolism\u2014glycolysis, ATP production, and pyruvate biosynthesis\u2014pointing to energy production. Additional terms for heme biosynthesis and cellular responses to insulin, epinephrine, lithium, and heat suggest regulation by nutrient sensing and stress/hormonal signals. Together they describe a metabolism-focused cluster tied to energy output and nutrient/hormone signaling.","confidence":"High","size":10,"edges":41,"triangles":92,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0042866","count":4},{"id":"GO:0007584","count":4},{"id":"GO:0019878","count":4},{"id":"GO:0032869","count":3},{"id":"GO:0006782","count":3}]},{"hash":"171908928386731646","title":"RNA and Protein Methylation","description":"The top terms cluster on methylation-related processes across both RNA and proteins (rRNA methylation, tRNA wobble modification, mRNA capping, and various protein methylations such as peptidyl-lysine and peptidyl-arginine methylation), with supporting biosynthetic methyltransferase roles (cobalamin and chlorophyll biosynthesis). This suggests a group of methyltransferase enzymes acting on diverse substrates, making \"RNA and Protein Methylation\" a coherent, specific label.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031167","count":4},{"id":"GO:0018027","count":4},{"id":"GO:0009236","count":4},{"id":"GO:0018013","count":3},{"id":"GO:0019919","count":3}]},{"hash":"708339505229392343","title":"Membrane Transporters","description":"The top GO terms indicate transport across the plasma membrane for diverse substrates (xenobiotics, glucose, phosphate, urate, selenite, ascorbate) and vesicular loading of neurotransmitters, pointing to a membrane-transport/facilitated-substrate trafficking cluster; a single term about high light response is less central but could reflect related photoreceptor transport processes.","confidence":"Medium","size":10,"edges":15,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0071486","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0098700","count":2},{"id":"GO:0042908","count":2},{"id":"GO:0044381","count":2}]},{"hash":"1050954021521739677","title":"Phosphatase-regulated TGF and NF-\u03baB signaling","description":"The top terms cluster around dephosphorylation of threonine residues and negative regulation of TGF-beta signaling, plus cellular response to TGF-beta and non-canonical NF-\u03baB signaling. This suggests a common theme of signaling pathway control by phosphatases. Some other terms (vacuole fusion, photosystem stoichiometry, meristem identity) are broader or plant-related and may be incidental. Overall, the core connection is phosphatase-mediated modulation of signaling cascades.","confidence":"Medium","size":10,"edges":39,"triangles":81,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0030512","count":10},{"id":"GO:0042347","count":10},{"id":"GO:0035970","count":10},{"id":"GO:0061191","count":10},{"id":"GO:0010991","count":10}]},{"hash":"512989130302641512","title":"RNA processing and translation regulation","description":"The terms center on RNA metabolism and gene expression control: ncRNA-mediated silencing, splicing via the spliceosome, mRNA export, and ribosome biogenesis, alongside initiation and regulation of translation. This suggests a cohesive module focused on RNA processing and how translation is initiated and regulated.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0006446","count":3}]},{"hash":"1192264958553327935","title":"Developmental morphogenesis and differentiation","description":"Top terms point to embryonic morphogenesis and lineage specification (embryonic body morphogenesis, glial cell fate determination, midbrain dopaminergic neuron differentiation) and tissue development (lung, heart, oogenesis). There are also adhesion (desmosome assembly) and vesicle dynamics (vacuole inheritance/fusion) processes, suggesting a shared theme of morphogenesis and cell differentiation across tissues. The label captures this broad pattern, though the diversity of terms yields only moderate confidence.","confidence":"Medium","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:1904948","count":10},{"id":"GO:0098911","count":10},{"id":"GO:0030720","count":10},{"id":"GO:0060916","count":10},{"id":"GO:0002159","count":10}]},{"hash":"24856136434229271","title":"Amino acid biosynthesis and vitamin pathways","description":"The top GO terms are centered on biosynthetic processes for amino acids (tyrosine, histidine) and vitamins/cofactors (biotin, cobalamin), with additional related catabolic steps linking to central metabolism. This pattern suggests a cluster of proteins involved in assembling amino acids and vitamins rather than degradation or signaling, justifying the label.","confidence":"High","size":10,"edges":25,"triangles":36,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006633","count":3},{"id":"GO:0019518","count":3},{"id":"GO:0033512","count":3},{"id":"GO:0009102","count":2}]},{"hash":"1130846019545179894","title":"P-body mediated mRNA decay","description":"The top GO terms point to mRNA turnover processes\u2014deadenylation-dependent decapping and decay, poly(A) tail shortening, and P-body assembly\u2014with additional links to miRNA-mediated silencing, all highlighting post-transcriptional regulation via mRNA decay pathways. While there is a minor association with transcription regulation, the dominant theme is P-body\u2013associated mRNA degradation. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033962","count":1},{"id":"GO:0000290","count":1},{"id":"GO:0045944","count":1},{"id":"GO:0035195","count":1},{"id":"GO:0000289","count":1}]},{"hash":"610294544301679577","title":"Epithelial differentiation and membrane transport","description":"Two GO terms point to differentiation of epithelial cells (intestinal epithelial cells and keratinocytes), while others describe transport across the plasma membrane (amino acids and calcium). The cluster seems to center on epithelial cell function with surface transport, with a few miscellaneous terms that are less related. Overall, the label reflects the prominent epithelial differentiation and membrane transport themes.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032973","count":2},{"id":"GO:1990034","count":2},{"id":"GO:0060575","count":1},{"id":"GO:0080182","count":1},{"id":"GO:2000146","count":1}]},{"hash":"343786101456429211","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0042273","count":8},{"id":"GO:0000463","count":8},{"id":"GO:0000480","count":8},{"id":"GO:0000466","count":8},{"id":"GO:0000398","count":8}]},{"hash":"813735015332527215","title":"Ribosome biogenesis and translation","description":"This cluster is strongly enriched for ribosome-related processes: translation, ribosome biogenesis, and ribosomal small subunit assembly, with an additional rRNA export term. A few actin-related terms appear, but the dominant signal points to protein synthesis and ribosome assembly, justifying a label centered on ribosome biogenesis and translation.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006407","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0000028","count":1},{"id":"GO:0007121","count":1}]},{"hash":"1671975746888394079","title":"Unknown","description":"There are no shared GO terms or network connections for this cluster; the Top Terms list is empty and there are 0 edges/triangles, so there is no clear functional theme among the proteins, and the ReCIPE re-addition does not establish a recognizable function.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"194427203347327139","title":"Transmembrane Ion Transport and pH Response","description":"The top terms cluster around ion movement across membranes (sodium and proton transport) and pH-related responses, pointing to a membrane transport and pH-homeostasis theme. Some terms appear unrelated or broad, but the strongest shared function is transmembrane ion transport coupled with pH regulation, making this label representative.","confidence":"Medium","size":10,"edges":11,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0035725","count":1},{"id":"GO:0015992","count":1},{"id":"GO:0046909","count":1},{"id":"GO:0060548","count":1},{"id":"GO:0001890","count":1}]},{"hash":"46309910806545408","title":"Unknown","description":"The GO terms are highly diverse, including calcium and potassium ion transport, vasopressin secretion, heart rate regulation, and several stress/response terms (cold, capsazepine, antipsychotic drug), plus a cell-cycle localization term. There\u2019s no single cohesive function uniting these proteins, and the lack of edges further suggests heterogeneous roles; thus a confident, succinct label is not supported.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0098703","count":5},{"id":"GO:0009409","count":5},{"id":"GO:0045013","count":5},{"id":"GO:0010754","count":5},{"id":"GO:0097332","count":5}]},{"hash":"156520732945087572","title":"Calcium signaling in heart and nervous system","description":"The terms cluster around calcium handling (import and release) and calcium-dependent signaling in both cardiac (SA node) and neural (synaptic plasticity) contexts, with additional related signals like GPCR pathways and mechanotransduction, suggesting a unifying theme of calcium-driven signaling across heart and brain.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098907","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0010745","count":3},{"id":"GO:0071260","count":2},{"id":"GO:0098703","count":2}]},{"hash":"1535165802590379323","title":"Synaptic Exocytosis and Vesicle Trafficking","description":"The terms cluster around neurotransmitter release machinery and secretory pathway trafficking\u2014exocytosis, receptor localization to the synapse, Golgi localization, and regulation by Rho/GTPase signaling and dephosphorylation\u2014pointing to synaptic vesicle transport and synapse assembly. Some terms are broader or less directly tied (exploration behavior, barrier establishment), but the dominant theme is neuronal exocytosis and vesicle trafficking.","confidence":"Medium","size":10,"edges":9,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0035640","count":4},{"id":"GO:0006887","count":3},{"id":"GO:0097120","count":3},{"id":"GO:0019933","count":3},{"id":"GO:0006470","count":3}]},{"hash":"21867733103306069","title":"Diverse membrane transporters for sugars, ions, and nitrates","description":"The GO terms are dominated by transmembrane transport across various substrates (nitrate, sugars, sodium, phosphate, etc.) and a vesicular neurotransmitter loading process, indicating a cluster of membrane transporter proteins with broad substrate specificity rather than a single metabolic pathway.","confidence":"High","size":10,"edges":9,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":3},{"id":"GO:0015757","count":3},{"id":"GO:0098700","count":3},{"id":"GO:0015706","count":3},{"id":"GO:0006004","count":3}]},{"hash":"574822485549520044","title":"Unfolded protein and dsRNA stress response","description":"This cluster is driven by GO terms for cellular response to exogenous dsRNA and response to unfolded protein, which point to a shared theme of cellular stress and protein quality control. Additional terms about protein localization, heterooligomerization, and cell-cycle regulation are present but weaker signals, and several terms are obsolete, so the connection is plausible but not highly cohesive. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071360","count":2},{"id":"GO:0006986","count":2},{"id":"GO:2001162","count":2},{"id":"GO:0051291","count":2},{"id":"GO:0016576","count":2}]},{"hash":"648355046747890087","title":"Neural development and ER-Golgi transport","description":"The proteins show strong signals for brain development and neural tube closure, and for ER-to-Golgi vesicle transport, suggesting a role in neuronal development with active secretory pathway functioning. Additional hints of actin dynamics, translation initiation, and ubiquitination point to broader regulatory processes during development. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0001843","count":3},{"id":"GO:0051301","count":3},{"id":"GO:2000601","count":2}]},{"hash":"1740814966058324189","title":"Meiotic DNA Break Formation and Repair","description":"Top GO terms are dominated by meiotic DSB formation (GO:0010780) and repair (GO:1990918), along with a mitotic DNA damage checkpoint signaling term (GO:0031573), indicating a cluster centered on meiotic recombination and genome maintenance. A few other terms (cell adhesion, ER-Golgi transport, translation regulation) appear less related and may reflect annotation noise.","confidence":"High","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032508","count":2},{"id":"GO:0010780","count":1},{"id":"GO:1990918","count":1},{"id":"GO:0098609","count":1},{"id":"GO:0051533","count":1}]},{"hash":"280251110563654106","title":"RNA and ribosome methylation with cofactor biosynthesis","description":"The cluster is dominated by GO terms for methylation (tRNA, rRNA, protein, and peptidyl-arginine methylation) and ribosomal processes (ribosomal subunit export), pointing to RNA and ribosome modification as the core theme. The vitamin biosynthesis terms (cobalamin and biotin) suggest involvement of cofactor biosynthetic pathways that can intersect with methyltransferase activity, reinforcing a cohesive theme around methylation-driven RNA/protein processing and ribosome function. Confidence: High.","confidence":"","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":3},{"id":"GO:0009236","count":3},{"id":"GO:0006479","count":3},{"id":"GO:0030488","count":3},{"id":"GO:0019919","count":2}]},{"hash":"1022673951227523076","title":"Translation and mRNA turnover","description":"The cluster shows a strong emphasis on translation-related processes: translation, translational termination, ribosome disassembly, and mitochondrial translation, along with an mRNA decay term. This suggests proteins connected to the ribosome, translation machinery, and RNA metabolism. Other single terms are less coherent but don\u2019t override the primary theme. Overall, a coherent label is translation-centric with RNA processing implications.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0014009","count":1},{"id":"GO:0006449","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0001514","count":1},{"id":"GO:0070125","count":1}]},{"hash":"1819368522693415955","title":"Bacterial Energy Metabolism and Vitamin Biosynthesis","description":"The cluster includes central energy pathways (glycolysis, TCA cycle, beta-oxidation) and multiple amino-acid catabolic routes (valine, lysine, phenylacetate), along with biosynthesis of quinones (menaquinone, phylloquinone) and even antibiotic biosynthesis. This pattern points to a metabolism-focused module typical of bacteria, combining energy production with cofactor/vitamin biosynthesis and some secondary metabolism. ","confidence":"Medium","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":5},{"id":"GO:0006635","count":4},{"id":"GO:0006096","count":4},{"id":"GO:0006099","count":3},{"id":"GO:0006574","count":3}]},{"hash":"862706095405593363","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":33,"triangles":66,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":5},{"id":"GO:0033129","count":5},{"id":"GO:0070935","count":5},{"id":"GO:0002741","count":4},{"id":"GO:0035607","count":4}]},{"hash":"370753063269475102","title":"Triglyceride catabolism and lipid remodeling","description":"This cluster is dominated by triglyceride-focused metabolism terms (triglyceride catabolic process, triglyceride mobilization, positive regulation of triglyceride catabolic process) and lipid remodeling (triglyceride acyl-chain remodeling, phosphatidylethanolamine and phosphatidylcholine catabolism), suggesting a cohesive lipid metabolism module. Some secondary terms (nitrogen utilization, uracil catabolic process, biotin biosynthetic process) are less represented and may reflect broader metabolic connections rather than a separate pathway.","confidence":"High","size":9,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":4},{"id":"GO:0019740","count":3},{"id":"GO:0006212","count":3},{"id":"GO:0006642","count":2},{"id":"GO:0036153","count":2}]},{"hash":"503666565720124329","title":"Bone Remodeling and Ossification","description":"Dominant GO terms point to bone resorption, intramembranous ossification, collagen catabolic process, and basement membrane disassembly, all central to skeletal development and matrix remodeling. Wnt signaling localization to the extracellular region supports osteogenic signaling; a few other terms (neural precursor proliferation, thyroid hormone response, immune-related processes) may reflect broader developmental signaling but do not outweigh the bone-centric terms. Overall, the cluster represents bone remodeling and extracellular matrix turnover.","confidence":"High","size":9,"edges":35,"triangles":77,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0045453","count":9},{"id":"GO:0035593","count":9},{"id":"GO:0001957","count":9},{"id":"GO:0030574","count":9},{"id":"GO:0034769","count":9}]},{"hash":"368135036625091059","title":"RNA Pol II Transcription Regulation & Chromatin Modification","description":"Most of the prominent GO terms in this cluster relate to transcription control by RNA polymerase II (elongation and negative regulation) and to chromatin-state alterations (histone ubiquitination and H3-K27 methylation). This pattern suggests a cohesive theme around transcriptional regulation mediated by chromatin modifications, with a few peripheral terms touching on broader regulatory roles such as growth hormone secretion and heart development.","confidence":"High","size":9,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006368","count":3},{"id":"GO:0033697","count":2},{"id":"GO:0036091","count":2},{"id":"GO:0071894","count":2},{"id":"GO:0000122","count":2}]},{"hash":"1747689403386943850","title":"Intracellular Trafficking and Protein Regulation","description":"The top terms point to intracellular transport processes (intraciliary retrograde transport; ER-Golgi vesicle transport) and protein regulation/modification (ubiquitination; histone methylation; actin nucleation), with a couple of differentiation/pigmentation terms that may reflect broader cellular remodeling. Together, they suggest a cluster of proteins involved in moving cellular cargo and coordinating protein function inside the cell, rather than a single specialized process. Confidence: Medium","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035721","count":2},{"id":"GO:0045444","count":2},{"id":"GO:0001731","count":1},{"id":"GO:2000601","count":1},{"id":"GO:0051567","count":1}]},{"hash":"309197447583465079","title":"Immune signaling with TGF-beta regulation","description":"Prominent GO terms point to immune signaling, including innate immunity and T cell receptor pathways, plus responses related to transforming growth factor beta (TGF-beta) signaling and its regulation, suggesting a cluster of proteins involved in cytokine- and receptor-mediated immune signaling with modulation of TGF-beta pathways. A developmental cue (heart development) likely reflects TGF-beta's broader roles, reinforcing the theme of signaling regulation rather than a single enzyme or process.","confidence":"High","size":9,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0071560","count":2},{"id":"GO:0050852","count":2},{"id":"GO:0071732","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0031666","count":2}]},{"hash":"1054934457093524794","title":"Ribosome biogenesis and cell division","description":"The cluster is enriched for ribosome-related processes (ribosome biogenesis, ribosomal subunit biogenesis/export) and cell division/cell cycle terms (cell division, cell cycle, cell septum assembly), suggesting a group of proteins coordinating ribosome production with progression through growth and division. Some peripheral terms like iron transport and stress response appear less central but may reflect broader metabolic regulation.","confidence":"High","size":9,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0000055","count":2},{"id":"GO:0000747","count":2},{"id":"GO:1903833","count":2},{"id":"GO:1901001","count":2}]},{"hash":"1007264957396585829","title":"Meiotic recombination and germ cell DNA repair","description":"The cluster is dominated by GO terms related to meiosis (meiotic mismatch repair, gene conversion, mating-type locus conversion, germ cell development) and genome maintenance (double-strand break repair, replication fork arrest, helicase activity regulation), suggesting a cohesive theme around meiotic recombination and DNA repair in germ cells. A couple of terms point to broader stress responses (innate immune response, amino acid starvation) and are likely peripheral noise. Confidence: High.","confidence":"","size":9,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0034198","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0097274","count":3},{"id":"GO:0010777","count":2},{"id":"GO:0006311","count":2}]},{"hash":"1234655509781751428","title":"ER Protein Folding and Quality Control","description":"This cluster is dominated by GO terms tied to protein folding, ER chaperones, and degradation via the ubiquitin-proteasome system, i.e., ER stress and quality control pathways (response to unfolded protein, protein folding in ER, chaperone-dependent refolding, and membrane targeting). A couple of outliers (mesoderm formation, tRNA import) are less central but do not override the main theme.","confidence":"High","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006986","count":4},{"id":"GO:0071630","count":4},{"id":"GO:0070389","count":4},{"id":"GO:0031204","count":4},{"id":"GO:0001707","count":4}]},{"hash":"1486232446818700221","title":"ER-Golgi-Endosome Vesicle Trafficking","description":"Most frequent GO terms cluster around intracellular transport between ER, Golgi, vacuole, endosomes, and melanosomes, plus endocytosis, indicating a coherent vesicle trafficking and cargo-sorting module. Protein ubiquitination and heterooligomerization support regulatory aspects of this trafficking, with occasional cell cycle signals likely reflecting broader cellular context. ","confidence":"Medium","size":9,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006623","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0006897","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0000278","count":2}]},{"hash":"1624905473348669289","title":"Epigenetic Chromatin Regulation","description":"This cluster is dominated by histone modification and DNA methylation terms (H3-K27 trimethylation, H2B ubiquitination, CHH methylation), heterochromatin assembly, and transcriptional regulation, pointing to epigenetic control of gene expression. A few non-epigenetic terms appear but do not define the cluster.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033697","count":1},{"id":"GO:0036091","count":1},{"id":"GO:0071894","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0060123","count":1}]},{"hash":"931385789346835611","title":"RNA processing and transcription regulation under stress","description":"This cluster is enriched for RNA metabolism activities: mRNA splicing via spliceosome (GO:0045292) and its positive regulation (GO:0048026), mRNA stability and catabolic processes (GO:0010610, GO:0006402), regulatory ncRNA-mediated gene silencing (GO:0031047), and transcription-related terms (GO:0006351, GO:0031564), indicating a core group of proteins involved in RNA processing, turnover, and transcription control, particularly in stress responses.","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":4},{"id":"GO:0045292","count":4},{"id":"GO:0006402","count":4},{"id":"GO:0090503","count":4},{"id":"GO:0031047","count":3}]},{"hash":"1429956319906710936","title":"ER Protein Folding and Quality Control","description":"This cluster is dominated by GO terms related to unfolded protein response, ER chaperone-assisted folding, ER protein folding, and ubiquitin-proteasome\u2013mediated quality control, pointing to a proteostasis/ER folding theme. A few outliers (e.g., mesoderm formation, tRNA import) are less connected to this core function, but the overall signal fits ER folding and quality control best.","confidence":"High","size":9,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006986","count":2},{"id":"GO:0071630","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0031204","count":2},{"id":"GO:0001707","count":2}]},{"hash":"1199357205729112295","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by translation- and ribosome-related terms: translation (GO:0006412) with multiple proteins, 90S preribosome assembly (GO:0097394), and positive regulation of translational initiation (GO:0045948), as well as protein-containing complex assembly (GO:0006461). These point to involvement in ribosome production and the protein synthesis machinery, with a few ancillary terms possibly reflecting broader RNA processing events. Overall, the theme is ribosome biogenesis and translation.","confidence":"Medium","size":9,"edges":10,"triangles":2,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0009236","count":2},{"id":"GO:0006461","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0097394","count":1}]},{"hash":"533777168867314452","title":"RNA processing and translation initiation machinery","description":"Top terms converge on mRNA maturation and processing (polyadenylation, splicing and spliceosome assembly), mRNA modification and stress-related stability, and core translation initiation steps (preinitiation complex formation and IRES-driven initiation), indicating a cluster of RNA metabolism proteins linked to translation start.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":3},{"id":"GO:0010610","count":3},{"id":"GO:0031047","count":2},{"id":"GO:0016556","count":2},{"id":"GO:0034462","count":2}]},{"hash":"2285919238599061255","title":"Protein quality control and degradation","description":"Predominant GO terms point to proteostasis activities: proteasome regulatory particle assembly, deubiquitinase signaling, SCF complex dynamics, and chaperone-related unfolding/refolding. Additional terms include protein import into peroxisomes and protein unfolding, suggesting a focus on maintaining protein homeostasis. A few terms about DNA replication and centriole elongation may reflect broader cell-cycle context or annotation noise rather than a core function of the cluster.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070682","count":5},{"id":"GO:0006272","count":3},{"id":"GO:1903007","count":3},{"id":"GO:2001171","count":3},{"id":"GO:1903724","count":3}]},{"hash":"905496352838005941","title":"Unknown","description":"This cluster has no top GO terms listed, so there is no evident shared function among the nine proteins. While there are interactions (8 edges), there is no clear functional theme to name.","confidence":"","size":9,"edges":8,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[]},{"hash":"22747114642197641","title":"Synaptic signaling and plasticity","description":"The most represented GO terms cluster around neuronal signaling: calcium ion import, long-term synaptic potentiation, trans-synaptic signaling, and regulation of synaptic transmission, suggesting the proteins group around synaptic communication and plasticity. Brain-related pathways (FGFR signaling in orbitofrontal cortex development and insulin receptor signaling) support a neuronal context, while a few terms like mitotic spindle organization may reflect background annotations. Overall, the cluster is best described as synaptic signaling and plasticity.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070509","count":3},{"id":"GO:0060291","count":3},{"id":"GO:0002741","count":2},{"id":"GO:0035607","count":2},{"id":"GO:0008286","count":2}]},{"hash":"1580157569167067145","title":"Mitochondrial energy metabolism","description":"Based on the Top Terms, several GO terms point to mitochondrial energy production: cytochrome complex assembly, mitochondrial electron transport (succinate to ubiquinone), the TCA cycle, and aerobic respiration. These collectively indicate a cluster centered on mitochondrial respiration and energy generation. Other terms such as vesicle transport and synaptic membrane insertion may reflect ancillary cellular processes or dataset noise, but do not outweigh the clear mitochondrial energy signal.","confidence":"High","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0017004","count":1},{"id":"GO:0006121","count":1},{"id":"GO:0006099","count":1},{"id":"GO:0009060","count":1},{"id":"GO:0098967","count":1}]},{"hash":"132685389292477185","title":"Oxidative Stress and ER Stress Response","description":"The proteins are enriched for redox-related processes (redox homeostasis and oxidant detoxification) and ER stress response, suggesting a coordinated role in managing oxidative stress and the unfolded protein response. Secondary signals of transcriptional regulation and nuclear transport appear, but redox/ER stress themes dominate. ","confidence":"Medium","size":9,"edges":16,"triangles":11,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045454","count":5},{"id":"GO:0000122","count":4},{"id":"GO:0098869","count":4},{"id":"GO:0046826","count":4},{"id":"GO:0055114","count":4}]},{"hash":"2227760053467185151","title":"Cardiac signaling and contraction","description":"The cluster\u2019s top GO terms center on heart development and cardiac muscle contraction, coupled with calcium ion import and cellular responses to mechanical stimuli, which together point to cardiomyocyte signaling and contractile function. GPCR-related signaling and guanylate cyclase regulation further support a cardiac signaling theme, while ubiquitination and cell migration appear as ancillary processes. Confidence: High","confidence":"","size":9,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":3},{"id":"GO:2001275","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0007507","count":2}]},{"hash":"2056658800197739208","title":"Peptide processing and hormone maturation","description":"The top terms cluster around proteolytic processing of peptide precursors (dibasic protein processing, enkephalin processing, peptide pheromone maturation), pointing to maturation of bioactive peptides. While LDL receptor\u2013related terms appear, the dominant theme is peptide processing and hormone maturation, with some noise from receptor regulation terms. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090472","count":1},{"id":"GO:0010989","count":1},{"id":"GO:0001920","count":1},{"id":"GO:1905596","count":1},{"id":"GO:0007354","count":1}]},{"hash":"327430455617908832","title":"Ribosome Biogenesis and Nuclear Export","description":"These proteins are linked by GO terms for ribosomal small subunit biogenesis and export from the nucleus, pointing to a shared role in ribosome assembly and nucleocytoplasmic transport, with a secondary signal of cell size regulation. Peripheral terms like DNA endoreduplication and ATP export are less representative of the core theme.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042023","count":1},{"id":"GO:1904669","count":1},{"id":"GO:0042274","count":1},{"id":"GO:0045793","count":1},{"id":"GO:0000056","count":1}]},{"hash":"705437248385857045","title":"ER Protein Folding and Quality Control","description":"These proteins cluster around proteostasis: responses to unfolded proteins, heat, and ER-specific folding, plus ubiquitin-proteasome\u2013mediated quality control and chaperone-assisted refolding. The dominant GO terms point to protein folding and maturation across compartments (ER and nucleus), with membrane targeting also tied to maturation. A few development-related terms are present but do not define the core function of this group.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006986","count":3},{"id":"GO:0071630","count":3},{"id":"GO:0070389","count":3},{"id":"GO:0031204","count":3},{"id":"GO:0001707","count":3}]},{"hash":"119052807166779058","title":"TLR4-TRAM Signaling and Cytokine Production","description":"The proteins are enriched for GO terms centered on TLR4 signaling, particularly TRAM-dependent pathways, and on regulation of multiple cytokines and chemokines (IL-6, IL-18, CCL5, CXCL1, IL-15). An accompanying term for antifungal peptide production suggests antimicrobial peptide output. Together, these terms indicate a module of innate immune signaling and inflammatory mediator production driven by TLR4.","confidence":"High","size":9,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0071650","count":4},{"id":"GO:0002781","count":4},{"id":"GO:0071651","count":4},{"id":"GO:2000494","count":4},{"id":"GO:0090073","count":4}]},{"hash":"370962759428848041","title":"Yeast meiosis and nuclear organization","description":"The top GO terms are dominated by nuclear-related processes (maintenance of rDNA, transcription termination, telomere attachment to the nuclear envelope, nuclear inner membrane organization, female meiotic nuclear division) and yeast-specific metabolism (glycolytic fermentation to ethanol, thiamine biosynthesis). This suggests a cluster centered on nuclear events during meiosis in yeast, with some metabolic context. Some terms (e.g., Notch signaling, obsolete terms) appear noisy but do not override the main theme.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043007","count":1},{"id":"GO:0006353","count":1},{"id":"GO:0070197","count":1},{"id":"GO:0071765","count":1},{"id":"GO:0090180","count":1}]},{"hash":"383442373786346667","title":"Mitochondrial Protein Import and Cofactor Biosynthesis","description":"The cluster is anchored by mitochondrial localization terms (protein insertion into inner membrane and targeting to mitochondrion), hinting at mitochondrial protein import. It also includes several biosynthetic processes for cofactors and metabolites (ubiquinone, GDP-mannose, ADP-L-glycero-beta-D-manno-heptose), suggesting a broader mitochondrial metabolism/cofactor biosynthesis theme.","confidence":"Medium","size":9,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0045039","count":2},{"id":"GO:0072321","count":2},{"id":"GO:0006626","count":2},{"id":"GO:0001081","count":2}]},{"hash":"130406024029010757","title":"Methionine cycle and one-carbon metabolism","description":"Most frequent terms center on methionine metabolism and one-carbon chemistry (L-methionine cycle, methionine catabolic process, SAH-related catabolic process, and one-carbon metabolic process). While a few terms point to lipid metabolism or stress/inflammatory responses, the core signal is methionine-cycle\u2013driven metabolism.","confidence":"High","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0006730","count":2},{"id":"GO:1903758","count":2},{"id":"GO:0009087","count":2},{"id":"GO:0006641","count":2}]},{"hash":"558798944674211261","title":"Transcriptional and chromatin regulation","description":"This cluster centers on regulation of gene expression and chromatin state. Top GO terms include negative regulation of transcription, chromatin silencing and heterochromatin maintenance (telomere and rDNA), and signaling pathways that modulate transcriptional activity, with a muscle adaptation-related regulatory term also present. Together, these suggest proteins that govern transcriptional control and chromatin dynamics as a cohesive theme.","confidence":"High","size":8,"edges":27,"triangles":50,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060766","count":8},{"id":"GO:0045668","count":8},{"id":"GO:0014894","count":7},{"id":"GO:0031939","count":7},{"id":"GO:0006344","count":7}]},{"hash":"1781441875511966811","title":"RNA and protein methyltransferases","description":"The GO terms are dominated by methylation-related processes, including RNA methylation (rRNA methylation, mRNA capping, guanine-N7 methylation, tRNA wobble modification) and protein methylation (peptidyl-lysine dimethylation, peptidyl-arginine dimethylation), indicating a cohesive function in methylation enzymes acting on both RNA and proteins.","confidence":"High","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031167","count":3},{"id":"GO:0018013","count":3},{"id":"GO:0018027","count":3},{"id":"GO:0019919","count":2},{"id":"GO:0002098","count":2}]},{"hash":"856316168047582518","title":"Unknown","description":"This cluster shows a mix of disparate GO terms (DNA replication, meiotic recombination, mRNA export, vesicle transport, peroxisome import, cell adhesion, and calcium/NFAT signaling) with little cohesive function, making a single representative label inappropriate. Confidence: None","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0016558","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0019079","count":2},{"id":"GO:0006406","count":2}]},{"hash":"645524747082771652","title":"Chromatin methylation and heterochromatin formation","description":"The proteins are tied to chromatin state modifications, including rDNA heterochromatin formation and various methylation events (histone lysine, N-terminal peptidyl-glycine, and rRNA methylation), suggesting a cluster of chromatin-modifying enzymes involved in establishing or maintaining heterochromatin.","confidence":"High","size":8,"edges":10,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":6},{"id":"GO:0031167","count":5},{"id":"GO:0018013","count":5},{"id":"GO:0018023","count":5},{"id":"GO:0018027","count":5}]},{"hash":"1946243665286601885","title":"Neuroimmune and Xenobiotic Response","description":"This cluster centers on inflammatory mediators such as interleukin-6 production and prostaglandin secretion, along with neural signaling via nitric oxide and a xenobiotic response profile (response to xenobiotic stimulus and organofluorine metabolism). The combination suggests a theme of neuroimmune communication intertwined with chemical detoxification pathways. While some terms are obsolete or broad, the dominant terms point to inflammation and xenobiotic metabolism as a cohesive thread. Confidence: Medium","confidence":"","size":8,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0072604","count":1},{"id":"GO:0042493","count":1},{"id":"GO:0070988","count":1},{"id":"GO:0032310","count":1},{"id":"GO:0055114","count":1}]},{"hash":"1303680441817630792","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000453","count":1},{"id":"GO:0002938","count":1},{"id":"GO:0034975","count":1},{"id":"GO:0018401","count":1},{"id":"GO:0045454","count":1}]},{"hash":"840614132387194545","title":"Nucleotide Interconversion and Salvage","description":"The top GO terms are dominated by nucleotide metabolism activities\u2014purine ribonucleotide interconversion, AMP salvage, various nucleotide phosphorylations, and biosynthetic processes for CDP/ADP/ITP\u2014suggesting a core function in nucleotide metabolism. Brain and liver development terms are present but likely reflect tissue-specific roles rather than the primary function of the cluster. Overall, the prevailing theme is nucleotide interconversion and salvage, justifying this label.","confidence":"High","size":8,"edges":12,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0046939","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0015951","count":3},{"id":"GO:0044209","count":3},{"id":"GO:0046705","count":3}]},{"hash":"617188611094847023","title":"Proteostasis and ubiquitin\u2013proteasome regulation","description":"The cluster is dominated by terms tied to protein quality control and turnover: proteasome regulatory particle assembly, various ubiquitin-related regulation (Lys63-specific deubiquitinase activity), protein unfolding/refolding, chaperone-dependent processes, and peroxisomal protein import. While a couple of terms touch on DNA replication/centriole dynamics, the strongest signal is proteostasis and ubiquitin\u2013proteasome pathways, suggesting a cohesive module around maintaining protein homeostasis. ","confidence":"High","size":8,"edges":7,"triangles":2,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006272","count":7},{"id":"GO:0070682","count":7},{"id":"GO:1903007","count":7},{"id":"GO:2001171","count":7},{"id":"GO:1903724","count":7}]},{"hash":"1386298090165712696","title":"Brain Development and Synaptic Signaling","description":"This cluster is dominated by neural-related GO terms such as FGFR signaling involved in orbitofrontal cortex development, trans-synaptic signaling, regulation of axon regeneration, and potassium ion transport, pointing to brain development and synaptic communication. There are also metabolic and cell-cycle signals (insulin receptor signaling, DNA replication, mitotic spindle organization) that may reflect broader cellular roles or annotation noise. Overall, the prominent theme is brain development and neural signaling.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0006813","count":7},{"id":"GO:0002741","count":6},{"id":"GO:0035607","count":6},{"id":"GO:0008286","count":6}]},{"hash":"1566899755323556161","title":"Chromatin dynamics and genome maintenance","description":"The cluster combines terms linked to chromatin regulation and genome integrity: heterochromatin formation and histone ubiquitination point to chromatin state control; meiotic gene conversion, DNA rewinding, and endodeoxyribonuclease activity reflect DNA processing and recombination; protein polyubiquitination supports broader regulatory control; and telomeric RNA transcription regulation ties to telomere maintenance. An outlier term about heart morphogenesis appears incidental rather than central to the cluster.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006311","count":8},{"id":"GO:0071894","count":8},{"id":"GO:0003226","count":8},{"id":"GO:0036292","count":8},{"id":"GO:0032079","count":8}]},{"hash":"370481005953880443","title":"Cardiac conduction and heart morphogenesis","description":"The cluster is dominated by GO terms related to heart development and cardiac electrical activity, including heart morphogenesis, ventricular cardiac muscle morphogenesis, regulation of cardiac conduction, and neural action potential propagation, plus calcium release from the sarcoplasmic reticulum\u2014together pointing to cardiac electrophysiology and contractile function. A single outlier term on homoserine biosynthesis is likely noise; overall the pattern supports a cardiac-centric function.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901710","count":2},{"id":"GO:0003007","count":2},{"id":"GO:0086064","count":2},{"id":"GO:0055010","count":2},{"id":"GO:0000412","count":2}]},{"hash":"181203076488081333","title":"Chromatin remodeling and transcription regulation","description":"This cluster centers on chromatin state control: chromatin remodeling with histone modifications (ubiquitination and acetylation), nucleosome density/mobilization, and regulation of RNA polymerase II transcription (initiation and termination). Together, these terms point to a cohesive module coordinating chromatin structure with transcriptional control, with mRNA processing/export as a related nuclear event.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":5},{"id":"GO:0071894","count":4},{"id":"GO:0006369","count":4},{"id":"GO:0060303","count":4},{"id":"GO:0042766","count":4}]},{"hash":"629886428506478618","title":"Neuronal exocytosis and GPCR trafficking","description":"The cluster\u2019s terms strongly point to regulated secretion and receptor trafficking, with several entries for synaptic vesicle priming and dense core granule exocytosis, plus G protein-coupled receptor internalization. Other terms (insulin signaling, vasoconstriction, Rac regulation) suggest broader neuroendocrine/metabolic signaling, while some immune-related terms may reflect cross-talk rather than core function. Overall, the dominant theme is neuronal secretion and GPCR trafficking.","confidence":"Medium","size":8,"edges":10,"triangles":0,"max_degree":3,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0032094","count":4},{"id":"GO:0035655","count":4},{"id":"GO:0016082","count":4},{"id":"GO:0002031","count":4},{"id":"GO:0008286","count":4}]},{"hash":"2054761063356932758","title":"Kallikrein-kinin pathway and vascular remodeling","description":"The cluster centers on plasma kallikrein-kinin cascade activity with supporting signals for endothelial cell migration, angiogenesis in wound healing, and blood pressure regulation, all tied together by proteolysis. While there are metabolic terms (glucose and energy homeostasis) and ROS regulation, the strongest cohesive theme is kallikrein-kinin signaling modulating vascular remodeling and related inflammatory processes.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0043535","count":1},{"id":"GO:0003085","count":1},{"id":"GO:0060055","count":1},{"id":"GO:0042593","count":1}]},{"hash":"1996082508854813910","title":"Histone Modification & Chromatin Regulation","description":"The top GO terms are dominated by histone methylation/demethylation (H3K36 and H3K4) and chromatin-related processes (such as regulation of rDNA heterochromatin formation), with additional signals for RNA processing and post-translational protein methylation. Although a few terms are obsolete or plant-specific, the central theme is enzymes/modifiers that shape chromatin state and transcription through histone marks.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070544","count":2},{"id":"GO:0034720","count":2},{"id":"GO:0009236","count":1},{"id":"GO:0006396","count":1},{"id":"GO:0006479","count":1}]},{"hash":"726830206271143509","title":"TGF-beta/SMAD signaling regulators","description":"The GO terms point to negative regulation of TGF-beta receptor signaling and cellular responses to TGF-beta, with supporting references to SMAD complex assembly regulation and threonine dephosphorylation, indicating modulation of the TGF-beta/SMAD pathway. Some terms appear plant-specific or obsolete, suggesting annotation noise, but the dominant theme is signaling modulation via the TGF-beta/SMAD axis.","confidence":"Medium","size":8,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0030512","count":3},{"id":"GO:0042347","count":3},{"id":"GO:0035970","count":3},{"id":"GO:0061191","count":3},{"id":"GO:0010991","count":3}]},{"hash":"1443256504880595633","title":"Meiosis and spermatogenesis","description":"Based on GO terms, the cluster centers on meiotic processes (DSB repair in meiotic recombination, chiasma assembly, cohesion regulation) and sperm development (spermatogonial division, seminiferous tubule development), with some embryonic organ development signals. The cohesive theme is meiosis and gametogenesis, justifying this label.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:1904430","count":1},{"id":"GO:0045876","count":1},{"id":"GO:1990918","count":1},{"id":"GO:0048568","count":1}]},{"hash":"1561517140661457651","title":"Chromosome maintenance and centromere assembly","description":"The GO terms point to nuclear functions centered on chromosome stability: CENP-A\u2013containing chromatin assembly, mitotic sister chromatid cohesion, and homologous recombination repair, plus DNA-templated transcription. While other terms relate to cytoplasmic processes (translation initiation, ER-to-Golgi transport, microtubule severing), the core appears to be chromatin dynamics and chromosome maintenance. Confidence: Medium","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0051013","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0000724","count":2}]},{"hash":"1229078364653055739","title":"Calcium and Ion Transport in Muscle and Neurons","description":"The terms show a clear focus on calcium signaling and ion transport (Ca2+, Na+, K+, mitochondrial Ca2+), linked to regulation of skeletal and heart muscle contraction and neuronal plasticity (long-term potentiation). This suggests a coherent functional cluster centered on calcium- and ion-driven signaling essential for muscle and neuronal activity.","confidence":"High","size":8,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0014819","count":3},{"id":"GO:0048022","count":3},{"id":"GO:0010163","count":3},{"id":"GO:0098703","count":3},{"id":"GO:0098735","count":3}]},{"hash":"771239175855565030","title":"Virus life-cycle proteins","description":"This cluster is dominated by GO terms related to viral entry, uncoating, replication, and assembly (e.g., uncoating of virus, virion assembly, fusion of viral membranes with host membranes, RNA-templated DNA biosynthesis, host-mediated activation of viral genome replication), indicating proteins involved in the viral life cycle and host\u2013virus interactions.","confidence":"High","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1901407","count":3},{"id":"GO:0006457","count":2},{"id":"GO:0019061","count":2},{"id":"GO:0006278","count":2},{"id":"GO:0010849","count":2}]},{"hash":"675382024168760024","title":"Splicing and Translation Initiation Machinery","description":"The proteins are enriched for spliceosome- and splicing-related processes (mRNA splicing, alternative splicing, small-subunit processome assembly, and spliceosome regulation) together with translation initiation roles (preinitiation complex formation, eIF4F complex assembly, and IRES-dependent initiation), indicating a cohesive cluster linking RNA processing to the start of translation.","confidence":"High","size":8,"edges":26,"triangles":45,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":5},{"id":"GO:0045292","count":5},{"id":"GO:0031047","count":4},{"id":"GO:0016556","count":4},{"id":"GO:0034462","count":4}]},{"hash":"833059324761287934","title":"Transmembrane transport of ions and metabolites","description":"The cluster's top GO terms are dominated by various transmembrane transport activities, including sodium and potassium ion transport, galactose and fucose transport, nitrate and phosphate transport, xenobiotic transport, and specifically neurotransmitter loading into synaptic vesicles. This indicates a group of membrane-embedded transport proteins handling diverse substrates, rather than a single canonical pathway. Therefore, a concise label is \"Transmembrane transport of ions and metabolites.\" ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098700","count":5},{"id":"GO:0035435","count":5},{"id":"GO:0006855","count":5},{"id":"GO:0015706","count":5},{"id":"GO:1900754","count":5}]},{"hash":"1162786848620476571","title":"ER proteostasis and unfolded protein response","description":"This cluster centers on proteostasis: unfolded protein response, ER protein folding, and ubiquitin-proteasome\u2013mediated quality control, plus heat-stress response and chaperone-related refolding terms. Together these terms point to protein folding/refolding capacity and ER-associated quality control as the shared function, with a few unrelated terms likely representing broader cellular processes or annotation noise.","confidence":"High","size":8,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006986","count":5},{"id":"GO:0071630","count":5},{"id":"GO:0070389","count":5},{"id":"GO:0031204","count":5},{"id":"GO:0001707","count":5}]},{"hash":"237622614370111029","title":"Unknown","description":"The top terms mix transcription-related processes (DNA-templated transcription) and a signaling pathway (Notch signaling) with several distinct metabolic biosynthesis pathways (biotin, cobalamin, amino acid biosynthesis/catabolism). This lack of a single, cohesive functional theme makes it unclear what function ties the cluster together, so the label is Unknown with no confidence.","confidence":"","size":8,"edges":9,"triangles":2,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0007219","count":4},{"id":"GO:0009102","count":3},{"id":"GO:0097053","count":3},{"id":"GO:0006571","count":3}]},{"hash":"217993129648226708","title":"Hormone Regulation and Reproductive Development","description":"The top GO terms point to endocrine-related activities, including aldosterone-regulated blood volume, progesterone metabolism, and uterus development, suggesting a hormonal regulatory and reproductive biology theme. Some plant-specific terms and digestive-related terms appear, which may reflect annotation noise, but the core signal centers on hormonal processes and reproductive tissue development.","confidence":"Medium","size":8,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0002017","count":2},{"id":"GO:0042448","count":2},{"id":"GO:0032094","count":2},{"id":"GO:0048565","count":2},{"id":"GO:0060065","count":2}]},{"hash":"1234924878255917491","title":"Amino Acid and Cofactor Biosynthesis","description":"The cluster shows enrichment for biosynthetic processes of amino acids (tyrosine, histidine, lysine, threonine, glutamate) and cofactors (biotin, cobalamin) as well as porphyrin precursor production, indicating a cohesive module focused on building cellular metabolites rather than degradation.","confidence":"Medium","size":8,"edges":8,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":2},{"id":"GO:0097053","count":2},{"id":"GO:0006571","count":2},{"id":"GO:0009236","count":2},{"id":"GO:0019518","count":2}]},{"hash":"1965707597927217690","title":"Skin development and proliferative signaling","description":"The terms show recurring references to skin development, broader multicellular development, and mitotic cell cycle, complemented by enrichment for signals controlling kinase activity and GTPase regulation. Although some terms like mRNA transport and hypoxia response are more general, the cluster consistently points to developmental processes in the epidermis governed by signaling pathways and proliferation control, suggesting a group of proteins involved in epidermal development and growth signaling.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0043588","count":3},{"id":"GO:0051028","count":3},{"id":"GO:0071456","count":3}]},{"hash":"184599368320508915","title":"Cofactor Biosynthesis and RNA Modification","description":"Most terms indicate biosynthesis of cofactors and vitamins (thiamine, biotin, menaquinone, molybdopterin) and related RNA/base modification processes (tRNA queuosine biosynthesis, rRNA base methylation). A single antibiotic response term is present but does not define the cluster. Overall, the proteins appear tied to small-molecule biosynthesis and nucleotide modification.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018339","count":1},{"id":"GO:0006782","count":1},{"id":"GO:0009102","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0008616","count":1}]},{"hash":"241862496556078395","title":"Neuronal vesicle trafficking and exocytosis","description":"The cluster is enriched for GO terms tied to vesicle trafficking and synaptic function (regulation of endosome-to-lysosome transport, ER-to-Golgi vesicle transport, synaptic vesicle budding and exocytosis, calcium-dependent exocytosis) and neural development (brain development, dendritic spine development). These together point to processes governing synaptic vesicle handling and neuronal connectivity, making a neuronal vesicle trafficking/exocytosis label most representative.","confidence":"High","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:1902307","count":2},{"id":"GO:1902824","count":2},{"id":"GO:0034379","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0060999","count":2}]},{"hash":"698108753768217750","title":"Cofactor and Nucleotide Biosynthesis","description":"Top GO terms indicate biosynthesis of tRNA queuosine, biotin, menaquinone, and GMP, pointing to a shared function in generating essential cofactors and nucleotides. The other GO terms related to responses and proteolysis appear ancillary noise rather than central to the cluster\u2019s primary role. Overall, the cluster centers on biosynthetic processes rather than signaling or degradation.","confidence":"Medium","size":7,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0008616","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009102","count":2},{"id":"GO:0009234","count":2},{"id":"GO:0006177","count":1}]},{"hash":"2185763883958768824","title":"Neurodevelopment and Cell Cycle Regulation","description":"The cluster shows strong enrichment for mitotic cell cycle terms (G1/S and G2/M transitions) alongside nervous system development, axon extension and regeneration, and signaling pathways (FGFR, insulin) relevant to neural contexts, suggesting proteins that coordinate cell division with neural development. This dual theme justifies a label that captures both processes succinctly.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":7},{"id":"GO:0030097","count":7},{"id":"GO:0045773","count":7},{"id":"GO:0007399","count":7},{"id":"GO:0000086","count":7}]},{"hash":"1723737674566186706","title":"Amino acid biosynthesis and sulfur metabolism","description":"This cluster is dominated by GO terms for amino acid biosynthesis (threonine, tryptophan, serine) and related sulfur metabolism processes (transsulfuration, homocysteine catabolism, hydrogen sulfide biosynthesis). The co-occurrence suggests a group of proteins involved in amino acid biosynthetic pathways, particularly those linked to sulfur-containing amino acids and related metabolites.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0009088","count":4},{"id":"GO:0019343","count":4},{"id":"GO:0000162","count":4},{"id":"GO:0043418","count":4},{"id":"GO:0046360","count":4}]},{"hash":"748878583452062688","title":"Steroid and retinoid lipid biosynthesis","description":"The top GO terms point to lipid- and steroid-related metabolism, including testosterone biosynthesis and retinoid metabolism (retinol/retinal/retinoic acid) alongside very long-chain fatty acid biosynthesis. There are some antibiotic-related terms present, but the dominant signal is lipid- and steroid-associated biosynthesis, justifying a label focused on steroid and retinoid/lipid metabolism rather than broader or unknown functions.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":5},{"id":"GO:0030961","count":3},{"id":"GO:0042761","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0055114","count":3}]},{"hash":"2213435163763926731","title":"Nuclear Chromatin Regulation and RNA Surveillance","description":"This cluster centers on nuclear processes, including chromatin regulation (histone modification, DNA methylation, nucleosome remodeling), protein import into the nucleus, and RNA quality control pathways (nuclear mRNA, tRNA, and rRNA surveillance) that drive RNA decay via TRAMP-related mechanisms.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006311","count":7},{"id":"GO:0071894","count":7},{"id":"GO:0006306","count":7},{"id":"GO:0017038","count":7},{"id":"GO:0071049","count":7}]},{"hash":"1079583163983074289","title":"Teichoic acid\u2013driven Gram-positive cell wall biosynthesis","description":"This cluster is dominated by GO terms tied to cell wall construction, especially teichoic acid biosynthesis (GO:0019350) and general cell wall organization (GO:0071555), with UDP-glucose metabolic process (GO:0006011) providing sugar donors for wall polysaccharides. While a few terms (xenobiotic response, DNA recombination, etc.) are more tangential or cross-species annotations, the core signal points to bacterial cell wall biosynthesis in Gram-positive organisms, centered on teichoic acid pathways.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":2},{"id":"GO:0006011","count":2},{"id":"GO:0005989","count":2},{"id":"GO:0006486","count":2},{"id":"GO:0019350","count":2}]},{"hash":"570082171250745703","title":"Cell Fate Signaling and Differentiation","description":"The cluster centers on signaling pathways that govern cell growth, differentiation, and survival (Wnt and Hippo signaling; GTPase activity regulation; transcriptional control; apoptosis). It also includes terms tied to lineage-specific differentiation (keratinocytes, lung epithelium) and neuronal morphology (dendrite extension), pointing to a general theme of cell fate decisions across tissues.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090263","count":3},{"id":"GO:0032465","count":3},{"id":"GO:0030216","count":3},{"id":"GO:1903861","count":3},{"id":"GO:0006915","count":3}]},{"hash":"447668869088739341","title":"Unknown","description":"The top terms include spermidine and putrescine biosynthesis and polyamine transport, which could hint at polyamine metabolism, but several other terms such as kidney development, trans-Golgi network organization, and iron-sulfur cluster assembly show unrelated biological contexts. Given there is no single cohesive function tying all terms together and the cluster has no reported interactions, there isn\u2019t a clear theme to assign a descriptive name. ","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008295","count":1},{"id":"GO:0033387","count":1},{"id":"GO:0045312","count":1},{"id":"GO:0001822","count":1},{"id":"GO:0098629","count":1}]},{"hash":"573228962746616048","title":"Proteostasis and protein quality control","description":"The GO terms cluster around protein folding/unfolding, chaperone/cofactor-dependent refolding, proteasome assembly, ubiquitin signaling (SCF disassembly, Lys63 deubiquitinase activity) and peroxisomal protein import, together indicating a proteostasis network governing protein quality control and turnover.","confidence":"Medium","size":7,"edges":11,"triangles":6,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006272","count":4},{"id":"GO:0070682","count":4},{"id":"GO:1903007","count":4},{"id":"GO:2001171","count":4},{"id":"GO:1903724","count":4}]},{"hash":"577451152980162043","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":6,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0035753","count":2},{"id":"GO:0031573","count":2},{"id":"GO:0051321","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0006296","count":2}]},{"hash":"614437420313618451","title":"Neuronal Growth Signaling and Axon Regeneration","description":"The top GO terms cluster around neural development and axon biology, including neurotrophin TRK receptor signaling, positive and regulatory roles in axon regeneration, and a brain development\u2013related FGFR signaling link. While some terms touch on broader developmental signaling (e.g., insulin receptor signaling, myotube differentiation), the strongest signal centers on neuronal growth, axon maintenance, and regeneration, suggesting a cohesive neural growth\u2013regeneration theme.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048011","count":3},{"id":"GO:0014902","count":3},{"id":"GO:0006939","count":3},{"id":"GO:0048680","count":3},{"id":"GO:0002741","count":2}]},{"hash":"943856680889594758","title":"DNA Replication and Genome Maintenance","description":"The top GO terms point to core DNA replication (replication initiation and elongation, mitotic replication, fork-associated processes) and related repair/chromatin regulation (telomere silencing, helicase activity regulation), with a species-specific chorion gene amplification term as a peripheral note. This indicates a cohesive group of proteins involved in DNA replication and genome stability.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0000727","count":5},{"id":"GO:0007307","count":5},{"id":"GO:0006271","count":5},{"id":"GO:0048478","count":5}]},{"hash":"1441613145354564733","title":"CDK Regulation and Spindle Checkpoint","description":"The GO terms cluster around cell-cycle control and mitosis, including peptidyl-threonine dephosphorylation, cell cycle, negative regulation of CDK activity, and mitotic spindle assembly checkpoint signaling, pointing to coordinated regulation of CDK activity during mitosis. Some terms appear peripheral (RNA localization, cerebellar structure), but the core theme centers on cell-cycle regulation and mitotic control.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035970","count":4},{"id":"GO:0007049","count":4},{"id":"GO:0009190","count":4},{"id":"GO:0045736","count":4},{"id":"GO:0033624","count":3}]},{"hash":"551633674080506160","title":"Core metabolism and antimicrobial stress responses","description":"Top terms indicate central metabolism (glycolysis and TCA cycle) and various biosynthetic pathways (thiamine, menaquinone, retinol, poly-hydroxybutyrate). They also include antimicrobial-related terms (antibiotic biosynthesis and response to antibiotic) and a lipopolysaccharide response, suggesting a link between metabolism and antimicrobial stress signaling. Therefore, the cluster seems to group proteins involved in core metabolic processes with antimicrobial stress responses.","confidence":"Medium","size":7,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0042619","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0042572","count":2},{"id":"GO:0017000","count":2}]},{"hash":"652746212000133496","title":"ER Protein Folding and Quality Control","description":"The terms cluster around proteostasis: unfolded protein response, ER chaperone- and ubiquitin-proteasome\u2013mediated quality control, ER-associated folding/maturation, and related stress responses; a few development-related terms are present but not central. Overall, the cluster reflects ER-based protein folding and quality control processes.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006986","count":6},{"id":"GO:0071630","count":6},{"id":"GO:0070389","count":6},{"id":"GO:0031204","count":6},{"id":"GO:0001707","count":6}]},{"hash":"1650643337978817738","title":"Cortical development and synapse assembly","description":"GO terms indicate cerebral cortex layer formation, neurogenesis, and promotion of synapse assembly, with supporting signals from Wnt pathway regulation and cell proliferation. This suggests proteins are involved in neural development, particularly cortical layering and synapse formation, rather than other processes. ","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048701","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0090394","count":3},{"id":"GO:0000278","count":2},{"id":"GO:0034446","count":2}]},{"hash":"1635699956835260749","title":"Unknown","description":"The GO terms are diverse (endodermal differentiation, cilium assembly, tRNA modification) with one obsolete term, indicating no clear shared function or pathway linking these proteins. The small, heterogeneous set does not support a cohesive label beyond Unknown.","confidence":"","size":7,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0035987","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0002943","count":1},{"id":"GO:0060271","count":1}]},{"hash":"316306954162857234","title":"Proteasome Assembly and Ubiquitination","description":"The top GO terms are dominated by proteasome regulatory particle assembly and various ubiquitin-related processes (ERAD, autoubiquitination, and K63-linked ubiquitination), pointing to a cluster of proteins involved in ubiquitin-proteasome\u2013mediated proteostasis. A couple of terms about differentiation and cell cycle appear less central, suggesting some background annotations but the core signal is proteasome/ubiquitin function.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070682","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0030579","count":3},{"id":"GO:0070534","count":3}]},{"hash":"370349838655459717","title":"Triglyceride and phospholipid remodeling and catabolism","description":"The top GO terms are dominated by triglyceride catabolic processes (including mobilization and acyl-chain remodeling) and phospholipid catabolism (phosphatidylethanolamine and phosphatidylcholine), indicating a coherent theme of lipid breakdown and remodeling. A few other lipid-related or regulatory terms appear with low support, but the strongest signal centers on triglyceride and phospholipid turnover.","confidence":"High","size":7,"edges":10,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":4},{"id":"GO:0006642","count":3},{"id":"GO:0036153","count":3},{"id":"GO:0046338","count":3},{"id":"GO:0010898","count":3}]},{"hash":"1395260684035687632","title":"Neuronal Ca2+ Signaling and Secretion","description":"Top GO terms point to calcium signaling events (calcium import across plasma membrane; release of sequestered calcium into cytosol) and a neuroendocrine secretory process (vasopressin secretion) with a related note on synaptic plasticity. This pattern suggests a cluster focused on Ca2+-dependent neuronal signaling and secretion, despite a few unrelated terms.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":1},{"id":"GO:0098703","count":1},{"id":"GO:0009409","count":1},{"id":"GO:0051209","count":1},{"id":"GO:1900383","count":1}]},{"hash":"2016189736575255254","title":"Ubiquitin-Dependent Protein Turnover","description":"The cluster is dominated by GO terms for ubiquitin-dependent protein catabolic processes (and ubiquitination) and histone catabolic processes, pointing to a core theme of proteostasis and chromatin turnover. While a peroxisomal protein import term and dosage-compensation-related terms appear, the strongest signal centers on ubiquitin-mediated degradation, making protein turnover a representative label. Some terms may reflect broader regulatory roles, but the central theme remains proteolysis and protein quality control.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:0036205","count":4},{"id":"GO:0016558","count":4},{"id":"GO:0046621","count":4},{"id":"GO:0009048","count":4}]},{"hash":"2195738150651732661","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":7,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":4},{"id":"GO:0000462","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0000466","count":3}]},{"hash":"2265137763833359883","title":"Unknown","description":"Top terms are not provided, so there is no GO-based theme to tie these seven proteins together; without shared annotations, I cannot assign a meaningful cluster name.","confidence":"","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[]},{"hash":"82131669243735026","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0033280","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0000209","count":2},{"id":"GO:0007014","count":2}]},{"hash":"381349046260061021","title":"Neural signaling and social/vocal behavior","description":"The cluster's top GO terms are dominated by neural and behavioral processes: sensory perception of sound, vocalization behavior, social behavior, grooming, exploration, and general regulation of behavior. Additional terms like retrograde signaling by nitric oxide, regulation of Wnt signaling, and protein dephosphorylation point to neuronal signaling and synaptic regulation, while protein localization to adherens junctions relates to cell connections at synapses. The combination suggests a module of proteins involved in neural signaling that underpins social and vocal behaviors in animals, with a metabolic component (carnitine transport) supporting neuron function. Therefore the label 'Neural signaling and social/vocal behavior' captures the common theme.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0006470","count":5},{"id":"GO:0015879","count":5},{"id":"GO:0098924","count":5},{"id":"GO:0030111","count":5},{"id":"GO:0007605","count":5}]},{"hash":"1558021920054885574","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":9,"triangles":7,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0006369","count":3},{"id":"GO:0048701","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0070935","count":2}]},{"hash":"1303854985086463977","title":"Translation and transcription linked to DNA replication","description":"The top GO terms cluster around core gene expression (translation and transcription) together with DNA replication and translesion synthesis, suggesting proteins that operate at the intersection of gene expression and genome maintenance/replication. While translation/transcription are primary signals, the TLS and replication terms indicate a broader role in replication-associated processes, justifying a label that highlights this intersection.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0070987","count":2},{"id":"GO:0042276","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0001023","count":1}]},{"hash":"799221284380443478","title":"Unknown","description":"There are no GO terms listed for this cluster, so there is no clear shared function, process, or component to label the group. Without enrichment signals, a reliable, specific label cannot be inferred.","confidence":"","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[]},{"hash":"47952841261253676","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009561","count":1},{"id":"GO:0042274","count":1},{"id":"GO:0000472","count":1},{"id":"GO:0000480","count":1},{"id":"GO:0000447","count":1}]},{"hash":"1102858536848384493","title":"RNA transcription and ribosome biogenesis","description":"The GO terms are dominated by transcription-related processes across RNA polymerases I, II, and III, plus RNA-templated transcription and ribosome biogenesis (rRNA transcription/processing context), suggesting a cohesive role in transcription machinery and ribosome production. Metabolic terms appear only as minor outliers.","confidence":"High","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006360","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0070893","count":1},{"id":"GO:0006354","count":1},{"id":"GO:0006369","count":1}]},{"hash":"886834682324521373","title":"Synaptic vesicle trafficking and receptor insertion","description":"This cluster centers on ER-to-Golgi and Golgi-associated vesicle trafficking, SNARE complex assembly, and exocytic insertion of neurotransmitter receptors into the postsynaptic membrane, all linked to synaptic plasticity such as long-term potentiation.","confidence":"High","size":7,"edges":7,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0098967","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0060291","count":2},{"id":"GO:0035493","count":2},{"id":"GO:0090161","count":2}]},{"hash":"1499963333520861413","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006368","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0043044","count":2},{"id":"GO:0046963","count":1},{"id":"GO:0036085","count":1}]},{"hash":"13156938754890957","title":"Unknown","description":"The GO terms span transcription regulation, stress response to arsenic, translation initiation, actin nucleation regulation, various histone methylation processes (obsolete), ER-Golgi trafficking, ubiquitination, and pigmentation, with no single dominant function unifying the cluster. Because there is no coherent theme or pathway that clearly connects these terms, there isn\u2019t a specific, informative label beyond Unknown.","confidence":"","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0045892","count":1},{"id":"GO:0046685","count":1},{"id":"GO:0001731","count":1},{"id":"GO:2000601","count":1},{"id":"GO:0051567","count":1}]},{"hash":"1232561272102315775","title":"Secondary metabolite biosynthesis and catabolism","description":"This cluster is enriched for terms related to biosynthesis (antibiotics, ectoine, biotin, alkaloids, verruculogen) and catabolic processing (stilbene catabolic, fatty acid oxidation). The mix points to a broad theme of specialized metabolite production and breakdown rather than a single pathway or direct protein\u2013protein interaction, leading to the label \u201cSecondary metabolite biosynthesis and catabolism.\u201d","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0001561","count":1},{"id":"GO:0042400","count":1},{"id":"GO:1902181","count":1}]},{"hash":"661777166358272013","title":"Unknown","description":"The GO terms span diverse metabolic and regulatory processes (lipid/retinoid metabolism, hormone biosynthesis, PHB production, sporulation, antibiotic response, transcription regulation) with little cohesive overlap, suggesting no single shared function for the cluster.","confidence":"","size":7,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0042761","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0042574","count":1},{"id":"GO:0002138","count":1}]},{"hash":"293017138638986727","title":"Unknown","description":"The GO terms for this cluster span several unrelated processes (lipid signaling, cell cycle, sporulation membrane formation, GTPase regulation, cell shape, phosphorylation/dephosphorylation, apoptosis, development, memory, and myoblast fusion), with no clear single function tying them together. Because of this heterogeneity and lack of a cohesive theme, there isn\u2019t a defensible specific label for the cluster.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048015","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0032120","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0008360","count":1}]},{"hash":"968989845630738312","title":"Translation Initiation Machinery","description":"The top GO terms cluster around cap-dependent and IRES-dependent translational initiation, formation and regulation of translation initiation complexes, and preinitiation complex assembly, indicating proteins that function in starting protein synthesis (including viral translation contexts). A few transport-related terms appear ancillary. ","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002191","count":1},{"id":"GO:0001732","count":1},{"id":"GO:0006446","count":1},{"id":"GO:0075525","count":1},{"id":"GO:0001731","count":1}]},{"hash":"1965149527059844946","title":"Vesicle trafficking and autophagy","description":"The cluster shows enrichment for endosome-to-lysosome transport, protein targeting to vacuole, and localization to phagophore assembly sites, plus tubulin complex assembly and actin filament branching. These together suggest a coherent module coordinating vesicle trafficking, autophagy initiation, and cytoskeletal remodeling, with occasional overlap into signaling pathways (Wnt/Smoothened) that may reflect multifunctional proteins. ","confidence":"Medium","size":7,"edges":7,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1902824","count":2},{"id":"GO:0006623","count":2},{"id":"GO:1903435","count":2},{"id":"GO:0007224","count":2},{"id":"GO:0090135","count":2}]},{"hash":"1726293521488854274","title":"Ubiquitin-Proteasome System and Protein Modification","description":"This cluster centers on ubiquitination-related processes (protein deubiquitination, sumoylation), proteasome core assembly, and proteasomal degradation, pointing to regulation of protein turnover via the ubiquitin-proteasome system. Additional terms related to stress and signaling (salt response, T cell receptor signaling, Wnt modulation) may reflect broader regulatory roles, but the dominant theme is protein modification and degradation.","confidence":"High","size":7,"edges":17,"triangles":19,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":3},{"id":"GO:0030433","count":2},{"id":"GO:0016925","count":2},{"id":"GO:0080129","count":2},{"id":"GO:0010499","count":2}]},{"hash":"924699762390906075","title":"ER Protein Folding and Redox Homeostasis","description":"The top GO terms cluster around endoplasmic reticulum\u2013associated protein folding, redox balance, and oxidative stress responses (including protein oxidation detoxification and prolyl hydroxylation). These point to a shared function in ER-assisted protein maturation coordinated with maintaining redox homeostasis, despite some peripheral terms like viral processes or transcription regulation appearing in the list. ","confidence":"High","size":7,"edges":4,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0034975","count":4},{"id":"GO:0045454","count":4},{"id":"GO:0018401","count":3},{"id":"GO:0043388","count":3},{"id":"GO:1903206","count":3}]},{"hash":"791839827019728864","title":"Proteostasis and Microtubule Assembly","description":"The cluster centers on protein folding and quality control (protein folding, chaperone-mediated assembly, ubiquitin-proteasome quality control) and cytoskeletal organization (tubulin complex assembly, cortical microtubule organization), suggesting a coordinated role in maintaining proteome integrity while assembling microtubules. While limb development appears among the terms, the dominant signals point to proteostasis and cytoskeletal dynamics as the core theme, with development-related terms possibly reflecting broader physiological contexts.","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0060173","count":2},{"id":"GO:0006457","count":1},{"id":"GO:0043622","count":1},{"id":"GO:0007021","count":1},{"id":"GO:0032968","count":1}]},{"hash":"150476656787369318","title":"Unknown","description":"GO terms span vertebrate embryonic development (fin morphogenesis, endoderm development, skeletal joint development), BMP signaling, plant-specific biosynthetic processes, and signaling, with no clear single function tying the proteins together. The lack of a cohesive theme and absence of interactions suggests no interpretable cluster function can be assigned.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035118","count":1},{"id":"GO:0010417","count":1},{"id":"GO:0009863","count":1},{"id":"GO:0035884","count":1},{"id":"GO:0008101","count":1}]},{"hash":"2024225493587208993","title":"Unknown","description":"Top GO terms are highly scattered across disparate processes (retina development, gibberellin signaling, cobalamin biosynthesis, lipid metabolism, synapse organization) with several obsolete entries, and there are no connecting edges among the proteins. This lack of a coherent shared function or pathway suggests the cluster does not reflect a single interpretable biological theme. ","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0060041","count":2},{"id":"GO:0009236","count":2},{"id":"GO:0042493","count":1},{"id":"GO:0042136","count":1}]},{"hash":"1309735576937697732","title":"Genome stability and telomere maintenance","description":"The cluster is enriched for telomere maintenance, DNA recombination and repair, and mitotic checkpoint signaling, pointing to genome stability and telomere length regulation as the core theme. Some terms related to lysylation and tRNA modification appear, but the dominant signal is telomere maintenance and genome integrity.","confidence":"High","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071915","count":2},{"id":"GO:0010833","count":2},{"id":"GO:0006310","count":2},{"id":"GO:0070200","count":2},{"id":"GO:0072581","count":2}]},{"hash":"367924071075963244","title":"Microtubule dynamics and spindle organization","description":"The GO terms point to microtubule behavior (plus/minus end depolymerization and sliding) and key mitotic spindle processes (centrosome separation, kinetochore attachment, polarity establishment), as well as cytokinesis-related actomyosin ring assembly. While there are ancillary terms involving dendritic transport and integrin regulation, the dominant signal is cytoskeletal/microtubule dynamics governing cell division.","confidence":"High","size":6,"edges":13,"triangles":13,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0070462","count":4},{"id":"GO:0000915","count":4},{"id":"GO:0098971","count":4},{"id":"GO:0031534","count":4},{"id":"GO:0031535","count":4}]},{"hash":"1755348616513134071","title":"Photosynthesis Light Harvesting and Light Response","description":"These proteins are annotated with GO terms tied to photosynthesis and light harvesting in PSI and PSII, plus various light-responsive processes (nonphotochemical quenching, responses to blue, red, and far-red light, as well as responses to light intensity). The cohesive theme centers on light capture and regulation within the photosynthetic apparatus, suggesting chloroplast light-harvesting or photosystem-associated functions. This makes the label representative of the cluster's function.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010196","count":2},{"id":"GO:0009768","count":2},{"id":"GO:0009637","count":2},{"id":"GO:0010218","count":2},{"id":"GO:0071486","count":2}]},{"hash":"450491147478296493","title":"Cytoskeleton dynamics and intracellular transport","description":"The cluster highlights Arp2/3-mediated actin nucleation regulation and mitotic spindle assembly, pointing to cytoskeleton remodeling and cell division. It also includes endoplasmic reticulum to Golgi vesicle transport and ubiquitination, suggesting roles in intracellular trafficking and protein regulation. Translation initiation appears less cohesive with these themes, and several methylation terms are obsolete, likely reflecting annotation noise. Overall, the shared theme centers on core cellular logistics involving the cytoskeleton and trafficking pathways.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":1},{"id":"GO:2000601","count":1},{"id":"GO:0051567","count":1},{"id":"GO:2001162","count":1},{"id":"GO:0061087","count":1}]},{"hash":"1552991114610832138","title":"DNA replication and cell cycle machinery","description":"The top GO terms cluster around DNA replication, DNA-templated transcription, leading strand elongation, and cell division, with supporting signals from centriole elongation and ubiquitin-proteasome regulation (SCF complex and proteasome assembly) and stress responses. This suggests a cohesive role in DNA replication/cell cycle control, coupled with proteostasis and energy/chaperone support during these processes. ","confidence":"High","size":6,"edges":4,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0006272","count":4},{"id":"GO:0070682","count":4}]},{"hash":"2107311404513977509","title":"Transsulfuration and sulfur amino acid biosynthesis","description":"These terms cluster around amino acid biosynthesis with a strong emphasis on sulfur-containing amino acids and transsulfuration (cysteine via cystathionine, homocysteine, hydrogen sulfide), plus related pathways like threonine and tryptophan biosynthesis.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009088","count":2},{"id":"GO:0019343","count":2},{"id":"GO:0000162","count":2},{"id":"GO:0043418","count":2},{"id":"GO:0046360","count":2}]},{"hash":"2040255962308287861","title":"Mitochondrial RNA maturation and methylation","description":"This cluster is dominated by GO terms for mitochondrial RNA processing and RNA modification, including maturation of mitochondrial rRNA and methylation of rRNA and tRNA, plus mitochondrial transcription initiation/regulation. The combined signals point to proteins involved in mitochondrial RNA maturation and RNA modification, with some link to transcription control within mitochondria. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":2},{"id":"GO:0031167","count":2},{"id":"GO:0006479","count":2},{"id":"GO:0030488","count":2},{"id":"GO:0014075","count":2}]},{"hash":"386863921409365470","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007417","count":2},{"id":"GO:0019673","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009243","count":2},{"id":"GO:0042619","count":2}]},{"hash":"2298094370335790960","title":"Cardiac conduction and calcium signaling","description":"The terms are dominated by heart-related processes: heart morphogenesis, ventricular myocardium morphogenesis, regulation of cardiac conduction, and electrical signaling in cardiac tissue. Additionally, the explicit calcium-release term from the sarcoplasmic reticulum points to calcium handling during cardiac excitation-contraction. A few unrelated single-term GO entries exist but do not override the clear cardiac electrophysiology theme.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901710","count":1},{"id":"GO:0003007","count":1},{"id":"GO:0086064","count":1},{"id":"GO:0055010","count":1},{"id":"GO:0000412","count":1}]},{"hash":"2122104792868343677","title":"Mitophagy and ubiquitin-mediated mitochondrial proteostasis","description":"This cluster is dominated by terms tied to mitochondrial protein quality control and degradation, including autophagy of mitochondrion (mitophagy), ubiquitin-dependent proteasomal pathways (including ERAD-associated processes), and mitochondria-associated ubiquitin-dependent catabolic activity, with supporting evidence from sumoylation-related regulation. While there are a few additional terms related to cell cycle and immune signaling, the core theme points to mitochondria-focused proteostasis via ubiquitin-proteasome and autophagy pathways.","confidence":"High","size":6,"edges":8,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1901799","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0000422","count":3},{"id":"GO:0016925","count":2},{"id":"GO:0070651","count":2}]},{"hash":"1535116549867679411","title":"Stress-Response Signaling and Transcription Regulation","description":"The terms cluster around regulation of signaling pathways and transcription in response to stress (salt stress, hypoxia/HIF-1alpha, interferon signaling) and include broader regulatory processes like transcription control and metabolic adjustments; this suggests a theme of stress-responsive signaling and gene regulation, despite some unrelated terms such as otolith tethering. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006457","count":1},{"id":"GO:0010105","count":1},{"id":"GO:0097411","count":1},{"id":"GO:0060338","count":1},{"id":"GO:0035889","count":1}]},{"hash":"895545200748600544","title":"Embryonic eye and forebrain development","description":"This cluster is dominated by GO terms pointing to embryonic development of ocular and neural structures (embryonic camera-type eye development, forebrain development, retinoic acid/retinoic acid biosynthesis) with related gland/brain morphogenesis terms, suggesting a cohesive theme around eye and neural development, despite a few metabolic terms that are less central.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055129","count":6},{"id":"GO:0030900","count":6},{"id":"GO:0003007","count":6},{"id":"GO:0015976","count":6},{"id":"GO:0006069","count":6}]},{"hash":"1601195874765610388","title":"Microtubule Dynamics and Spindle Organization","description":"Terms like plus-end and minus-end microtubule dynamics, polarity establishment, spindle/centrosome activities, and transport along microtubules point to a theme of cytoskeleton organization, especially microtubule dynamics and spindle functions that drive cell division and intracellular transport.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0070462","count":6},{"id":"GO:0000915","count":6},{"id":"GO:0098971","count":6},{"id":"GO:0031534","count":6},{"id":"GO:0031535","count":6}]},{"hash":"1428969069734663047","title":"Ribosome Translation & RNA Modification","description":"GO terms overwhelmingly point to translation and ribosome-related RNA modifications (translation; tRNA and rRNA methylation; ribosome-associated protein quality control and ubiquitin-dependent degradation). Some peripheral terms appear unrelated (cobalamin biosynthesis, telomerase regulation), but the core theme is ribosome function and RNA modification.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0030488","count":1},{"id":"GO:0009236","count":1},{"id":"GO:0070476","count":1},{"id":"GO:0006479","count":1}]},{"hash":"1807793623926681636","title":"Root hair cell wall biosynthesis","description":"The dominant GO terms are RG-II biosynthesis and cell wall organization, together with root hair cell development, indicating a plant-specific process focused on root hair formation and cell wall biosynthesis. A few transcription and stress-related terms appear but seem secondary to the primary theme.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010306","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0080147","count":3},{"id":"GO:0006355","count":2},{"id":"GO:0006351","count":1}]},{"hash":"796595561931545371","title":"Unknown","description":"The top GO terms show a scattered mix of metabolic biosynthetic processes across plants, microbes, and animals, along with neuronal differentiation and exocytosis signals. This lack of a cohesive, single-function theme makes it hard to assign a specific label to the cluster.","confidence":"","size":6,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0042572","count":2},{"id":"GO:0042208","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0009718","count":2}]},{"hash":"2025416996609101031","title":"RNA Splicing and Translation Initiation Regulation","description":"The terms cluster around mRNA processing and splicing (spliceosome assembly, alternative splicing regulation, splice site recognition) and the assembly/activation of translation initiation machinery (preinitiation complex, eIF4F complex, IRES-dependent initiation), plus ncRNA-mediated regulation of gene expression. This points to a cohesive theme of RNA processing coupled with translational control. Despite no edges, the GO signals consistently link splicing machinery with initiation factors and miRNA/Regulatory ncRNA\u2013mediated silencing, suggesting a functionally connected set of RNA-processing and translation-regulation proteins.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":1},{"id":"GO:0016556","count":1},{"id":"GO:0034462","count":1},{"id":"GO:0000380","count":1},{"id":"GO:0001731","count":1}]},{"hash":"928990172632414127","title":"DNA damage response and RNA processing","description":"The terms show a core of nucleic acid maintenance and stress response (nucleotide-excision repair, SOS response, antibiotic response) alongside RNA metabolism (regulatory ncRNA silencing, mRNA splicing via spliceosome, ribosome biogenesis), suggesting a cohesive cluster around DNA damage response coupled with RNA processing. Some terms (e.g., meiotic gene conversion) are related to genome maintenance, supporting this theme, though there is some noise from signaling terms like excitatory postsynaptic potential regulation.","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0090394","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0009432","count":2}]},{"hash":"1306763828610477315","title":"Cardiac Ion Homeostasis and EC Coupling","description":"The top GO terms point to ion transport and membrane electrochemical gradient maintenance (K+ import, Na+ export, membrane repolarization), along with T-tubule organization and calcium-dependent exocytosis, all central to cardiac muscle excitability and excitation-contraction coupling. While a couple of terms are less cardiac-specific, the overall theme centers on cardiac membrane potential regulation and calcium signaling.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903243","count":4},{"id":"GO:0010248","count":4},{"id":"GO:1990573","count":4},{"id":"GO:1903233","count":4},{"id":"GO:0033292","count":4}]},{"hash":"167182243427870352","title":"Chromatin modification and ribosome biogenesis","description":"Proteins in this cluster show links to chromatin-level regulation (negative regulation of transcription by RNA polymerase II; histone demethylation) and to ribosome biogenesis/assembly (rRNA base methylation; cytosolic ribosome assembly). Although some terms are obsolete, the recurring themes are histone modification affecting transcription and components involved in ribosome production, suggesting a module that coordinates gene expression with ribosome biogenesis.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0030961","count":2},{"id":"GO:0034720","count":2},{"id":"GO:0045668","count":2},{"id":"GO:0070544","count":2}]},{"hash":"1318083956567926647","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by translation-related terms across cytoplasmic and mitochondrial contexts, along with ribosome biogenesis (e.g., preribosome assembly) and translation initiation regulation. Fe-S cluster assembly terms further link to mitochondrial-associated translation machinery. A couple of peripheral terms (intraciliary transport and NGF response) exist but do not outweigh the central theme.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0032543","count":1},{"id":"GO:1990090","count":1},{"id":"GO:0002181","count":1},{"id":"GO:0090070","count":1}]},{"hash":"728848167141862481","title":"Ubiquitin-Dependent Immune Regulation","description":"The main GO terms point to ubiquitin-mediated proteolysis (ubiquitin-dependent degradation, ERAD, autoubiquitination) with immune-related processes (B cell homeostasis, germinal center regulation, TNF signaling), suggesting a theme where ubiquitin-driven protein turnover modulates immune signaling; some terms are less central but do not override the core pattern.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0016558","count":3},{"id":"GO:0060816","count":3},{"id":"GO:0001782","count":3}]},{"hash":"1795931667893366192","title":"Unknown","description":"The top GO terms span diverse processes (oocyte maturation, translation initiation, actin nucleation regulation, histone methylation, neural tube closure, ubiquitin-dependent protein catabolism, and ER-Golgi transport) with no single shared function or interaction pattern among the six proteins, and no edges linking them, making it not possible to assign a cohesive, representative label.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":1},{"id":"GO:0001731","count":1},{"id":"GO:2000601","count":1},{"id":"GO:0051567","count":1},{"id":"GO:0021993","count":1}]},{"hash":"2119002608313932743","title":"Unknown","description":"The GO terms span transcription, DNA replication, protein folding/unfolding, proteasome assembly, ubiquitin-related regulation, peroxisome import, centriole elongation, and stress response, with no clear, cohesive function tying the cluster together. Therefore no single representative label; mark as Unknown.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0030961","count":2},{"id":"GO:0006272","count":1},{"id":"GO:0070682","count":1},{"id":"GO:1903007","count":1}]},{"hash":"1056881530743832734","title":"DNA replication and chromatin-RNA regulation","description":"This cluster centers on nucleic acid metabolism and genome maintenance. Frequent terms include DNA replication (and primer synthesis), RNA processing of ribosomal RNA, and ncRNA-mediated gene silencing, alongside chromatin-related activity (histone H2B ubiquitination). A SOS response tag also aligns with DNA damage handling, supporting a cohesive theme of DNA replication, RNA-level regulation, and chromatin control of gene expression.","confidence":"Medium","size":6,"edges":5,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0000462","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0006605","count":2},{"id":"GO:0006311","count":2}]},{"hash":"545481206944272125","title":"ER Protein Folding and Quality Control","description":"The cluster is strongly linked by GO terms about responding to unfolded proteins, ER-specific protein folding, and ubiquitin-proteasome\u2013mediated quality control, as well as post-translational targeting to membranes, pointing to a cohesive group of ER-associated folding and QC machinery. A few terms related to development (mesoderm formation, neural tube patterning) and nuclear tRNA import appear less central, suggesting some peripheral or unrelated annotations in this small set. Overall, the dominant theme is protein folding and quality control within the secretory/ER pathway.","confidence":"Medium","size":6,"edges":9,"triangles":4,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006986","count":3},{"id":"GO:0071630","count":3},{"id":"GO:0070389","count":3},{"id":"GO:0031204","count":3},{"id":"GO:0001707","count":3}]},{"hash":"1519735038325154384","title":"Unknown","description":"This cluster shows a highly heterogeneous mix of GO terms (propylene catabolic process, various metabolism terms, aging, gastrulation, cell division, mitochondrial electron transport, megakaryocyte differentiation) and several obsolete annotations. There are no edges or shared functional connections among the proteins (Edges 0, Triangles 0, Max Degree 0), suggesting no cohesive single function. Given the lack of a clear unifying theme, a specific label cannot be confidently assigned.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042208","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0007568","count":3},{"id":"GO:0007369","count":3},{"id":"GO:0016575","count":3}]},{"hash":"165933568453238233","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061180","count":1},{"id":"GO:0030728","count":1},{"id":"GO:0070509","count":1},{"id":"GO:0002115","count":1},{"id":"GO:0006406","count":1}]},{"hash":"682141686413782255","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0000463","count":1},{"id":"GO:0000480","count":1},{"id":"GO:0000472","count":1},{"id":"GO:0000447","count":1}]},{"hash":"1622057793184151069","title":"SRP-dependent cotranslational protein targeting to membrane","description":"The top GO terms are all SRP-dependent cotranslational protein targeting to membrane, including signal sequence recognition and translocation. This strongly suggests the proteins function together in the SRP pathway that targets nascent polypeptides to the ER membrane, making the SRP-targeting cluster the best-fitting label despite no reported interactions.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006617","count":1},{"id":"GO:0006616","count":1},{"id":"GO:0006614","count":1}]},{"hash":"1910548345855624658","title":"Vacuolar Ion Transport and Homeostasis","description":"The GO terms cluster around vacuolar processes (protein targeting to vacuole, vacuole organization, vacuolar acidification) and diverse ion transport and energy-related activities (magnesium, copper, sodium, proton transport; proton motive force-driven ATP synthesis). This suggests a coherent theme of maintaining ion balance within vacuoles and related organelles, with associated trafficking and energy coupling. ","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002377","count":1},{"id":"GO:0015693","count":1},{"id":"GO:0006878","count":1},{"id":"GO:0006623","count":1},{"id":"GO:0042777","count":1}]},{"hash":"2022130932306012591","title":"Plant light signaling and calcium signaling","description":"The Top Terms show photomorphogenesis regulation, responses to blue and red light, and calcium import/release, indicating a core function in light perception linked to calcium signaling. Ethylene signaling and cold response align with broader environmental responses in plants, supporting a cohesive plant light-response theme, though some terms (miRNA processing, mechanical stimulus, synaptic regulation) appear as weaker, broader connections. Overall, the dominant theme is light-driven signaling with calcium involvement.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010099","count":1},{"id":"GO:0009637","count":1},{"id":"GO:0009873","count":1},{"id":"GO:0010114","count":1},{"id":"GO:0035196","count":1}]},{"hash":"1832500060870132484","title":"Epigenetic Transcriptional Regulation","description":"The top GO terms point to chromatin modification and transcription control (histone ubiquitination, H3K27 trimethylation, DNA methylation) and regulation of transcription by RNA polymerase II, indicating an epigenetic regulation focus. A couple terms relate to heart development or circulation, but the overarching signal is chromatin-state\u2013driven transcriptional regulation.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033697","count":1},{"id":"GO:0036091","count":1},{"id":"GO:0071894","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0060123","count":1}]},{"hash":"1790946485090818436","title":"Neural development and synaptic signaling","description":"This cluster is driven by terms related to brain development (orbitofrontal cortex development), neural signaling (trans-synaptic signaling, axon regeneration), and signaling pathways (FGFR, insulin receptor) plus transcriptional regulation, suggesting a set of proteins involved in neural development and synaptic communication, with supporting transcriptional activity.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0060716","count":4},{"id":"GO:0042220","count":4},{"id":"GO:0002741","count":3},{"id":"GO:0035607","count":3}]},{"hash":"1221546821222409882","title":"Neurodevelopmental Signaling","description":"These proteins cluster around signaling and development, especially neural development and axon-related processes (Smoothened pathway regulation, FGF signaling in cortex development, trans-synaptic signaling, axon regeneration) plus related growth and immune signaling terms. The common theme is developmental signaling with a neural focus, hence Neurodevelopmental Signaling.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901621","count":3},{"id":"GO:0000082","count":3},{"id":"GO:0060434","count":3},{"id":"GO:0002741","count":2},{"id":"GO:0035607","count":2}]},{"hash":"1792846876729712724","title":"Unknown","description":"The GO terms span lipid and sterol metabolism (unsaturated fatty acid biosynthesis, ergosterol-related regulation, sphingolipid metabolism) alongside nitrogen assimilation, nitric oxide biosynthesis, and tissue-specific processes (mitochondrion inheritance, myelin maintenance, sebaceous gland differentiation). There isn\u2019t a single cohesive function or pathway tying these terms together, suggesting a heterogeneous set of roles rather than a dedicated cluster. None","confidence":"","size":6,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006636","count":2},{"id":"GO:0006675","count":2},{"id":"GO:0000001","count":2},{"id":"GO:0001949","count":2}]},{"hash":"1323514415457986346","title":"Vesicular trafficking regulation","description":"Most top GO terms point to positive regulation of vesicle transport between compartments (endosome-lysosome, endosome-plasma membrane, ER-to-Golgi), indicating members of the cluster mainly regulate intracellular trafficking and membrane dynamics. Additional terms related to polarity and cytoskeletal organization echo trafficking roles; overall the theme is regulation of vesicle transport.","confidence":"High","size":6,"edges":6,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1902824","count":4},{"id":"GO:1902307","count":4},{"id":"GO:1905751","count":4},{"id":"GO:1902953","count":4},{"id":"GO:0061000","count":4}]},{"hash":"2041963403573679961","title":"Glycan biosynthesis and cell wall assembly","description":"The top GO terms point to polysaccharide and glycoprotein synthesis and modification (teichoic acid, cellulose, hyaluronan biosynthesis; UDP-glucose metabolism; O- and N-linked glycosylation), suggesting a shared function in building or decorating the cell envelope and extracellular matrix. A few terms (tRNA methylation, immunoglobulin production) are less consistent with this theme and may reflect annotation noise, but the dominant signal supports glycan synthesis and cell wall-related processes.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030488","count":1},{"id":"GO:0030213","count":1},{"id":"GO:0018242","count":1},{"id":"GO:0036108","count":1},{"id":"GO:0071555","count":1}]},{"hash":"1881165673037766427","title":"Postsynaptic receptor trafficking and synaptic plasticity","description":"The GO terms point to delivery and recycling of receptors at the postsynaptic membrane (exocytic insertion, receptor recycling), coupled with synaptic potentiation (LTP) and vesicle transport through the Golgi and ER-Golgi pathway, suggesting a cluster focused on neuronal receptor trafficking and synaptic strengthening. Some terms (vacuolar fusion, hindgut contraction) are peripheral noise relative to this core theme.","confidence":"Medium","size":6,"edges":6,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0098967","count":1},{"id":"GO:0042144","count":1},{"id":"GO:1902259","count":1},{"id":"GO:1900483","count":1},{"id":"GO:0006888","count":1}]},{"hash":"1462875843303116347","title":"Xenobiotic and nutrient transmembrane transport","description":"This cluster shows strong representation of transmembrane transport terms across diverse substrates\u2014xenobiotics, vitamins, phosphate ions, urate, glucose import in response to insulin, and even neurotransmitter loading into synaptic vesicles\u2014suggesting a unifying role in membrane transport processes or transporter regulation.","confidence":"High","size":6,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":6},{"id":"GO:0035461","count":6},{"id":"GO:0042891","count":5},{"id":"GO:0098700","count":4},{"id":"GO:0042908","count":4}]},{"hash":"2044703452379815343","title":"Cardiac Development and Electrophysiology","description":"The top GO terms point to heart development (GO:0007507), SA node action potential regulation (GO:0098907), and clustering of voltage-gated potassium channels (GO:0045163), with supporting signals in angiogenesis and multicellular development. Together these suggest roles in heart formation and cardiac electrical activity, including ion channel organization and signaling modulation, rather than a single metabolic pathway. The lack of edges means this is a functional grouping based on annotations rather than direct protein\u2013protein interactions.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":3},{"id":"GO:0035987","count":2},{"id":"GO:0045163","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0001525","count":2}]},{"hash":"337325430860179350","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006398","count":1},{"id":"GO:0033260","count":1},{"id":"GO:0034316","count":1},{"id":"GO:0071354","count":1},{"id":"GO:0021766","count":1}]},{"hash":"1975127938929793560","title":"Meiotic DSB formation and repair","description":"The top GO terms are dominated by meiotic processes: programmed double-strand break formation and repair in meiotic recombination, indicating the proteins co-function in meiotic chromosome processing. Other terms (cell-cell adhesion, calcium signaling regulation, ER\u2013Golgi transport, translation initiation control) are less central and may reflect multifunctionality or annotation noise. Overall, the cluster most reasonably maps to meiotic recombination and DNA damage response.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010780","count":5},{"id":"GO:1990918","count":5},{"id":"GO:0098609","count":5},{"id":"GO:0051533","count":5},{"id":"GO:0060316","count":5}]},{"hash":"226786169084098909","title":"Meiotic Chromosome Dynamics","description":"This cluster centers on meiosis-related processes: synaptonemal complex organization, chiasma assembly, and DNA double-strand break processing, with associated chromatin remodeling (histone ubiquitination/phosphorylation), indicating roles in meiotic chromosome pairing and recombination; a couple of terms (prolactin secretion, peroxisomal protein import) appear as noise rather than core signals.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0070459","count":5},{"id":"GO:0016558","count":5},{"id":"GO:0071894","count":5},{"id":"GO:0051026","count":5},{"id":"GO:0071455","count":5}]},{"hash":"1422022038955070943","title":"Neural and Epithelial Differentiation","description":"The cluster is dominated by GO terms for differentiation of multiple tissues, notably neuron differentiation and epithelial lineages (lung, intestinal, keratinocyte). This suggests a shared function in guiding cell fate across neural and epithelial lineages, with other terms likely reflecting broader cell-cycle and regulation aspects rather than a single tissue-specific process. Some histone modification terms are obsolete, but the core signal points to differentiation across tissues. ","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030182","count":3},{"id":"GO:0060487","count":3},{"id":"GO:0060575","count":2},{"id":"GO:0080182","count":2},{"id":"GO:2000146","count":2}]},{"hash":"2147568863725915630","title":"Epithelial differentiation with GTPase and ubiquitin regulation","description":"The cluster is strongly linked to epithelial differentiation, with GO terms for intestinal epithelial and keratinocyte differentiation. It also includes signaling and cytoskeletal regulation (positive regulation of GTPase activity, regulation of cell motility, and cytokinesis) and protein turnover via ubiquitin pathways, suggesting a theme of differentiation coordinated with cytoskeletal dynamics and ubiquitin-mediated regulation. Some histone modification terms are obsolete, but they do not overturn the main theme.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0060575","count":3},{"id":"GO:0080182","count":3},{"id":"GO:2000146","count":3},{"id":"GO:0097198","count":3}]},{"hash":"231088105771438985","title":"B Cell Activation and IgG Class Switching","description":"This cluster's strongest GO terms point to B cell\u2013driven immune activation, with cytokine production, inflammatory regulation, and IgG isotype switching, suggesting antibody-related responses as the core function; other terms (mitochondrial import, telomere/RNA localization) appear less central.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0002368","count":5},{"id":"GO:0050729","count":5},{"id":"GO:1903427","count":5},{"id":"GO:0048291","count":5},{"id":"GO:0045041","count":5}]},{"hash":"465155436118935165","title":"Microtubule dynamics and spindle organization","description":"This cluster is dominated by GO terms tied to microtubule function and cytoskeletal dynamics, including plus- and minus-end\u2013directed movement, microtubule sliding, polarity establishment, spindle-kinetochore attachments, and actomyosin ring assembly. The dendritic transport term reflects microtubule-based cargo movement as part of the same cytoskeletal theme, suggesting a cohesive focus on microtubule-driven processes during cell division and transport.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000742","count":3},{"id":"GO:0070462","count":2},{"id":"GO:0000915","count":2},{"id":"GO:0098971","count":2},{"id":"GO:0031534","count":2}]},{"hash":"1762002816441398503","title":"Unknown","description":"The top terms span lipid metabolism, dephosphorylation, serine biosynthesis, stilbene catabolism, testosterone response, calcium homeostasis, and metal ion transport, with no single unifying process. The diversity suggests either multifunctional proteins or noisy annotations, so a coherent cluster label cannot be assigned.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":2},{"id":"GO:0097755","count":2},{"id":"GO:0016311","count":2},{"id":"GO:0046839","count":2},{"id":"GO:0006564","count":2}]},{"hash":"818309180331423528","title":"Karyogamy and DNA replication","description":"This cluster is dominated by terms for karyogamy (nuclear fusion during mating) and DNA replication, with additional signals of protein folding and membrane-associated protein targeting, suggesting a group tied to nuclear events and genome maintenance with proteostasis aspects. Some terms are peripheral (e.g., hematopoietic differentiation), but the core theme centers on nuclear fusion and genome replication. ","confidence":"Medium","size":5,"edges":5,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000742","count":3},{"id":"GO:0070389","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0000902","count":2},{"id":"GO:1902037","count":2}]},{"hash":"219937300985278111","title":"Cardiac morphogenesis and excitation-contraction coupling","description":"The top terms cluster around heart development and cardiac function: heart morphogenesis, ventricular cardiac muscle tissue morphogenesis, and electrical conduction via cardiac coupling, plus action potential propagation and calcium release from the sarcoplasmic reticulum, all pointing to cardiac morphogenesis and excitation-contraction signaling. Some terms are obsolete or tangential (e.g., oxidative-reduction, histone isomerization), but the visible pattern supports a cardiac-focused theme.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:1901710","count":1},{"id":"GO:0003007","count":1},{"id":"GO:0086064","count":1},{"id":"GO:0055010","count":1}]},{"hash":"240187893517907708","title":"Cytoskeletal dynamics and organelle inheritance","description":"The terms cluster around actin nucleation, cell shape/polarity, cytokinesis, spindle orientation, and organelle inheritance (peroxisome and vacuole), indicating a shared role in cytoskeletal organization and organelle inheritance during cell division.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045033","count":2},{"id":"GO:0006930","count":2},{"id":"GO:0051127","count":2},{"id":"GO:0071963","count":2},{"id":"GO:0007107","count":2}]},{"hash":"574903308449209495","title":"Fatty acid biosynthesis and lipid metabolism","description":"The top GO terms are dominated by fatty acid biosynthetic and metabolic processes, including long-chain and medium-chain fatty acid metabolism and transport, plus lipoteichoic acid biosynthesis, pointing to a lipid metabolism-focused cluster. Some terms reference seed development or bioluminescence, which appear as outliers or broader annotations, but the strongest signal is lipid-related pathways.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006633","count":2},{"id":"GO:0019654","count":2},{"id":"GO:0010030","count":2},{"id":"GO:0010214","count":2},{"id":"GO:1902987","count":2}]},{"hash":"1957884364590429998","title":"Mitosis and cell cycle regulation","description":"This cluster centers on mitosis-related processes and cell cycle control, with specific emphasis on spindle attachment to kinetochores, sister chromatid biorientation, and broader cell cycle regulation. Dephosphorylation and GTPase activity terms suggest signaling modulation coordinating these processes. A few terms (apoptotic signaling, interferon signaling, mRNA capping) are less directly tied to mitosis, but the dominant pattern is spindle- and cell cycle\u2013related.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0035335","count":2},{"id":"GO:0098783","count":2},{"id":"GO:0035970","count":2},{"id":"GO:0051229","count":2}]},{"hash":"1596011165007684667","title":"RNA and Protein Methylation","description":"The top GO terms cluster around RNA and protein methylation (rRNA methylation, peptidyl methylations, and tRNA modification), suggesting the proteins function as methyltransferases or methylation-related modifiers; a few ancillary terms appear unrelated but do not outweigh the dominant theme.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031167","count":2},{"id":"GO:0018013","count":2},{"id":"GO:0018027","count":2},{"id":"GO:0035498","count":1},{"id":"GO:0018023","count":1}]},{"hash":"507924416520856595","title":"Amino acid biosynthesis and metabolism","description":"The top GO terms point to biosynthetic and metabolic activities, notably antibiotic biosynthesis, L-tyrosine biosynthesis, and the L-methionine cycle, with additional general metabolic processes like one-carbon metabolism. Sporulation appears only once, suggesting no single, dominant specialized pathway beyond metabolism. Therefore, a label focused on biosynthesis and amino acid-related metabolism fits best.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0006730","count":1},{"id":"GO:1903758","count":1},{"id":"GO:0006571","count":1}]},{"hash":"1993842348502759924","title":"Unknown","description":"The listed GO terms are scattered across meiosis-specific DNA repair and various unrelated cellular processes (adhesion, signaling, transport, translation control), with no single dominant function connecting the cluster; therefore a cohesive, intuitive label cannot be assigned.","confidence":"","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0010780","count":1},{"id":"GO:1990918","count":1},{"id":"GO:0098609","count":1},{"id":"GO:0051533","count":1},{"id":"GO:0060316","count":1}]},{"hash":"1904852051433456881","title":"Ubiquitin-mediated immune signaling","description":"GO terms in this cluster cluster around ubiquitination processes (ubiquitin-dependent protein catabolic process, protein autoubiquitination, K6-linked ubiquitination) and immune pathways (adaptive immune response, NF-kappaB signaling regulation, and modulation of RIG-I signaling), suggesting a cohesive role in ubiquitin-regulated immune signaling and NF-kB control.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043123","count":2},{"id":"GO:0036205","count":2},{"id":"GO:0009048","count":2},{"id":"GO:0090073","count":2},{"id":"GO:0042787","count":2}]},{"hash":"1358393835568498486","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000453","count":1},{"id":"GO:0002938","count":1},{"id":"GO:0070475","count":1}]},{"hash":"2239362148926225790","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":3},{"id":"GO:0006364","count":3},{"id":"GO:0090503","count":3},{"id":"GO:0018189","count":2},{"id":"GO:1903999","count":2}]},{"hash":"854578918792144720","title":"Cell Signaling","description":"The proteins are linked to multiple signaling-related GO terms, including cytokine production, FGFR signaling, insulin signaling, and trans-synaptic signaling, along with related cellular responses to stimuli. This suggests a theme of signal transduction and communication, even though a few terms touch on division or fertilization; overall, the dominant pattern is signaling pathways, justifying the label \"Cell Signaling.\"","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002741","count":2},{"id":"GO:0035607","count":2},{"id":"GO:0008286","count":2},{"id":"GO:0048679","count":2},{"id":"GO:1904628","count":2}]},{"hash":"1819202388027561751","title":"Unknown","description":"These five proteins do not share a single clear function. The top GO terms cover sodium ion transport, various metabolic/catabolic processes and energy production, plus several endothelial/vasculature development terms that don\u2019t point to one cohesive theme. Thus there isn\u2019t a single representative label to assign.","confidence":"","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006814","count":3},{"id":"GO:0006124","count":2},{"id":"GO:0045602","count":2},{"id":"GO:0007595","count":2},{"id":"GO:0009115","count":2}]},{"hash":"683508242366606160","title":"Purine nucleotide metabolism and salvage","description":"This cluster is dominated by GO terms related to nucleotide phosphorylation and purine nucleotide interconversion and biosynthesis (ADP, CDP, AMP, ITP, NAD+), with occasional tissue terms (brain/liver) likely reflecting expression rather than core function. The shared theme is purine nucleotide metabolism and salvage pathways.","confidence":"High","size":5,"edges":7,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0046939","count":4},{"id":"GO:0007420","count":4},{"id":"GO:0046041","count":4},{"id":"GO:0044209","count":4},{"id":"GO:0046705","count":4}]},{"hash":"2216449108147410302","title":"Microtubule dynamics and cytoskeleton organization","description":"The top GO terms cluster around microtubule behavior (plus/minus-end dynamics, depolymerization, sliding), spindle and centrosome functions (centrosome separation, kinetochore attachment), cytoskeletal polarity, and related transport processes, with some links to actomyosin-based cytokinesis and neuronal receptor transport. This points to a cohesive role in microtubule-based cytoskeletal remodeling across division and trafficking.","confidence":"High","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0070462","count":4},{"id":"GO:0000915","count":4},{"id":"GO:0098971","count":4},{"id":"GO:0031534","count":4},{"id":"GO:0031535","count":4}]},{"hash":"693520608043611523","title":"Spliceosome and translation initiation assembly","description":"These proteins show strong enrichment for mRNA splicing and spliceosome components (splicing regulation, splice site recognition, small-subunit processome) as well as factors involved in initiating translation (translation preinitiation complex, EIF4F complex assembly, IRES-dependent initiation). This points to a cluster involved in RNA processing linked to the start of translation.","confidence":"High","size":5,"edges":4,"triangles":0,"max_degree":2,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":4},{"id":"GO:0031047","count":3},{"id":"GO:0016556","count":3},{"id":"GO:0034462","count":3},{"id":"GO:0000380","count":3}]},{"hash":"1375421502760217440","title":"DNA replication and repair","description":"Dominant GO terms center on DNA replication, repair, and genome maintenance (DNA replication, DNA repair, leading strand elongation, DNA recombination, DNA-templated transcription, SOS response). The inclusion of viral genome replication and related replication-associated processes suggests a module focused on genome maintenance and replication machinery. The lack of edges indicates these proteins are represented by dispersed terms rather than a tightly interconnected network in this dataset, but the core theme is replication/repair. ","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0019079","count":3},{"id":"GO:0018144","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006269","count":2}]},{"hash":"650842619980809731","title":"Androgen signaling and prostate development","description":"The key GO terms emphasize male sex differentiation, prostate gland development, and steroid hormone receptor complex assembly, indicating androgen receptor\u2013mediated control of male reproductive development. While other terms (cell division, dsRNA response, unfolded protein response, histone-related terms) are present but less cohesive, the strongest theme across the cluster is sex hormone signaling impacting prostate development.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046661","count":3},{"id":"GO:0006463","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0030850","count":3},{"id":"GO:0071360","count":2}]},{"hash":"181506066210801764","title":"RNA Processing and Ribosome Biogenesis","description":"This cluster is enriched for RNA-related processes: tRNA wobble uridine modification, tRNA methylation, and 7-methylguanosine mRNA capping, plus ribosomal small subunit export and cell growth, pointing to RNA processing and ribosome assembly. The presence of vitamin biosynthesis terms (cobalamin, biotin, ubiquinone) may reflect broader metabolic context rather than a single cohesive RNA-centered pathway. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":3},{"id":"GO:0019919","count":2},{"id":"GO:0009102","count":2},{"id":"GO:0002098","count":2},{"id":"GO:0016049","count":2}]},{"hash":"2135903651237760845","title":"Synaptic receptor trafficking and vesicle regulation","description":"The top GO terms point to neuronal membrane trafficking and synaptic dynamics: exocytic insertion of neurotransmitter receptors into postsynaptic membranes, positive regulation of receptor localization to synapse, and negative regulation of synaptic vesicle recycling, supported by ER-to-Golgi vesicle transport. While there are unrelated terms present (e.g., nucleotide biosynthesis, transcription regulation, immune processes), the strongest signal centers on synaptic receptor trafficking and vesicle regulation.","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019363","count":2},{"id":"GO:0045892","count":2},{"id":"GO:0098967","count":1},{"id":"GO:1903422","count":1},{"id":"GO:0007340","count":1}]},{"hash":"1334802950800285734","title":"Unknown","description":"The GO terms for this cluster are highly heterogeneous, ranging from cobalamin biosynthesis and complex assembly to ubiquitination pathways, immune signaling, and plant/hormone regulation. There is no clear, single biological theme tying the proteins together, so a cohesive functional label cannot be inferred with confidence.","confidence":"","size":5,"edges":5,"triangles":2,"max_degree":3,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0009236","count":4},{"id":"GO:0006461","count":4},{"id":"GO:0031943","count":1},{"id":"GO:0030433","count":1},{"id":"GO:0008626","count":1}]},{"hash":"1759997010829381682","title":"Plant photoreception and circadian regulation","description":"Most terms center on light-responsive processes (photosynthesis, blue light response, UV protection) and rhythms (circadian, locomotor rhythm), with supporting hints of photomorphogenesis (strigolactone response) and growth regulation. This points to proteins involved in plant light sensing and clock-controlled functions, rather than a general metabolic cluster.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0018298","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0042754","count":1},{"id":"GO:0010075","count":1},{"id":"GO:0045475","count":1}]},{"hash":"169412593919164547","title":"Nuclear DNA Repair and Chromatin Dynamics","description":"The terms cluster around nuclear processes: DNA replication/unwinding, DNA methylation, histone H2B ubiquitination, nucleosome mobilization, and RNA processing/surveillance, indicating genome maintenance and chromatin regulation. A few terms (e.g., SOS response) may be annotations or cross-species noise, but the core theme is nuclear DNA maintenance and chromatin remodeling.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009432","count":4},{"id":"GO:0006268","count":3},{"id":"GO:0006311","count":2},{"id":"GO:0071894","count":2},{"id":"GO:0006306","count":2}]},{"hash":"1205641846995010868","title":"Embryonic organogenesis (brain, heart, placenta)","description":"This cluster centers on organ development, with GO terms for hippocampus and cerebellar cortex development, heart development, and placenta morphogenesis, plus associated transcriptional regulation. The proteins appear to participate in embryonic organ formation across neural and cardiac tissues, rather than a single cohesive pathway.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0021766","count":2},{"id":"GO:0043433","count":2},{"id":"GO:0033138","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0021695","count":2}]},{"hash":"150242799912452030","title":"TGF-\u03b2/SMAD signaling regulation","description":"The top GO terms point to negative regulation of TGF-\u03b2 receptor signaling and SMAD complex activity, plus cellular responses to TGF-\u03b2 and a dephosphorylation step, all suggesting phosphatase-mediated modulation of the TGF-\u03b2/SMAD pathway. Some NF-\u03baB cross-talk terms appear, but the strongest theme is TGF-\u03b2 signaling regulation; a few other terms likely reflect annotation noise. ","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030512","count":3},{"id":"GO:0042347","count":3},{"id":"GO:0035970","count":3},{"id":"GO:0061191","count":3},{"id":"GO:0010991","count":3}]},{"hash":"1709617579093598227","title":"Ubiquitination and antiviral innate immunity","description":"The cluster is enriched for ubiquitination-related GO terms (K63-linked ubiquitination, protein autoubiquitination, protein ubiquitination) and innate antiviral defense terms (defense response to virus, innate immune response), suggesting a module centered on ubiquitin-mediated regulation of immune responses to viral threats. Some related terms (response to vitamin D, histone catabolic process) appear as ancillary links but do not override the dominant ubiquitination/innate-immunity theme.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070534","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0051607","count":3},{"id":"GO:0033280","count":3},{"id":"GO:0016567","count":3}]},{"hash":"695356517377554020","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:1902187","count":3},{"id":"GO:0046597","count":2},{"id":"GO:0061158","count":2},{"id":"GO:0035372","count":2}]},{"hash":"1279847228692647710","title":"Unknown","description":"The listed GO terms cover development, peroxisomal import, transcriptional and chromatin regulation, immune tolerance, and general regulatory processes, with no single coherent function tying the five proteins together. Therefore no specific, representative label can be assigned.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060669","count":1},{"id":"GO:0016558","count":1},{"id":"GO:0046621","count":1},{"id":"GO:0000122","count":1},{"id":"GO:2001040","count":1}]},{"hash":"1591872177497557032","title":"Ubiquitin-Dependent Protein Degradation","description":"The top GO terms cluster around ubiquitination-driven proteolysis, including ubiquitin-dependent protein catabolic process, autoubiquitination, K48-linked ubiquitination, and ERAD pathways, suggesting these proteins primarily participate in tagging and degrading substrates. Some terms about peroxisome import and X-chromosome processes appear ancillary or multifunctional annotations, but the dominant theme is ubiquitin-mediated protein turnover and receptor/quality-control degradation. ","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016558","count":2},{"id":"GO:0060816","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0030433","count":2}]},{"hash":"1191832227545043024","title":"Proteostasis and Complex Assembly","description":"The cluster is driven by GO terms related to protein folding and quality control (response to unfolded protein; chaperone-dependent protein refolding) and to protein complex formation (protein heterooligomerization), suggesting a shared function in maintaining protein homeostasis and assembling multiprotein complexes. Other terms (histone modification, snoRNP assembly, photoreceptor localization, leptin signaling) appear less cohesive and may reflect annotation noise or multi-functional proteins. Overall, proteostasis and complex assembly is the most consistent theme.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:0006986","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0051291","count":2},{"id":"GO:0061087","count":2}]},{"hash":"1916067622102527588","title":"Multisubstrate Transmembrane Transport","description":"The GO terms cluster around transport across the plasma membrane for diverse substrates (xenobiotics, sugars, ions, and metabolites) including glucose, nitrate, urate, selenite, and neurotransmitter loading, indicating a cohesive theme of broad substrate transmembrane transport likely by membrane transport proteins.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098700","count":4},{"id":"GO:0042908","count":4},{"id":"GO:0044381","count":4},{"id":"GO:0035435","count":4},{"id":"GO:0006855","count":4}]},{"hash":"1676956019647384687","title":"Nuclear DNA replication and chromatin regulation","description":"This cluster centers on nuclear genome maintenance: DNA replication (primer synthesis, unwinding), DNA damage response (SOS), DNA methylation, chromatin remodeling (histone ubiquitination, nucleosome mobilization), and related nuclear processes (protein import, mRNA surveillance). A single neural term appears as noise, but the dominant signal ties to DNA replication/repair and chromatin regulation.","confidence":"Medium","size":5,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006306","count":5},{"id":"GO:0006269","count":5},{"id":"GO:0009432","count":5},{"id":"GO:0006268","count":5},{"id":"GO:0006311","count":4}]},{"hash":"1926783721380816391","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060149","count":1},{"id":"GO:0000467","count":1},{"id":"GO:0071035","count":1},{"id":"GO:0070481","count":1},{"id":"GO:0070651","count":1}]},{"hash":"290646329805711059","title":"Diverse metabolism and signaling","description":"The top GO terms cover several distinct metabolic processes (retinal/retinol, progesterone, norepinephrine, arabinose), a cellular stress response (methylglyoxal), water homeostasis, and regulatory signaling (JAK-STAT) with a note on apoptotic regulation. The absence of links between proteins and the broad spread of functions suggest a general mix of metabolic activities and signaling rather than a single cohesive pathway, hence this broad label.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042574","count":2},{"id":"GO:0042572","count":2},{"id":"GO:0097238","count":1},{"id":"GO:0042448","count":1},{"id":"GO:0003091","count":1}]},{"hash":"1624466981818864267","title":"Unknown","description":"The five proteins are associated with a highly diverse set of GO terms, including bacterial flagellum assembly, arginine homeostasis, angiogenesis and endothelial migration, multiple proton-gradient\u2013driven ATP synthesis processes, transcription regulation/termination, and vacuolar acidification. This mix does not point to a single coherent function or pathway, so a confident, representative label cannot be assigned.","confidence":"","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0044780","count":1},{"id":"GO:0090465","count":1},{"id":"GO:0043536","count":1},{"id":"GO:0042776","count":1},{"id":"GO:0001525","count":1}]},{"hash":"1246434477141950436","title":"Glycan and sugar biosynthesis","description":"The top terms cluster around glycosylation and carbohydrate metabolism, including mannosylation, protein glycosylation in the ER, GPI anchor biosynthesis, and other glycan-related biosynthetic processes, plus sugar metabolic processes like sucrose and starch biosynthesis. The presence of mycothiol and bacillithiol biosynthesis adds a broader biosynthesis theme for sugar-derived metabolites and redox cofactors in bacteria. Overall, the cluster is best described as glycan and carbohydrate biosynthesis.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097502","count":1},{"id":"GO:0010125","count":1},{"id":"GO:0009413","count":1},{"id":"GO:0033577","count":1},{"id":"GO:0006506","count":1}]},{"hash":"628042326519325478","title":"Protein Synthesis and RNA Decay","description":"Most terms converge on translation processes (translational initiation, elongation, termination, and general translation) and on mRNA metabolism (nuclear export of ribosomal subunits, deadenylation-dependent decay). The inclusion of selenocysteine incorporation further supports a focus on specialized translation. A pair of terms like glial cell proliferation and response to antibiotic may reflect broader cellular context or indirect effects, but the dominant signal across the cluster points to the protein synthesis machinery and RNA turnover.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001514","count":2},{"id":"GO:0006413","count":2},{"id":"GO:0014009","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0006415","count":2}]},{"hash":"334935819527548870","title":"Pseudouridine RNA Modification and Translation Initiation","description":"The cluster is driven by GO terms for tRNA and rRNA pseudouridine synthesis (pseudouridylation) and by translation-related processes, including translation initiation and formation of initiation complexes. This points to a cohesive function in RNA modification and the initiation phase of protein synthesis. While there are some metal detoxification terms present, they appear as minor annotations relative to the core RNA modification/translation theme.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031119","count":1},{"id":"GO:0098849","count":1},{"id":"GO:0010273","count":1},{"id":"GO:0000455","count":1},{"id":"GO:0010038","count":1}]},{"hash":"632671370240231683","title":"Unknown","description":"The top GO terms are cobalamin biosynthetic process and protein-containing complex assembly, each supported by only one protein and with no connecting edges, giving no clear single functional theme for the cluster. Therefore a definite label cannot be assigned with confidence.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":1},{"id":"GO:0006461","count":1}]},{"hash":"652969760910961375","title":"Actin Dynamics and Cell Motility Regulation","description":"This cluster's GO terms cluster around actin cytoskeleton remodeling\u2014regulation of actin filament assembly, barbed-end capping, and localization to the cell leading edge\u2014together with regulation of cell motility and related polarization processes. While oxidative stress and interleukin-1 responses appear, the dominant theme is actin-driven cytoskeletal dynamics governing cell migration.","confidence":"High","size":5,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0070301","count":2},{"id":"GO:0008360","count":1},{"id":"GO:0032232","count":1},{"id":"GO:2000147","count":1},{"id":"GO:0051511","count":1}]},{"hash":"292643595364973790","title":"Light-harvesting and light-response proteins","description":"The top GO terms cluster around photosynthesis and light-response processes, including nonphotochemical quenching, light harvesting in photosystems I and II, and responses to blue, red, far-red, and high/low light. This points to proteins involved in capturing and regulating light energy during photosynthesis, hence a label focusing on light harvesting and light responsiveness is appropriate.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010196","count":1},{"id":"GO:0009768","count":1},{"id":"GO:0009637","count":1},{"id":"GO:0010218","count":1},{"id":"GO:0071486","count":1}]},{"hash":"1818783501390306814","title":"Unknown","description":"No single shared function emerges: GO terms span endocytosis, extracellular transport, transcriptional regulation, and developmental processes (ureteric bud and CNS), each with only one occurrence. With edges = 0 and no cohesive theme, a meaningful cluster label cannot be assigned.","confidence":"","size":5,"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:0048662","count":1},{"id":"GO:0001658","count":1},{"id":"GO:0043392","count":1}]},{"hash":"49285705882956205","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904582","count":1},{"id":"GO:2000766","count":1},{"id":"GO:0043029","count":1},{"id":"GO:0061158","count":1},{"id":"GO:0031086","count":1}]},{"hash":"411551409324575372","title":"Unknown","description":"Top terms span very different biological areas (antibiotic biosynthesis, ubiquitin recycling, proteolysis regulation, mitochondrial respiration, insulin signaling, protein heterooligomerization, aerobic respiration, PQQ biosynthesis, pheromone maturation, viral process) with no clear unifying function or pathway. The network shows no edges, so there is no shared function tying the proteins together. Therefore a specific, representative label cannot be assigned; Unknown.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":2},{"id":"GO:0010992","count":1},{"id":"GO:0045861","count":1},{"id":"GO:0006122","count":1},{"id":"GO:0008286","count":1}]},{"hash":"308925848852436981","title":"Bacterial glycan biosynthesis and sugar metabolism","description":"These proteins\u2019 GO terms cluster around sugar metabolism (GDP-mannose and galactose metabolic processes) and cell-surface glycan assembly (O antigen and lipopolysaccharide biosynthetic processes), suggesting a shared function in bacterial glycan biosynthesis and related carbohydrate metabolism. Some other listed catabolic processes are peripheral to this core theme. ","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019673","count":1},{"id":"GO:0033212","count":1},{"id":"GO:0055114","count":1},{"id":"GO:1902987","count":1},{"id":"GO:0009243","count":1}]},{"hash":"790136048720137536","title":"Metabolic Diversity: Lipid/Valine Catabolism and Quinone Biosynthesis","description":"These proteins show enrichment for multiple metabolism-related processes, including fatty acid beta-oxidation, valine and phenylacetate catabolism, and biosynthesis of quinones (menaquinone, phylloquinone) as well as antibiotic biosynthesis. The common thread is broad metabolic capability, spanning both catabolic pathways and specialized biosynthesis (quinones and antibiotics), rather than a single, cohesive pathway. ","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006635","count":1},{"id":"GO:0006574","count":1},{"id":"GO:0017000","count":1},{"id":"GO:0009234","count":1},{"id":"GO:0042372","count":1}]},{"hash":"2135149153887627581","title":"Unknown","description":"This cluster has no GO terms listed, so there is no identifiable shared function or process to name it; without functional annotations, the 5 proteins and their network connections cannot be linked to a cohesive biological theme.","confidence":"","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[]},{"hash":"321682736978196212","title":"Unknown","description":"The cluster has 5 proteins but no GO terms are shown and no common functional signal emerges; therefore a reliable label cannot be inferred.","confidence":"","size":5,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[]},{"hash":"1926663766231202877","title":"Morphogenesis Across Tissues","description":"The most representative terms point to morphogenesis across multiple tissues (hippocampus development, atrial septum morphogenesis, embryonic placenta morphogenesis), suggesting the cluster relates to developmental shaping in different organs. Other terms (protein turnover via the N-end rule pathway, leucine response, drug response) are more ancillary and do not form a single cohesive function for all members. Thus, the label captures the strongest shared theme, but overall support is limited.","confidence":"Low","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071233","count":1},{"id":"GO:1901718","count":1},{"id":"GO:0071596","count":1},{"id":"GO:0021766","count":1},{"id":"GO:0060669","count":1}]},{"hash":"2102868052240108671","title":"Neural development and kinase signaling regulation","description":"The cluster shows enrichment in forebrain development and multiple terms tied to regulation of kinase activity (positive/negative regulation, autophosphorylation, GTPase activity), plus mitotic cycle and proliferation hints. Together these suggest a theme of neural development with coordinated signaling pathway control, despite some broader terms like mRNA transport. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0071456","count":2}]},{"hash":"1418880980380115153","title":"Neuronal development and GABAergic signaling","description":"GO terms emphasize neural development and inhibitory signaling (dendrite morphogenesis; midbrain dopaminergic neuron differentiation; GABAergic synaptic transmission), with other terms reflecting general cellular processes. The neural-centric terms dominate, suggesting proteins involved in neuronal maturation and inhibitory signaling, though some noise exists.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0043552","count":2},{"id":"GO:0006813","count":2},{"id":"GO:0048813","count":2},{"id":"GO:0016032","count":1}]},{"hash":"809954274460157868","title":"Unknown","description":"The GO terms are diverse (exocytosis regulation, phosphorylation, metabolism, and multiple differentiation processes) with no clear, cohesive function tying the four proteins together, so a specific label cannot be confidently assigned.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045920","count":2},{"id":"GO:0006186","count":2},{"id":"GO:0006228","count":2},{"id":"GO:0018106","count":2},{"id":"GO:0010976","count":2}]},{"hash":"578255554074365469","title":"Proteostasis and protein quality control","description":"This cluster centers on protein maintenance and turnover: proteasome assembly, unfolding/refolding by chaperones, ubiquitin-mediated proteolysis, and ribosome quality control (nonfunctional rRNA decay). A few terms touch on energy and organelle protein targeting, but the dominant theme is proteostasis.","confidence":"Medium","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006272","count":4},{"id":"GO:0070682","count":4},{"id":"GO:1903007","count":4},{"id":"GO:2001171","count":4},{"id":"GO:1903724","count":4}]},{"hash":"1828983399525522509","title":"Polyamine and collagen biosynthesis","description":"The top GO terms are dominated by spermidine biosynthesis and putrescine biosynthesis, indicating polyamine biosynthesis as a central function. The presence of collagen biosynthetic process and other biosynthetic terms suggests a broader role in synthesizing extracellular matrix components and related molecules; xenobiotic and metal ion response terms appear as ancillary annotations.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0008295","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0032964","count":2},{"id":"GO:0033388","count":2},{"id":"GO:0070207","count":2}]},{"hash":"1628112904543604032","title":"Meiotic DSB Formation and Repair","description":"The top GO terms explicitly describe meiotic double-strand break formation and repair during recombination, which is the clearest shared function among the proteins. While other terms touch on signaling and trafficking, the dominant signal points to meiotic recombination processes, especially DSB formation and repair.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010780","count":4},{"id":"GO:1990918","count":4},{"id":"GO:0098609","count":4},{"id":"GO:0051533","count":4},{"id":"GO:0060316","count":4}]},{"hash":"1227407705956567939","title":"Protein quality control and autophagy","description":"The cluster shows strong representation of proteostasis-related processes: protein sumoylation, ERAD, aggrephagy, and autophagosome maturation, which together point to protein quality control and turnover. There are additional, less central terms related to signaling regulation and cell-cycle/DNA repair, but the core theme aligns with maintaining protein homeostasis.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0016925","count":2},{"id":"GO:0034140","count":2},{"id":"GO:1904378","count":2},{"id":"GO:0035973","count":2}]},{"hash":"52101427855345201","title":"Unknown","description":"GO terms point to mitochondrial metabolism and apoptosis (fatty acid beta-oxidation, propionyl-CoA biosynthetic process, and regulation of mitochondrial membrane permeability) but also include sporulation and organ development terms, yielding a highly heterogeneous set with no single shared function.","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006635","count":3},{"id":"GO:0009725","count":3},{"id":"GO:1902109","count":3},{"id":"GO:1902860","count":3},{"id":"GO:0014070","count":3}]},{"hash":"132170220214008064","title":"RNA and protein methylation","description":"This cluster centers on methylation-related processes: tRNA wobble uridine modification, rRNA methylation, and various protein methylations (N-terminal, arginine). Although there are additional biosynthetic and other processes present, the strongest and most coherent signal is RNA- and protein-methylation activity, suggesting a set of methyltransferase\u2013type functions driving the cluster.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0039654","count":1},{"id":"GO:0002098","count":1},{"id":"GO:0019919","count":1},{"id":"GO:1901052","count":1},{"id":"GO:0009102","count":1}]},{"hash":"1445396601633385473","title":"Neuronal proteostasis and ER stress regulation","description":"The dominant GO terms point to protein quality control and stress response pathways: regulation of proteasomal degradation (both inhibition and promotion), ubiquitin-dependent proteolysis, ER-associated degradation and unfolded protein response, and ER stress\u2013related apoptotic signaling. These components tie together around maintaining protein homeostasis, especially in neural contexts, with some additional neuronal development signals present. Overall, a coherent theme is proteostasis regulation with links to ER stress and cell fate in neurons.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1902260","count":4},{"id":"GO:1902236","count":4},{"id":"GO:0043433","count":4},{"id":"GO:0014070","count":4},{"id":"GO:0034140","count":4}]},{"hash":"727625031127326697","title":"Cell cycle transcription and replication control","description":"The listed GO terms cluster around cell cycle regulation and transcriptional control, including G2/M transcription, DNA replication initiation, and mitotic spindle checkpoint signaling, with supporting signals in RNA processing and chromatin regulation. While some terms relate to tissue-specific processes and signaling pathways, the core theme is regulation of proliferation through transcriptional and replication control.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0033624","count":2},{"id":"GO:0051237","count":2},{"id":"GO:0090282","count":2},{"id":"GO:0021685","count":2},{"id":"GO:0044810","count":2}]},{"hash":"160786718591988881","title":"ER Protein Folding and Redox Stress Response","description":"The top GO terms point to endoplasmic reticulum\u2013associated protein folding and responses to oxidative stress, including redox homeostasis and detoxification, suggesting a cluster centered on ER protein quality control under oxidative conditions. Some terms (viral process, transcription regulation) are less cohesive with this theme, but the dominant signals support ER folding combined with redox/stress management. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034975","count":1},{"id":"GO:0018401","count":1},{"id":"GO:0045454","count":1},{"id":"GO:0043388","count":1},{"id":"GO:1903206","count":1}]},{"hash":"74862497811095740","title":"DNA replication and meiotic recombination","description":"Based on the top GO terms, the proteins in this cluster show a stronger association with DNA replication and meiotic recombination processes (DNA replication; meiotic DSB formation and repair). Other terms appear only once and likely reflect secondary or incidental functions, so the core theme is genome maintenance during replication and meiosis.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0010780","count":1},{"id":"GO:1990918","count":1},{"id":"GO:0098609","count":1},{"id":"GO:0051533","count":1}]},{"hash":"1342785098589530159","title":"Metabolic Pathways: Fatty acid and amino acid catabolism","description":"This cluster shows enrichment for fatty acid beta-oxidation and various amino acid/phenylacetate catabolic processes, along with biosynthesis steps for quinones and antibiotics. The common thread is metabolism\u2014both energy-production pathways and secondary metabolite biosynthesis\u2014across bacteria, suggesting these proteins function as metabolic enzymes involved in diverse pathways.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006635","count":4},{"id":"GO:0006574","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0009234","count":4},{"id":"GO:0042372","count":4}]},{"hash":"842771923849357323","title":"RNA and protein methyltransferases","description":"This cluster is dominated by GO terms for methylation across RNA (rRNA, tRNA wobble) and proteins (peptidyl-lysine/arginine, N-terminal glycine), with an additional link to chromatin regulation via rDNA heterochromatin formation. The shared theme is enzymatic methylation activities influencing RNA processing, translation, and chromatin state.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031167","count":3},{"id":"GO:0018013","count":3},{"id":"GO:0000183","count":3},{"id":"GO:0018023","count":3},{"id":"GO:0018027","count":3}]},{"hash":"174264217315143762","title":"Plant Telomere Maintenance and Shelterin Assembly","description":"The top terms cluster around telomere biology: negative regulation of protein localization to telomeres, positive regulation of shelterin complex assembly, telomeric loop formation, and G-quadruplex DNA formation. These collectively point to a coherent theme of telomere maintenance in plants, with a few auxiliary terms reflecting broader cellular contexts. ","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904850","count":2},{"id":"GO:1904792","count":2},{"id":"GO:0071919","count":2},{"id":"GO:0031627","count":2},{"id":"GO:0009723","count":2}]},{"hash":"2233941979362019204","title":"Endoplasmic reticulum protein folding and ERAD","description":"The cluster shows enrichment for ER-associated protein folding and quality-control processes (ER folding, chaperone cofactor-dependent refolding, and ERAD-related terms), suggesting a theme around ER proteostasis. The presence of a mix of unrelated terms (DNA replication, axon guidance, various catabolic processes) makes the signal weak, so the label is plausible but not strongly supported.","confidence":"Low","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070389","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0031290","count":2}]},{"hash":"408408790029269142","title":"Virus life cycle","description":"The proteins are enriched for GO terms across multiple stages of viral infection and replication (uncoating, genome replication, virion assembly, membrane fusion, release, and overall viral life cycle). While a few general terms appear, the dominant theme ties to viral entry, replication, assembly, and propagation.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":"protein folding","top_go_terms":[{"id":"GO:0006457","count":3},{"id":"GO:0019061","count":3},{"id":"GO:0006278","count":3},{"id":"GO:0010849","count":3},{"id":"GO:0044829","count":3}]},{"hash":"819051563766168366","title":"Spliceosome Assembly and Translation Initiation","description":"The GO terms center on spliceosome assembly, alternative mRNA splicing, and splice-site recognition, plus formation of translation preinitiation complexes and eIF4F complex assembly, with IRES-dependent initiation. This points to a cluster of proteins involved in RNA processing and the early steps of translation, consistent with a coherent RNA-processing/translation initiation module. The inclusion of ncRNA-mediated silencing terms suggests additional regulation of mRNA fate.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":1},{"id":"GO:0016556","count":1},{"id":"GO:0034462","count":1},{"id":"GO:0000380","count":1},{"id":"GO:0001731","count":1}]},{"hash":"1359213915097449732","title":"Ubiquitin-regulated signaling and cell fate","description":"This cluster centers on ubiquitination (protein ubiquitination and polyubiquitination) and broad regulatory themes\u2014cell cycle control, apoptosis/necroptosis regulation, transcriptional regulation, immune signaling (TLR), and responses to vitamin D, mechanical cues, and calcium. Taken together, this suggests proteins acting as regulators that link ubiquitin turnover to signaling and cell fate decisions, rather than a single specific pathway.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033280","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0000209","count":2},{"id":"GO:0071157","count":2},{"id":"GO:0060544","count":2}]},{"hash":"1558358309423999123","title":"Fatty acid metabolism and energy production","description":"This cluster is dominated by GO terms for fatty acid and CoA-related metabolism (malonyl-CoA biosynthesis, long-chain fatty acid biosynthesis, acyl-CoA metabolic process) combined with central energy pathways (gluconeogenesis, pyruvate metabolism, ketone body biosynthesis). The overall theme points to lipid synthesis and energy generation, with a secondary, less central term for sodium ion transport. ","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006552","count":2},{"id":"GO:0006094","count":2},{"id":"GO:0006814","count":2},{"id":"GO:2001295","count":2},{"id":"GO:0042759","count":2}]},{"hash":"898866501959190015","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042273","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0000398","count":3}]},{"hash":"2235368857219480674","title":"Environmental stress response and gene regulation","description":"This cluster is enriched for GO terms related to responses to xenobiotic and other environmental stimuli (response to xenobiotic stimulus, response to cold, response to ethanol, response to herbicide, response to lipopolysaccharide) and includes regulatory processes such as positive regulation of chromatin binding and alternative mRNA splicing, suggesting a module that links environmental sensing to changes in gene expression. Some terms (thiamine diphosphate biosynthetic process, megakaryocyte differentiation) are less cohesive with the rest, but the dominant theme is stress-response and transcriptional/chromatin regulation.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":2},{"id":"GO:0009409","count":2},{"id":"GO:0035563","count":2},{"id":"GO:0009229","count":2},{"id":"GO:0045471","count":2}]},{"hash":"378961860255404890","title":"Proteostasis and protein turnover","description":"The cluster shows enrichment for protein unfolding, proteasome regulatory particle assembly, ubiquitin-related regulation (SCF complex disassembly, deubiquitinase activity), and peroxisomal protein import, all central to protein quality control and turnover. While a few terms relate to other cellular processes (DNA replication, centriole elongation), the dominant theme is maintaining proteome homeostasis, especially under stress, via degradation and processing pathways.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009086","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006272","count":1},{"id":"GO:0070682","count":1},{"id":"GO:1903007","count":1}]},{"hash":"333935877629851339","title":"Chromatin remodeling and transcription regulation","description":"Dominant GO terms point to nuclear gene expression control, with chromatin remodeling (GO:0043044) and transcription regulation (GO:0034244, GO:0090282) being the strongest signals. While there are additional terms related to cell cycle checkpoints and signaling (NF-kappaB) or tissue-specific processes, the core theme across the cluster appears to be chromatin-based regulation of transcription. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":2},{"id":"GO:0033624","count":1},{"id":"GO:0051237","count":1},{"id":"GO:0090282","count":1},{"id":"GO:0021685","count":1}]},{"hash":"75405142524629471","title":"Sensory Nervous System Development and Signaling","description":"This cluster shows a clear emphasis on nervous system functions and sensory processes: development, pain and touch perception, optic nerve organization, and calcium signaling, coupled with transcriptional regulation and nuclear export that support neuronal differentiation and signaling. The few heart-related GO terms likely reflect shared ion-channel and action-potential dynamics rather than a cardiac-specific function. Overall, the dominant theme is neural development and sensory signaling.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0019233","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0046827","count":2},{"id":"GO:0086045","count":2}]},{"hash":"707148384209645405","title":"Synaptic Vesicle Trafficking and Receptor Localization","description":"The cluster centers on vesicle trafficking and membrane fusion related to synaptic signaling: exocytic insertion of neurotransmitter receptors, regulation of synaptic vesicle priming and recycling, and receptor localization to the synapse. The inclusion of ER-to-Golgi vesicle transport and the acrosome reaction supports a broader vesicle trafficking/exocytosis theme, tying these proteins to synaptic receptor delivery and exocytic processes.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0098967","count":1},{"id":"GO:1903422","count":1},{"id":"GO:0007340","count":1},{"id":"GO:1902685","count":1},{"id":"GO:0001916","count":1}]},{"hash":"799377991920617417","title":"Growth Factor Signaling and Cell Cycle","description":"The top GO terms include FGFR signaling, insulin receptor signaling, trans-synaptic signaling, and various stimulus responses, suggesting a theme of growth-related signaling. Coupled with DNA replication and mitotic spindle organization, there is a clear connection to cell cycle processes. Overall, the proteins appear linked to signaling pathways that regulate growth and proliferation, with possible ties to neural development contexts.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0002741","count":3},{"id":"GO:0035607","count":3},{"id":"GO:0008286","count":3},{"id":"GO:0048679","count":3}]},{"hash":"1325931962540191209","title":"Ubiquitin-dependent regulation of innate immune signaling","description":"The top GO terms highlight ubiquitination processes (ubiquitin-dependent protein catabolic process, autoubiquitination, K63-linked ubiquitination) together with immune-signaling regulation (negative regulation of type I interferon production, negative regulation of RIG-I signaling, and regulation of the JNK cascade). This points to a cluster of proteins that modulate antiviral responses through ubiquitin-mediated pathways, possibly dampening RIG-I/IFN signaling and affecting MAPK/JNK activity. A few terms about ERAD or chromatin modification appear incidental.","confidence":"High","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0032480","count":2},{"id":"GO:0070534","count":2},{"id":"GO:0046328","count":2}]},{"hash":"299750916173778822","title":"Unknown","description":"The four proteins show a mix of nuclear processes (DNA methylation, histone ubiquitination, nucleosome mobilization, RNA processing) along with a few neuronal/behavioral terms, and several annotations are marked obsolete. There isn\u2019t a clear, shared function tying the majority of terms together, so there isn\u2019t a distinct, interpretable theme to name the cluster.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006311","count":2},{"id":"GO:0071894","count":2},{"id":"GO:0006306","count":2},{"id":"GO:0017038","count":2},{"id":"GO:0071049","count":2}]},{"hash":"1589581751465802677","title":"Transcription Regulation and Histone Modification","description":"The GO terms cluster around control of gene expression, including DNA-templated transcription and RNA polymerase II\u2013mediated transcription, with hints of chromatin state regulation via histone demethylation. Although several terms are marked obsolete, they collectively imply transcriptional regulation and chromatin remodeling, with developmental processes like myoblast differentiation and vasculogenesis that are commonly governed by transcription networks.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042264","count":2},{"id":"GO:0042265","count":2},{"id":"GO:0045663","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0070544","count":2}]},{"hash":"856506281772939959","title":"Ubiquitin-Dependent Protein Degradation","description":"The top terms point to ubiquitin-centric processes: ubiquitin-dependent ERAD, autoubiquitination, K63-linked ubiquitination, SCF complex assembly, and ubiquitin-driven protein catabolism, indicating a cluster of proteins involved in tagging substrates for degradation and proteostasis. ","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0070534","count":2},{"id":"GO:0036205","count":1},{"id":"GO:0046597","count":1}]},{"hash":"1189522826399060311","title":"Unknown","description":"The top terms span distinct processes: spliceosome/RNA processing and mitochondrial respiration/ETC assembly. With no shared function or interactions evident (edges 0, no triangles) and only one term per function, there isn\u2019t a cohesive theme to name beyond Unknown. ","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000387","count":1},{"id":"GO:0006396","count":1},{"id":"GO:1902600","count":1},{"id":"GO:0009060","count":1},{"id":"GO:0006122","count":1}]},{"hash":"1126314456002068668","title":"Ubiquitin-Proteasome Proteostasis","description":"The cluster shows strong enrichment for ubiquitin-dependent degradation and proteasomal pathways (SCF-dependent ubiquitin-proteasome catabolic process; protein ubiquitination; ERAD). Other terms touch on translation initiation/reinitiation and muscle differentiation, suggesting a proteostasis-focused module that links protein quality control with protein synthesis in muscle contexts.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0033280","count":2},{"id":"GO:0000715","count":2}]},{"hash":"1452487818146864737","title":"Ufmylation and Autophagy","description":"The top GO terms point to protein modification by small protein conjugation and, notably, K69-linked ufmylation, along with macroautophagy. This suggests a coherent theme around ubiquitin-like, ufmylation-dependent regulation of autophagy, possibly in response to cellular stress (hyperoxia). Other terms (tRNA thiolation, thiamine biosynthesis, cell cycle regulation) are more peripheral, but do not override the strongest signal linking ufmylation to autophagy, justifying the label as a small autophagy/ufe-modification\u2013focused cluster.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032446","count":1},{"id":"GO:0002143","count":1},{"id":"GO:0018192","count":1},{"id":"GO:0051726","count":1},{"id":"GO:0071455","count":1}]},{"hash":"1125501484186999791","title":"Transcription and ribosome biogenesis with proteostasis control","description":"This cluster centers on core gene-expression processes (DNA-templated transcription, RNA polymerase I transcription) and ribosome biogenesis, with enrichment also for proteasomal protein catabolic regulation. The presence of signaling (Wnt, JNK) and mitochondrial fission terms suggests broader regulatory coordination of transcription, protein turnover, and cellular stress responses, rather than a single narrow function. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000266","count":2},{"id":"GO:1903542","count":2},{"id":"GO:0032436","count":2},{"id":"GO:0090394","count":2}]},{"hash":"661668819239138663","title":"RNA splicing and translation initiation","description":"This cluster centers on post-transcriptional RNA processing and translation control, with strong signals for spliceosome-related activities (alternative splicing, splice site recognition, processome assembly) alongside components of translation initiation (preinitiation complex formation, eIF4F complex assembly, IRES-dependent initiation) and RNA silencing pathways (ncRNA- and miRNA-mediated silencing). The shared theme is regulation of mRNA fate from splicing through initiation and silencing. ","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":2},{"id":"GO:0016556","count":2},{"id":"GO:0034462","count":2},{"id":"GO:0000380","count":2},{"id":"GO:0001731","count":2}]},{"hash":"1823615064612224305","title":"Post-transcriptional regulation and P-body dynamics","description":"The top GO terms cluster around mRNA processing and translation control, especially P-body assembly, cytoplasmic mRNA processing body regulation, and negative regulation of translational initiation, with related neuronal and circadian aspects like circadian regulation of translation, habituation, and synaptic plasticity. This suggests a cohesive role in RNA metabolism and post-transcriptional regulation within neurons, centered on RNA granules and translational control.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043007","count":1},{"id":"GO:1905833","count":1},{"id":"GO:0033962","count":1},{"id":"GO:0045947","count":1},{"id":"GO:0010603","count":1}]},{"hash":"559383706755522212","title":"Ribosome Biogenesis and Translation","description":"Most terms point to ribosome production and function: rRNA pseudouridylation, ribosomal subunit biogenesis and export, and translation. While a couple terms (TNF response, base-excision repair, riboflavin biosynthesis) appear less central or reflect shared annotations, the dominant cluster signal is ribosome assembly and protein synthesis.","confidence":"High","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0031119","count":1},{"id":"GO:0000455","count":1},{"id":"GO:0006407","count":1},{"id":"GO:0061481","count":1},{"id":"GO:0006412","count":1}]},{"hash":"2205497292269436228","title":"Diverse carbon source metabolism","description":"This cluster shows broad metabolic processing of multiple carbon sources, including glycerol, alcohols, sugars, and lipids, as well as general carbon utilization. The mixed set of catabolic and biosynthetic GO terms suggests a general metabolic capacity rather than a single, cohesive pathway.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0015993","count":2},{"id":"GO:0019564","count":2},{"id":"GO:0042846","count":2},{"id":"GO:0006650","count":2},{"id":"GO:0008654","count":2}]},{"hash":"2085568591597401799","title":"Zinc Ion Homeostasis and Transport","description":"These proteins are enriched for GO terms tied to zinc ion response, zinc ion homeostasis, zinc transmembrane transport, and detoxification of zinc, with some related iron/cobalt ion terms. The shared theme is regulation and transport of zinc ions, i.e., zinc homeostasis and detoxification.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010043","count":2},{"id":"GO:1903874","count":2},{"id":"GO:0006877","count":2},{"id":"GO:0006882","count":2},{"id":"GO:0098849","count":2}]},{"hash":"214651154242221082","title":"Ribosome Biogenesis and SSU rRNA Maturation","description":"GO:0042254 and GO:0030490 indicate ribosome biogenesis and maturation of small-subunit rRNA, suggesting these proteins share a role in assembling the ribosome's small subunit; this reflects a cohesive functional theme for the cluster despite no observed edges.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":1},{"id":"GO:0030490","count":1}]},{"hash":"1900988124459896872","title":"Arp2/3-mediated actin nucleation and ER-Golgi trafficking","description":"Based on the top GO terms, this cluster centers on cytoskeletal dynamics and intracellular transport: positive regulation of Arp2/3 complex\u2013mediated actin nucleation and endoplasmic reticulum to Golgi vesicle\u2013mediated transport, with supportive signals from GTPase activity regulation and ubiquitination pathways. While some terms relate to growth or defense, the clearest common function is actin remodeling linked to vesicle trafficking, suggesting a cytoskeletal\u2013trafficking module.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035264","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0001731","count":2},{"id":"GO:2000601","count":2}]},{"hash":"885543261600242875","title":"Histone Methylation and Chromatin Regulation","description":"Most GO terms point to histone H3 methylation at multiple lysines (K4, K9, K27, K79), indicating chromatin modification and epigenetic regulation as the core function of this cluster. The presence of a few ancillary terms (translation preinitiation complex formation, actin nucleation, ER-Golgi transport, ubiquitination) may reflect shared cellular processes or annotation noise, but do not override the dominant chromatin-related signal. Therefore, the cluster is best described as related to histone methylation and chromatin regulation.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051568","count":2},{"id":"GO:0001731","count":1},{"id":"GO:2000601","count":1},{"id":"GO:0051567","count":1},{"id":"GO:2001162","count":1}]},{"hash":"1269036082284207864","title":"Sodium and Proton Transmembrane Transport","description":"This cluster centers on transmembrane movement of ions, specifically sodium and protons, as indicated by GO:0035725 and GO:0015992. The shared theme is ion transport across membranes, consistent with transporter or pump activities, though only a couple of GO terms are present and there are no interactions shown.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035725","count":1},{"id":"GO:0015992","count":1}]},{"hash":"2088618102876343826","title":"Vacuolar transport and proton homeostasis","description":"The top GO terms are centered on vacuolar processes (vacuole organization, protein targeting to vacuole, vacuolar acidification) and proton/ion transport (proton transmembrane transport, proton motive force\u2013driven ATP synthesis), with mentions of copper and phosphate ion homeostasis. This suggests a cohesive theme around vacuolar function and ion/proton transport rather than a single enzyme activity, so a label focusing on vacuolar transport and proton/ion homeostasis is most representative.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051604","count":1},{"id":"GO:0006817","count":1},{"id":"GO:2000185","count":1},{"id":"GO:0006878","count":1},{"id":"GO:0006623","count":1}]},{"hash":"1300061754979522325","title":"Teichoic acid transport and peptidoglycan turnover","description":"The dominant GO terms point to teichoic acid transport and peptidoglycan catabolic/turnover processes, indicating a function in bacterial cell wall remodeling, likely in Gram-positive organisms. The obsolete pteridine term is not informative for the main theme. Despite few connections (2 edges, 0 triangles), the core theme remains coherent around cell wall metabolism.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042068","count":1},{"id":"GO:0015777","count":1},{"id":"GO:0016998","count":1},{"id":"GO:0009254","count":1},{"id":"GO:0009253","count":1}]},{"hash":"1993612321662277651","title":"Dendritic spine morphogenesis and Wnt/Rho signaling","description":"The terms point to neuronal development and synaptic structure, especially dendritic spine morphogenesis (GO:0060997) and signaling pathways that regulate cytoskeletal dynamics, such as Wnt signaling (GO:0016055) and Rho signaling (GO:0035023), with supporting roles from protein dephosphorylation and broader growth/signal-regulation terms. Some terms appear less related (defense response, angiogenesis), likely reflecting broader or promiscuous associations rather than a single cohesive function, but the core cluster centers on neuronal signaling and spine formation.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":2},{"id":"GO:0045766","count":2},{"id":"GO:0071333","count":2},{"id":"GO:0016055","count":2},{"id":"GO:0014068","count":2}]},{"hash":"1223998490081880415","title":"Unknown","description":"The Top Terms span plant biosynthesis and signaling (glucuronoxylan, arabinan, xylogalacturonan, plant cell wall biogenesis; salicylic acid signaling) and animal/vertebrate development (BMP signaling, endoderm development, embryonic fin and joint morphogenesis, heparin proteoglycan biosynthesis), with no clear, shared function or interaction pattern. There are no edges or coherent enrichment, so a single representative function cannot be assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035118","count":1},{"id":"GO:0010417","count":1},{"id":"GO:0009863","count":1},{"id":"GO:0035884","count":1},{"id":"GO:0008101","count":1}]},{"hash":"649800310246431776","title":"Bacterial cell envelope biosynthesis and division","description":"The GO terms cluster around synthesis of cell wall components (peptidoglycan biosynthesis, cell wall organization), carbohydrate metabolism for wall precursors, and lipid biosynthesis (fatty acid and sterol), plus regulation of cell shape and cell cycle/division. This points to a cohesive theme of growth through envelope construction and cell division in bacteria, rather than a single narrow pathway.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1902321","count":2},{"id":"GO:0042759","count":2},{"id":"GO:0008360","count":2},{"id":"GO:0009252","count":2},{"id":"GO:0005975","count":2}]},{"hash":"2213119155300316307","title":"Unknown","description":"There are no GO terms listed for this cluster, and the proteins have no recorded interactions (no edges or triangles), so there is no discernible shared function or thematic enrichment to assign a label. Without functional terms or connectivity, a specific, representative name cannot be inferred.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2000919555615935107","title":"Unknown","description":"The top GO terms are sparse and cover unrelated processes (obsolete oxidation-reduction; alkane catabolic process; GPCR-PLC signaling). With no connections or shared function among proteins, there is no coherent theme to define a meaningful label.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":1},{"id":"GO:0043448","count":1},{"id":"GO:0007200","count":1}]},{"hash":"1336538777702125804","title":"Neuronal GPCR Trafficking and Synaptic Priming","description":"The top GO terms emphasize vesicle-related processes (synaptic vesicle priming, GPCR internalization) and trafficking (endosome-to-lysosome transport) with associated ion transport, suggesting a theme of neuronal signaling and vesicle regulation. Some terms are peripheral (fucose metabolism, IL-18 signaling), but the core cluster aligns with neuronal GPCR trafficking and synaptic vesicle priming.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042354","count":1},{"id":"GO:0036065","count":1},{"id":"GO:0019303","count":1},{"id":"GO:0060180","count":1},{"id":"GO:1902824","count":1}]},{"hash":"1138197336784042685","title":"Transmembrane Transport of Small Molecules","description":"This cluster is dominated by GO terms for transmembrane transport of various substrates (glycerophosphodiesters, long-chain fatty acids into peroxisomes, amino acids, cysteine, thiamine), plus related membrane-associated processes like bacteriocin transport and cytochrome complex assembly. Although there are outliers (SOS response, obsolete terms), the common theme is proteins involved in moving diverse small molecules across membranes.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006490","count":1},{"id":"GO:0006486","count":1},{"id":"GO:0001407","count":1},{"id":"GO:0015910","count":1},{"id":"GO:0043213","count":1}]},{"hash":"1557837270079072571","title":"Lipid biosynthesis in mesoderm development","description":"This cluster features lipid biosynthetic terms (glycolipid and phospholipid processes) together with mesoderm development terms (paraxial mesoderm, somitogenesis) and Notch signaling regulation, suggesting a role in membrane lipid biosynthesis linked to early developmental patterning.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009247","count":1},{"id":"GO:0097502","count":1},{"id":"GO:0009405","count":1},{"id":"GO:0008654","count":1},{"id":"GO:0045747","count":1}]},{"hash":"2014766322319942901","title":"Unknown","description":"The top GO terms span DNA replication (leading strand elongation), proteostasis (proteasome assembly, protein unfolding), organelle import (peroxisome matrix), ribosome/gene expression quality control, and stress responses, with no single cohesive function binding all three proteins. Therefore a precise, representative label isn\u2019t identifiable beyond Unknown.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006272","count":3},{"id":"GO:0070682","count":3},{"id":"GO:1903007","count":3},{"id":"GO:0090305","count":3},{"id":"GO:2001171","count":3}]},{"hash":"1872496852246571526","title":"Actin Cytoskeleton and Cell Polarity","description":"The dominant GO terms point to actin filament polymerization and actomyosin-based structures (contractile ring, thin filaments) as well as processes governing cell shape and polarity, indicating a cluster centered on actin cytoskeleton organization and polarity-driven remodeling across cellular contexts. Peripheral terms like retina homeostasis and ascospore wall assembly are less central to this core function.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071963","count":3},{"id":"GO:0001895","count":3},{"id":"GO:0000011","count":3},{"id":"GO:0030476","count":3},{"id":"GO:1904623","count":3}]},{"hash":"1269836810347161997","title":"Meiotic DSB Repair and Recombination","description":"The strongest GO signals are meiotic double-strand break formation and repair, pointing to roles in meiotic recombination and DNA damage response. Other terms present are either less representative or indicate possible secondary functions, but the core theme is meiotic DNA processing.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1990918","count":2},{"id":"GO:0061587","count":2},{"id":"GO:0010780","count":1},{"id":"GO:0098609","count":1},{"id":"GO:0051533","count":1}]},{"hash":"313749580978039679","title":"Mitotic division and cytokinesis","description":"The top GO terms point to cell division and mitosis (cell cycle, mitotic spindle midzone assembly, mitotic cytokinesis, FtsZ-dependent cytokinesis, etc.), indicating a cohesive theme of division machinery; a couple terms like neuron migration and cellular response to interleukin-4 appear as less central annotations but do not override the core division-related signal.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0071353","count":3},{"id":"GO:1902408","count":3},{"id":"GO:0051256","count":3},{"id":"GO:0090529","count":3}]},{"hash":"2269186030614791675","title":"Denervation-induced muscle adaptation","description":"This cluster\u2019s strongest term is \u201cresponse to denervation involved in regulation of muscle adaptation,\u201d pointing to a muscle adaptation module triggered by denervation. Other terms touch on muscle fiber development and stress signaling, supporting a muscle-regulatory theme, though several chromatin-related terms and obsolete annotations add noise. Overall, the label captures the central muscle adaptation connection.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0014894","count":3},{"id":"GO:0031939","count":3},{"id":"GO:0006344","count":3},{"id":"GO:0061188","count":3},{"id":"GO:0032874","count":3}]},{"hash":"1226143056487255076","title":"Meiotic DSB Repair","description":"Two of the top GO terms directly point to meiotic double-strand break formation and repair during recombination, suggesting a meiosis-associated DNA processing function for this cluster. Other terms (cell adhesion, signaling, and vesicle transport) appear less cohesive with this theme, so the dominant signal is meiosis-related DNA repair. ","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010780","count":3},{"id":"GO:1990918","count":3},{"id":"GO:0098609","count":3},{"id":"GO:0051533","count":3},{"id":"GO:0060316","count":3}]},{"hash":"2248478580855314636","title":"mRNA splicing and translation initiation machinery","description":"The GO terms show strong signals for spliceosome-mediated mRNA processing (spliceosome assembly, splice site recognition, alternative splicing regulation) and for translation initiation complex formation (preinitiation complex, eIF4F assembly, IRES-dependent initiation). There are also indicators of RNA silencing regulation. Taken together, the cluster centers on post-transcriptional mRNA processing and the initiation of translation, with regulatory RNA silencing involved.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":1},{"id":"GO:0016556","count":1},{"id":"GO:0034462","count":1},{"id":"GO:0000380","count":1},{"id":"GO:0001731","count":1}]},{"hash":"1126721290415192391","title":"Calcium signaling & ER-Golgi trafficking","description":"The cluster shows clear enrichment for calcium signaling-related terms (positive regulation of calcineurin-NFAT signaling, ryanodine receptor/calcium release) and ER-to-Golgi vesicle transport, pointing to a core theme of calcium-regulated intracellular trafficking. While there are outliers related to meiosis and other processes, the strongest and most coherent signal across terms is calcium signaling connected to vesicle transport and translation regulation. Confidence: Medium","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010780","count":3},{"id":"GO:1990918","count":3},{"id":"GO:0098609","count":3},{"id":"GO:0051533","count":3},{"id":"GO:0060316","count":3}]},{"hash":"1069219839525625193","title":"Unknown","description":"The terms span metabolism (TCA cycle), transcription regulation, RNA localization, signaling pathways, chromosome maintenance, and tissue-specific processes, with no clear, shared function binding the cluster. The diversity and lack of a cohesive theme suggest this is a heterogeneous set rather than a distinct biological module. ","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":1},{"id":"GO:0033624","count":1},{"id":"GO:0051237","count":1},{"id":"GO:0090282","count":1},{"id":"GO:0021685","count":1}]},{"hash":"798767638579030625","title":"Proteostasis and ER Stress Regulation","description":"Most terms point to regulation of proteasome-mediated protein degradation and ER stress responses (proteostasis), including UPS/ubiquitin-dependent degradation and ERAD-related processes. While a few terms are obsolete or less connected (e.g., certain signaling or development terms), the dominant theme ties to cellular protein quality control under stress. Therefore this label captures the core function of the cluster.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1902260","count":3},{"id":"GO:1902236","count":3},{"id":"GO:0043433","count":3},{"id":"GO:0014070","count":3},{"id":"GO:0034140","count":3}]},{"hash":"184242292276685765","title":"Unknown","description":"The top GO terms span a mix of signaling, metabolic, stress response, hormone-related, and even organism-specific processes with no clear shared pathway tying the proteins together, making it hard to assign a cohesive, representative label.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051897","count":2},{"id":"GO:0009414","count":2},{"id":"GO:0097238","count":1},{"id":"GO:0042448","count":1},{"id":"GO:0003091","count":1}]},{"hash":"1432255253045173626","title":"Unknown","description":"Top terms are highly diverse, including fatty acid metabolism, ectoine biosynthesis, verruculogen biosynthesis, and vertebrate development, across bacteria, fungi, and animals, with no protein-protein edges. This lack of a coherent shared function across the cluster prevents a meaningful, specific label.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001561","count":2},{"id":"GO:0042400","count":2},{"id":"GO:1902181","count":2},{"id":"GO:0097089","count":2},{"id":"GO:0019491","count":2}]},{"hash":"5738830640372788","title":"Unknown","description":"The GO terms are a mix of lignin biosynthesis, vitamin B12 biosynthesis, several amino acid biosynthetic pathways, and protein methylation, with no unifying function across the proteins. Because the terms point to disparate, context-specific processes and there are no edges or coherent network structure, there is no reliable cluster-level function to name.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009809","count":1},{"id":"GO:0042135","count":1},{"id":"GO:0009236","count":1},{"id":"GO:0006479","count":1},{"id":"GO:0006584","count":1}]},{"hash":"1729788839487799359","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051402","count":3},{"id":"GO:0009089","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0006096","count":3},{"id":"GO:0008615","count":3}]},{"hash":"1557724247957901566","title":"Mitochondrial protein synthesis and tRNA charging","description":"The cluster centers on mitochondrial tRNA aminoacylation (asparaginyl/aspartyl/lysyl) and translation, pointing to mitochondrial protein synthesis as the core function, with non-specific or obsolete terms contributing little clarity.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071915","count":2},{"id":"GO:0072581","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0070145","count":2},{"id":"GO:0070146","count":2}]},{"hash":"1424268658660164684","title":"Embryonic brain and sensory organ morphogenesis","description":"The top GO terms cluster around development of neural and sensory structures in the embryo (subpallium, trigeminal ganglion, habenula, rhombomere 3, metencephalon, camera-type eye) and related morphogenetic processes (somitogenesis regulation, myoblast proliferation). This points to a cohesive theme of embryonic neural/sensory tissue development, justifying a label focused on brain and sensory organ morphogenesis rather than unrelated processes.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0021544","count":2},{"id":"GO:0060272","count":2},{"id":"GO:0061551","count":2},{"id":"GO:0014807","count":2},{"id":"GO:2000288","count":2}]},{"hash":"1635328626714679081","title":"Unknown","description":"The top GO terms are scattered across very different biological contexts: lignan biosynthesis/catabolism (pinoresinol, lariciresinol) hints at phenylpropanoid metabolism, but other terms point to O antigen biosynthesis, GDP-mannose metabolism, poly-hydroxybutyrate biosynthesis, ubiquinone biosynthesis, and nitrogen catabolite repression\u2014no single pathway or function ties all terms together. With zero edges and only individual annotations, there isn\u2019t a coherent theme to name a specific cluster. ","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001081","count":1},{"id":"GO:1902125","count":1},{"id":"GO:0019673","count":1},{"id":"GO:0055114","count":1},{"id":"GO:1902129","count":1}]},{"hash":"1959899561363596953","title":"Unknown","description":"The top terms span both bacterial lipopolysaccharide biosynthesis and various animal cardiac and neural processes, with additional oxidative stress and calcium signaling terms. This broad mix shows no single cohesive function tying the cluster, so a concise, representative label cannot be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":2},{"id":"GO:1901710","count":1},{"id":"GO:0003007","count":1},{"id":"GO:0086064","count":1},{"id":"GO:0055010","count":1}]},{"hash":"691003222163189506","title":"RNA Modification and Gene Expression","description":"This cluster centers on gene expression with involvement in transcription and translation, and is enriched for RNA modification processes (tRNA methylation, wybutosine biosynthesis) that can regulate translation. Peripheral terms like cobalamin biosynthesis and histone methylation are less representative but do not override the core theme of RNA metabolism linked to expression control.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0019919","count":1},{"id":"GO:0090398","count":1},{"id":"GO:0016049","count":1}]},{"hash":"1260903108961831465","title":"Methylation-Driven Biosynthesis and Dopamine Regulation","description":"Primarily characterized by several methylation terms (protein, tRNA, general methylation), indicating a methylation-centric cluster. The presence of dopamine/catecholamine metabolism and regulation terms suggests a neuromodulatory context that could relate to methylation status, while plant/secondary metabolite biosynthesis terms are present but less connected to the core theme.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":2},{"id":"GO:0009809","count":1},{"id":"GO:0032259","count":1},{"id":"GO:0006584","count":1},{"id":"GO:0042135","count":1}]},{"hash":"1797125736032568490","title":"Nervous System Sensory Perception and Glial Migration","description":"The terms strongly point to nervous-system roles: sensory perception of sound, rhodopsin biosynthetic process (vision), and astrocyte cell migration (glial involvement in CNS). While other terms (reproduction, catabolic processes) appear, they are less cohesive with the core sensory/neural theme, making this label a good representation of the cluster\u2019s main function.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019953","count":2},{"id":"GO:0008049","count":2},{"id":"GO:0008360","count":2},{"id":"GO:0007040","count":2},{"id":"GO:0042340","count":2}]},{"hash":"839626251534642063","title":"Cellular Metabolism and Energy Production","description":"The proteins show annotations for core metabolic processes, including glycolysis, mitochondrial electron transport, lipoate metabolism, beta-alanine biosynthesis, and thymidine catabolic turnover, pointing to an energy-production/metabolic theme. Some regulatory terms (chromatin binding, alternative splicing) appear but are less central, suggesting metabolism is the primary common function with incidental regulation-related annotations.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009106","count":1},{"id":"GO:0019483","count":1},{"id":"GO:0035563","count":1},{"id":"GO:0000380","count":1},{"id":"GO:0006120","count":1}]},{"hash":"1057161000594756180","title":"Nuclear RNA Processing and Splicing","description":"The GO terms cluster around nuclear RNA maturation: mRNA splicing via the spliceosome, spliceosomal snRNP assembly, and related mRNA processing steps (including nuclear import and rRNA maturation). This indicates a cohesive function in nuclear RNA processing and splicing, with some peripheral terms likely reflecting broader contextual roles. ","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":3},{"id":"GO:0051170","count":2},{"id":"GO:0008334","count":2},{"id":"GO:0033962","count":2},{"id":"GO:1990141","count":2}]},{"hash":"1486027558096664463","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006189","count":1},{"id":"GO:0009116","count":1},{"id":"GO:0009113","count":1},{"id":"GO:0052704","count":1},{"id":"GO:0033050","count":1}]},{"hash":"202770227202223286","title":"Transcription and cell cycle regulation","description":"These proteins collectively relate to regulation of gene expression and cell cycle control: transcription elongation regulation, DNA replication initiation, and chromatin/silencing mechanisms; canonical NF-kappaB signaling ties into broader transcriptional control, and spindle checkpoint signaling connects to mitosis. Some terms are tissue-specific (cerebellar granule layer organization, cholangiocyte proliferation), but the dominant theme is transcriptional and cell-cycle regulation.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0033624","count":1},{"id":"GO:0051237","count":1},{"id":"GO:0090282","count":1},{"id":"GO:0021685","count":1},{"id":"GO:0044810","count":1}]},{"hash":"1291657301559864873","title":"Cadmium-responsive ubiquitin-proteasome proteostasis","description":"The top terms are dominated by ubiquitination and proteasomal degradation (protein polyubiquitination and SCF-dependent ubiquitin-proteasome catabolic process) and a clear cellular response to cadmium ion, pointing to a proteostasis and metal-stress theme. Other terms are auxiliary (translation initiation, vesicle transport, actin nucleation), but the ubiquitin-proteasome and cadmium response signals are the strongest thread. ","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0001731","count":1},{"id":"GO:2000601","count":1}]},{"hash":"82636320440849670","title":"Unknown","description":"The GO terms are too diverse to imply a single shared function for this small cluster. While there are transcription- and nucleus-related terms (DNA-templated transcription and maintenance of protein location in the nucleus), other terms touch on metabolism and development with no clear unifying theme. Therefore there is no coherent label that accurately represents the cluster\u2019s function.","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1903212","count":1},{"id":"GO:2001172","count":1},{"id":"GO:0090180","count":1},{"id":"GO:0048147","count":1},{"id":"GO:0007275","count":1}]},{"hash":"1858970216528334872","title":"Spliceosome and Translation Initiation Machinery","description":"The GO terms point to RNA splicing and spliceosome assembly (alternative splicing, splice-site recognition, spliceosome regulation) and to translation initiation processes (preinitiation complex formation, eIF4F complex assembly, IRES-dependent initiation). This combination suggests a cluster centered on mRNA processing and the start of protein synthesis.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":1},{"id":"GO:0016556","count":1},{"id":"GO:0034462","count":1},{"id":"GO:0000380","count":1},{"id":"GO:0001731","count":1}]},{"hash":"2212121348447698069","title":"Xenobiotic and drug-response cluster","description":"This cluster is dominated by GO terms for cellular response to xenobiotic stimuli and response to cocaine, indicating a shared function in handling external chemical stress. Additional terms for transcription regulation, protein folding, and stress signaling suggest a broader stress-response program rather than a single tightly defined pathway, so the label centers on xenobiotic/drug response as the core theme.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":2},{"id":"GO:0042220","count":2},{"id":"GO:0043007","count":1},{"id":"GO:0006457","count":1},{"id":"GO:0010105","count":1}]},{"hash":"2239651706082343603","title":"Unknown","description":"Three proteins show a scattered set of GO terms, including stilbene catabolic process, regulation of actin filament depolymerization, dephosphorylation, carbohydrate metabolism, intracellular calcium homeostasis, zinc ion transport, lipopolysaccharide biosynthesis, and cellular response to ATP. There is no clear shared pathway or functional theme, and the small size with no edges makes it difficult to assign a coherent label.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046272","count":1},{"id":"GO:0030836","count":1},{"id":"GO:0046839","count":1},{"id":"GO:0016311","count":1},{"id":"GO:0071318","count":1}]},{"hash":"534219123162642491","title":"Unknown","description":"The listed GO terms span ubiquitination, translation initiation, actin nucleation, ER-to-Golgi vesicle transport, and a cellular response to leucine, with several terms marked obsolete. There is no clear, cohesive functional theme connecting these terms for this small cluster, so assigning a specific common function is not supported. ","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071233","count":1},{"id":"GO:1901718","count":1},{"id":"GO:0071596","count":1},{"id":"GO:0001731","count":1},{"id":"GO:2000601","count":1}]},{"hash":"1163451895768843222","title":"Ribosome Biogenesis and Subunit Export","description":"The top GO terms are dominated by ribosome biogenesis and ribosomal subunit export from the nucleus, including both large and small subunit biogenesis. These points strongly indicate a cluster centered on ribosome assembly and maturation. The cell cycle and division terms may reflect growth-coupled regulation but are secondary to ribosome production. Overall, the cluster appears representative of ribosome biogenesis processes.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0000055","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0000747","count":1},{"id":"GO:1903833","count":1}]},{"hash":"1479890111500251396","title":"MEP Terpenoid Biosynthesis and SA Defense","description":"The GO terms highlight plastidic terpenoid biosynthesis via the methylerythritol phosphate pathway and salicylic acid\u2013mediated systemic acquired resistance, suggesting a plant metabolism linked to defense. The combination points to production of defense-related terpenoids coupled with SA signaling, despite one obsolete term present in the list.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016114","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0019288","count":1},{"id":"GO:0009862","count":1}]},{"hash":"273751232535188632","title":"Unknown","description":"The top GO terms are highly diverse and include translation initiation (GO:0001731), actin nucleation (GO:2000601), various histone methylation terms (GO:0051567, GO:2001162, GO:0061087; all marked obsolete), ER-to-Golgi vesicle transport (GO:0006888), protein ubiquitination (GO:0000209), pigmentation (GO:0043473), aging (GO:0007568; obsolete), and mitotic spindle assembly (GO:0090307). This wide mix suggests no single shared function or theme linking the proteins; with only one edge and no cohesive pathway signal, the cluster cannot be assigned a meaningful, unified function.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":1},{"id":"GO:2000601","count":1},{"id":"GO:0051567","count":1},{"id":"GO:2001162","count":1},{"id":"GO:0061087","count":1}]},{"hash":"1459419650524869514","title":"Photosynthesis Light Harvesting and Light Response","description":"The GO terms cluster around photosynthesis and light-response processes, including nonphotochemical quenching, light harvesting in PSI/II, and responses to blue, red, and far-red light, plus high light. These proteins are best labeled as chloroplast light-harvesting/photoprotection components.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010196","count":1},{"id":"GO:0009768","count":1},{"id":"GO:0009637","count":1},{"id":"GO:0010218","count":1},{"id":"GO:0071486","count":1}]},{"hash":"97642494686243623","title":"Neuronal development and synaptic signaling","description":"The cluster\u2019s GO terms cluster around neural development and communication: axonogenesis, retinal ganglion cell axon guidance, and neurogenesis point to neuronal formation; smoothened signaling and trans-synaptic signaling relate to neural signaling pathways and synaptic modulation; cell\u2013matrix adhesion supports neural cell interactions during development. While a few terms (e.g., prolactin signaling, T cell costimulation) are less central, the dominant pattern is neural development and synaptic signaling.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007224","count":3},{"id":"GO:0050772","count":3},{"id":"GO:0099557","count":3},{"id":"GO:1902955","count":3},{"id":"GO:2000525","count":3}]},{"hash":"1273222012406941312","title":"Neural Signaling and ECM Remodeling","description":"Top GO terms emphasize extracellular matrix interaction (hyaluronan metabolism, metallopeptidase activity, integrin signaling) together with neural signaling and growth factor pathways (FGFR, insulin receptor) and processes like axon regeneration and trans-synaptic signaling, suggesting a cluster of proteins that coordinate neural signaling with ECM remodeling and growth cues.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030212","count":3},{"id":"GO:1905050","count":3},{"id":"GO:0007229","count":3},{"id":"GO:0002741","count":2},{"id":"GO:0035607","count":2}]},{"hash":"660797531258347767","title":"Oxidative stress defense and DNA repair","description":"The cluster shows strong representation of cellular oxidant detoxification and glutathione metabolic process, along with nucleotide-excision repair and cell cycle regulation, which together suggest a unit focused on protecting the cell from oxidative/genotoxic stress and coordinating damage repair with growth control. Other terms such as prostaglandin biosynthesis and platelet aggregation hint at inflammatory context, while response to starvation reflects general metabolic stress. Overall, the common theme is stress response and maintenance of genomic integrity.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0060316","count":2},{"id":"GO:0009072","count":2},{"id":"GO:0042594","count":2}]},{"hash":"1071754251086579425","title":"Synaptic receptor trafficking and vesicle transport","description":"The top GO terms cluster around vesicle trafficking and receptor movement related to synaptic membranes, including exocytic insertion of neurotransmitter receptors at the postsynaptic site, receptor recycling, and Golgi- and ER-to-Golgi\u2013to\u2013plasma membrane transport. Additional terms about vesicle fusion and autophagosome docking support a broader vesicle-organization theme, pointing to proteins serving in synaptic receptor delivery and membrane trafficking.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0098967","count":1},{"id":"GO:0042144","count":1},{"id":"GO:1902259","count":1},{"id":"GO:1900483","count":1},{"id":"GO:0006888","count":1}]},{"hash":"1290853756968640045","title":"Unknown","description":"There are no shared GO terms, edges, or triangles to define a common function, and Top Terms are empty, so no cohesive functional theme is evident among the proteins (the RECIPE re-additions don\u2019t provide connectivity). ","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1981305460075142989","title":"Unknown","description":"There are no GO terms or interactions to anchor a shared function for these proteins; with no edges and an empty Top Terms list, a coherent theme cannot be inferred.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"880870633100920446","title":"Unknown","description":"The top terms span ubiquitin-dependent protein degradation, chromatin methylation regulation (obsolete), protein complex assembly, cell cycle regulation, photoreceptor localization, hormone signaling, and virus defense. They do not point to a single cohesive function or pathway, and there are no interactions among proteins, so a meaningful cluster label cannot be inferred.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":2},{"id":"GO:2001162","count":1},{"id":"GO:0051291","count":1},{"id":"GO:0061087","count":1},{"id":"GO:0045842","count":1}]},{"hash":"1004267636774375640","title":"Host ubiquitin-like modification and autophagy","description":"The GO terms cluster around host cell processes that are manipulated or modulated, notably ubiquitin-like protein modification, autophagy activation, and chromatin-related protein localization, which align with known host-microbe interaction strategies (symbiont/viral influences). This suggests the proteins may participate in host-pathogen/symbiont\u2013driven regulation of post-translational modification and autophagy, with some relation to chromatin-associated localization.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032364","count":1},{"id":"GO:0018401","count":1},{"id":"GO:0055114","count":1},{"id":"GO:1901874","count":1},{"id":"GO:0046496","count":1}]},{"hash":"2238622714072821895","title":"Regulated membrane trafficking","description":"The GO terms cluster around regulation of vesicle and membrane trafficking across endosomes, lysosomes, ER-Golgi, and plasma membrane (e.g., endosome-lysosome transport, ER-Golgi transport). Additional terms related to polarity and actin structures (podosomes, epithelial polarity) also tie to membrane dynamics, supporting a common theme of regulated membrane trafficking.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902824","count":1},{"id":"GO:1902307","count":1},{"id":"GO:1905751","count":1},{"id":"GO:1902953","count":1},{"id":"GO:0061000","count":1}]},{"hash":"1343087915172345065","title":"Phosphorylation-Related Proteins","description":"The shared top term is phosphorylation (GO:0016310), suggesting these proteins may participate in phosphorylation events; the other listed term\u2014obsolete pathogenesis\u2014provides little functional guidance. With only 3 proteins and no interactions observed, the evidence is weak, so the label reflects a general involvement in phosphorylation rather than a specific enzyme or pathway.","confidence":"Low","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009405","count":1},{"id":"GO:0016310","count":1}]},{"hash":"799369606252689534","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":1},{"id":"GO:0050884","count":1},{"id":"GO:0032225","count":1},{"id":"GO:0017001","count":1},{"id":"GO:0046929","count":1}]},{"hash":"810044142702898688","title":"Unknown","description":"The three proteins have a mix of GO terms (phosphorylation, amino acid biosynthesis, iron homeostasis, fructosamine metabolism, response to antibiotic, protein stabilization, and muscle differentiation) with no clear, single functional theme tying them together. Several terms are obsolete, suggesting noisy or inconsistent annotations, so a specific, representative label cannot be confidently assigned.","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019509","count":1},{"id":"GO:0016310","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0009088","count":1},{"id":"GO:0019284","count":1}]}]