[{"hash":"985084026152395367","title":"Placental and heart vascular development","description":"This cluster centers on placental development (maternal placenta development, labyrinthine layer blood vessel development) and heart development, with strong signals for angiogenesis and fibroblast migration, suggesting a shared program of vascular growth in placenta and heart. Other terms are broader cellular processes that do not override this cohesive theme.","confidence":"High","size":29,"edges":42,"triangles":11,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0007507","count":5},{"id":"GO:0031571","count":4},{"id":"GO:2001275","count":4},{"id":"GO:0001525","count":4}]},{"hash":"352997665794591756","title":"Oxidative stress and xenobiotic response","description":"This cluster is dominated by GO terms tied to cellular defense against chemical stress and redox balance, including responses to xenobiotics, hydrogen peroxide, cadmium ion, and general redox homeostasis. While some metabolic terms appear (nitrate assimilation, cAMP signaling), the prominent theme is oxidative/redox stress response.","confidence":"Medium","size":29,"edges":8,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":3},{"id":"GO:0042128","count":2},{"id":"GO:0045471","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0071320","count":2}]},{"hash":"959343388084781648","title":"RNA Processing and Ribosome Biogenesis","description":"Dominant terms cluster around RNA metabolism (transcription termination, splicing, tRNA processing, mRNA decay) and ribosome biogenesis/translation, with some chromatin and cell-cycle hints; together they point to RNA processing and protein synthesis.","confidence":"Medium","size":29,"edges":398,"triangles":3447,"max_degree":28,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006369","count":7},{"id":"GO:0070317","count":7},{"id":"GO:0042254","count":6},{"id":"GO:0006412","count":6},{"id":"GO:0008033","count":6}]},{"hash":"1385452222208278226","title":"Carbon-source-regulated transcription in fungi","description":"The cluster is dominated by GO terms for DNA-templated transcription and regulation of transcription from RNA polymerase II promoter, especially linked to carbon-source conditions (nonfermentable carbon sources). Additional terms about cellular respiration and amino acid biosynthesis (lysine, leucine) suggest a coordinated transcriptional program that connects metabolism to gene regulation in fungal cells, with ergosterol-related processes reinforcing the fungal context. This points to a functional theme of transcriptional control driven by metabolic state in fungi.","confidence":"High","size":29,"edges":17,"triangles":3,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0035961","count":3},{"id":"GO:1904741","count":3},{"id":"GO:0061415","count":3},{"id":"GO:2001196","count":3}]},{"hash":"2062979786832373022","title":"Chromatin Assembly and Mitotic Chromosome Segregation","description":"The cluster is strongly enriched for mitosis-related terms (mitotic cell cycle, mitotic sister chromatid segregation, CENP-A containing chromatin assembly) and chromatin maintenance during division, pointing to a core role in chromosome organization and segregation. There are additional links to ribosome biogenesis and rRNA maturation, suggesting nucleolar activities associated with proliferating cells, but the dominant theme appears to be chromatin and chromosome dynamics in mitosis.","confidence":"High","size":29,"edges":394,"triangles":3361,"max_degree":28,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":13},{"id":"GO:0030433","count":11},{"id":"GO:0000278","count":11},{"id":"GO:0042273","count":11},{"id":"GO:0051260","count":10}]},{"hash":"2045156221917860848","title":"Rho GTPase\u2013driven actin remodeling","description":"The cluster is dominated by terms linked to actin cytoskeleton dynamics, including lamellipodium and filopodium assembly, regulation of Rho signaling and GTPase activation, and TORC2 signaling, all pointing to actin remodeling and cell migration; other terms (adhesion, spreading) support this theme, with occasional developmental/immune terms present but secondary.","confidence":"High","size":29,"edges":6,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0060313","count":4},{"id":"GO:0030032","count":4},{"id":"GO:0043314","count":4},{"id":"GO:0038203","count":4},{"id":"GO:0035435","count":4}]},{"hash":"1333151930667729447","title":"Growth signaling and cytoskeletal dynamics","description":"This cluster centers on signaling pathways that regulate growth and cytoskeletal organization, including Rho signaling, Wnt signaling, and actin filament bundle assembly. It also includes related cell-cycle and transcription-related terms, suggesting coordinated control of proliferation and gene expression through signaling and cytoskeletal remodeling.","confidence":"Medium","size":29,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0035023","count":4},{"id":"GO:0048549","count":4},{"id":"GO:0006397","count":4},{"id":"GO:0045736","count":4},{"id":"GO:0051209","count":3}]},{"hash":"1679721883994521239","title":"Transmembrane Transporters for Sugars, Ions, and Nitrates","description":"The GO terms point to membrane transporter activities across a variety of substrates\u2014galactose, arabinose, nitrates/nitrites, vitamins, potassium ions, and other small molecules\u2014as well as neurotransmitter loading into synaptic vesicles. Together these suggest a cluster of membrane transporter proteins with broad substrate specificity, rather than a single substrate type, justifying a transport-focused label.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015757","count":4},{"id":"GO:0042128","count":4},{"id":"GO:0042891","count":4},{"id":"GO:0015706","count":4},{"id":"GO:0098700","count":4}]},{"hash":"286219564260620351","title":"ROS Production and Oxidative Stress Response","description":"Dominant GO terms cluster around redox metabolism and oxidative stress: oxygen metabolic process, superoxide anion generation, hydrogen peroxide biosynthesis, and oxidative stress\u2013related signaling, along with cellular stress response to acidic pH and protein repair. Some terms (otolith development, integrin biosynthetic regulation) are less clearly connected and may reflect broader annotation, but the central theme is management of redox balance and ROS. ","confidence":"Medium","size":28,"edges":175,"triangles":453,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0072592","count":5},{"id":"GO:0042554","count":5},{"id":"GO:0010467","count":5},{"id":"GO:0045726","count":5},{"id":"GO:0030091","count":5}]},{"hash":"571789989598351331","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":370,"triangles":3090,"max_degree":27,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009432","count":8},{"id":"GO:0042273","count":8},{"id":"GO:0006369","count":8},{"id":"GO:0000480","count":7},{"id":"GO:0000472","count":7}]},{"hash":"1843614793374678777","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":361,"triangles":2882,"max_degree":27,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000463","count":8},{"id":"GO:0042273","count":8},{"id":"GO:0042254","count":6},{"id":"GO:0000466","count":6},{"id":"GO:0000447","count":6}]},{"hash":"1311314644938217816","title":"Heart Development and Angiogenesis","description":"The cluster is enriched for heart development and angiogenesis (GO:0007507, GO:0001525), with transcriptional processes (GO:0006351) likely driving developmental programs. Additional terms like response to toxic substances and Schwann cell development suggest broader developmental and stress-related regulatory activity, but the strongest signal centers on cardiovascular development and vascular formation.","confidence":"Medium","size":28,"edges":26,"triangles":8,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0035729","count":5},{"id":"GO:0090400","count":5},{"id":"GO:0050830","count":5},{"id":"GO:0007507","count":5}]},{"hash":"1376959497772652065","title":"Mitochondrial Protein Import and Membrane Insertion","description":"The top GO terms map to mitochondrial processes, including import into the mitochondrial matrix and insertion of proteins into the outer mitochondrial membrane, with a related (though obsolete) hint at mitophagy regulation and protein targeting to mitochondria; together these terms suggest a cluster of proteins involved in mitochondrial import and membrane assembly rather than cytosolic processes.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098779","count":1},{"id":"GO:0030150","count":1},{"id":"GO:1903955","count":1},{"id":"GO:0045040","count":1}]},{"hash":"2256568142787026085","title":"Core Metabolism and Gene Expression Activities","description":"Top terms indicate involvement in fundamental gene expression (translation, DNA-templated transcription) and essential biosynthetic pathways (cholesterol, porphyrin/heme), with additional signals of stress and apoptosis (xenobiotic response, apoptotic process). This suggests a broad cellular metabolism/gene-expression theme rather than a single pathway, justifying a label that reflects both metabolism and gene regulation. Confidence: Medium","confidence":"","size":28,"edges":12,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0006695","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0000448","count":2},{"id":"GO:0055114","count":2}]},{"hash":"1891430732180730645","title":"Unknown","description":"The cluster's top GO terms cover sterol biosynthesis across fungi/plants, vesicle trafficking, general gene expression, metal ion import, hormone generation, and bone resorption\u2014spanning multiple kingdoms with no single cohesive function. Without a clear common theme, a specific label is not justified.","confidence":"","size":28,"edges":374,"triangles":3174,"max_degree":27,"top_function":null,"top_go_terms":[{"id":"GO:0006696","count":3},{"id":"GO:0006695","count":2},{"id":"GO:0016132","count":2},{"id":"GO:0032511","count":2},{"id":"GO:0010467","count":2}]},{"hash":"2070621622108043474","title":"Mitosis and DNA Replication Machinery","description":"The cluster is dominated by GO terms tied to the mitotic cell cycle, DNA replication initiation, and microtubule dynamics, with septin ring organization also involved in cytokinesis. These together point to proteins involved in cell division and genome duplication. A few terms (cholesterol biosynthesis, RNA processing) are present but less central, so the core theme remains cell division machinery.","confidence":"Medium","size":27,"edges":3,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:1900363","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0031116","count":2},{"id":"GO:0060211","count":2}]},{"hash":"1553216855894685381","title":"Xenobiotic and lipid transmembrane transporters","description":"The terms cluster around transmembrane transport of diverse substrates, including xenobiotics, antibiotics and drugs like doxorubicin, vitamins, taurine, monoatomic anions, and phospholipids, with related lipid metabolism and cholesterol absorption regulation. This points to a cohesive function as membrane transport proteins moving small molecules and lipids across membranes.","confidence":"High","size":27,"edges":45,"triangles":20,"max_degree":7,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0046677","count":6},{"id":"GO:0006855","count":6},{"id":"GO:0035461","count":6},{"id":"GO:0017004","count":5},{"id":"GO:1900753","count":5}]},{"hash":"683254358541689364","title":"Transcription and Cell Cycle Regulation","description":"The cluster contains multiple transcription-related terms (DNA-templated transcription, negative regulation of transcription by RNA polymerase II) together with cell-cycle signals (protein localization to kinetochore, mitotic spindle assembly checkpoint signaling, apoptotic process), suggesting a cohesive theme around nuclear gene expression control and checkpoint/mitosis. Other terms like tRNA wobble uridine modification support broader gene expression processes, while ubiquinone biosynthesis and response to cocaine appear as less central associations.","confidence":"Medium","size":27,"edges":10,"triangles":2,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0002098","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0000122","count":2},{"id":"GO:0006744","count":2}]},{"hash":"1865130933394959903","title":"Neuroimmune Signaling and Development","description":"The terms point to coordinated regulation of multiple signaling cascades (Wnt, ERK/JNK, TCR, ephrin) with neural development and plasticity (nervous system development, dendrite morphogenesis, dopamine response) as well as immune processes (beta selection). This suggests a module of proteins that modulate signaling across neural and immune contexts, linked to development and signal transduction.","confidence":"Medium","size":27,"edges":37,"triangles":17,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090263","count":7},{"id":"GO:0050852","count":6},{"id":"GO:0033138","count":6},{"id":"GO:0070374","count":6},{"id":"GO:0046330","count":5}]},{"hash":"1035564740053163100","title":"RNA and protein methylation","description":"The strongest shared signal among the top GO terms is methylation: rRNA methylation, peptidyl-arginine methylation, and histone methylation. This points to a cluster enriched for methyltransferase activity or methylation regulation. Other terms (biosynthetic processes, ER localization, growth/senescence) are present but appear secondary, making this a representative and specific label.","confidence":"High","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031167","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0019919","count":2},{"id":"GO:0090398","count":2},{"id":"GO:0046690","count":2}]},{"hash":"1445280370157916159","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":297,"triangles":2063,"max_degree":26,"top_function":null,"top_go_terms":[{"id":"GO:0009228","count":5},{"id":"GO:0009229","count":5},{"id":"GO:0043200","count":4},{"id":"GO:0061621","count":3},{"id":"GO:0001666","count":3}]},{"hash":"73259530898440820","title":"Transmembrane solute transporters","description":"Most of the top terms point to movement of diverse solutes across membranes (nitrate/nitrite, galactose, fucose, sialic acid, vitamins, potassium, xenobiotics) and even neurotransmitter loading into synaptic vesicles, indicating a cluster of membrane transporter proteins with a broad transport role rather than enzymes. Confidence is high that this label captures the common function of the cluster.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098700","count":12},{"id":"GO:0006855","count":12},{"id":"GO:0015706","count":12},{"id":"GO:0035461","count":12},{"id":"GO:0042128","count":12}]},{"hash":"520034795069758208","title":"Transcriptional Regulation and Cell Cycle Control","description":"The top GO terms emphasize negative regulation of transcription by RNA polymerase II and DNA-templated transcription, along with regulation of the cell cycle and cell division, pointing to a cluster of proteins involved in controlling gene expression during cell cycle progression. A few metabolic or obsolete terms appear but do not define the core theme. ","confidence":"Medium","size":26,"edges":30,"triangles":1,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0071157","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0097755","count":2}]},{"hash":"1825992152781940754","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":320,"triangles":2487,"max_degree":25,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000463","count":9},{"id":"GO:0000462","count":9},{"id":"GO:0042273","count":9},{"id":"GO:0000398","count":9},{"id":"GO:0000466","count":9}]},{"hash":"854583712721212141","title":"Placental Development and Membrane Lipid Regulation","description":"Plenty of GO terms point to placenta development (placenta and embryonic placenta), while several terms indicate regulation of lipid biosynthesis, especially phosphatidylcholine and phosphatidylglycerol, plus related membrane/barrier functions. This combination suggests a cluster centered on placental development with membrane lipid regulation as a key supporting theme.","confidence":"High","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001890","count":3},{"id":"GO:0046909","count":3},{"id":"GO:0006970","count":3},{"id":"GO:0001892","count":2},{"id":"GO:0090212","count":2}]},{"hash":"931934272471669264","title":"Mitosis and Transcription Machinery","description":"Based on the top GO terms, the cluster centers on mitotic processes (sister chromatid cohesion) and transcription-related assemblies (RNA polymerase II initiation and transcription), with a weaker tie to ribosome biogenesis suggesting growth-related gene expression. Some terms like spinal cord development and nutrient response may reflect broader regulatory roles rather than direct functions of all proteins in the group. Overall, it seems to capture the core theme of cell-cycle\u2013related cohesion and transcription machinery.","confidence":"Medium","size":26,"edges":33,"triangles":12,"max_degree":20,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0007064","count":3},{"id":"GO:0006366","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0021510","count":3}]},{"hash":"442281303587790135","title":"Embryonic development and organ morphogenesis","description":"These proteins span a broad set of embryonic development processes across multiple tissues and organs, including placenta formation, cartilage morphogenesis, endocrine and pancreatic development, cardiac EMT in endocardial cushion formation, left-right patterning, and autonomic nervous system development. The lone mRNA splicing term appears as a minor outlier, but the dominant theme is developmental differentiation and tissue morphogenesis, justifying this label.","confidence":"High","size":26,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0060806","count":1},{"id":"GO:0060536","count":1},{"id":"GO:0035270","count":1},{"id":"GO:0003323","count":1},{"id":"GO:0003198","count":1}]},{"hash":"673024541123879674","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":15,"triangles":6,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0046328","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0034605","count":2}]},{"hash":"1759844723999365865","title":"Nutrient-limited invasive growth in fungi","description":"The top GO terms point to fungal morphogenesis and stress responses driven by nutrient limitation, notably pseudohyphal/invasive growth, response to glucose limitation, and amino acid starvation, all coupled with regulatory processes like cell polarity establishment and signaling. Some terms (e.g., placenta/face development) are likely non-fungal annotations or incidental; however, the core theme centers on nutrient-stress\u2013induced growth form changes in fungi, supported by a few regulatory processing terms. This supports labeling the cluster as fungal nutrient-limited invasive/pseudohyphal growth.","confidence":"Medium","size":26,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000381","count":2},{"id":"GO:0006470","count":2},{"id":"GO:0060324","count":2},{"id":"GO:0009636","count":2},{"id":"GO:2000114","count":2}]},{"hash":"1717887442540295195","title":"Skeletal Muscle Development and RNA Processing","description":"The cluster combines GO terms tied to skeletal muscle tissue development with RNA processing and transcription (mRNA processing, DNA-templated transcription, mRNA stabilization). The co-occurrence suggests proteins involved in controlling gene expression during muscle development, spanning transcription initiation to mRNA maturation and stability. Obsolete terms can be ignored; the non-obsolete items point to a coherent theme of transcription-coupled RNA processing in muscle formation.","confidence":"High","size":26,"edges":11,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007519","count":3},{"id":"GO:0006397","count":3},{"id":"GO:0006351","count":3},{"id":"GO:1903586","count":2},{"id":"GO:1905663","count":2}]},{"hash":"993006789629341974","title":"Neural development and metabolic signaling","description":"This cluster centers on developmental processes in neural tissues, including neural crest cell development and neural tube development, plus endocrine/cardiac tissue development (pituitary gland and cardiac muscle). The accompanying metabolic and signaling GO terms (nutrient response, cAMP response, GABA catabolic, proline and polyamine metabolism, retinol metabolism) suggest these proteins participate in developmental programs that are tightly linked with metabolic regulation, particularly in neural and related endocrine tissues.","confidence":"Medium","size":25,"edges":298,"triangles":2255,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0007584","count":11},{"id":"GO:0051591","count":10},{"id":"GO:0009450","count":10},{"id":"GO:0055129","count":10},{"id":"GO:0009447","count":10}]},{"hash":"448985187808889296","title":"Ribosome Biogenesis and Translation","description":"Dominant GO signals are clearly about ribosome assembly and protein synthesis: ribosome biogenesis, LSU rRNA maturation, rRNA methylation, and cytoplasmic translation. This points to a cluster of ribosomal components and associated factors. A few terms like neural tube closure or B cell signaling are unlikely core functions but do not outweigh the central ribosome/translation theme.","confidence":"High","size":25,"edges":174,"triangles":565,"max_degree":21,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0042254","count":4},{"id":"GO:0002181","count":3},{"id":"GO:0031167","count":3},{"id":"GO:0042273","count":2}]},{"hash":"260791707885122544","title":"Transcription Regulation and RNA Processing","description":"The cluster is dominated by GO terms for DNA-templated transcription, regulation of transcription, and mRNA splicing/processing, pointing to a nucleus-wide program of transcription control and RNA maturation. Histone modification terms (even obsolete) further support chromatin-level regulation. A defense response term is present but not central to the cluster\u2019s main theme. Overall, the proteins likely include transcription factors, chromatin modifiers, and RNA processing factors.","confidence":"High","size":25,"edges":24,"triangles":13,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0043966","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0050830","count":3}]},{"hash":"1558417250586539642","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":64,"triangles":30,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0071276","count":3},{"id":"GO:0006412","count":2},{"id":"GO:0006400","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0051301","count":2}]},{"hash":"691744997189409258","title":"Neural development and cell-cycle signaling","description":"GO terms point to core nuclear processes (DNA replication, DNA-templated transcription, mitotic cell cycle) alongside neural development terms (nervous system development, neuron development) and developmental signaling pathways (Hippo, Wnt) that regulate progenitor proliferation and differentiation. The combination suggests a cluster of proteins coordinating neural development with cell-cycle control and growth signaling.","confidence":"Medium","size":25,"edges":31,"triangles":2,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0007399","count":3},{"id":"GO:0048666","count":3}]},{"hash":"15285222234451564","title":"Metal Ion Transport and Calcium Homeostasis","description":"This cluster is dominated by GO terms for intracellular calcium ion homeostasis and transmembrane transport of metal ions (copper, zinc, cadmium), pointing to a shared function in maintaining ion balance across membranes. Though some terms are more peripheral (lipid-related or organism-specific pathways), the strongest common theme is metal ion transport and calcium handling, justifying the label.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0006874","count":5},{"id":"GO:0006825","count":4},{"id":"GO:0097755","count":4},{"id":"GO:0071577","count":4},{"id":"GO:0019373","count":4}]},{"hash":"359195591251170940","title":"Vacuolar and Golgi trafficking and degradation","description":"This cluster centers on intracellular transport and turnover within endomembrane compartments: vacuole fusion, protein transport to the vacuole via ubiquitin-dependent sorting, autophagy, and Golgi lumen transport (including UDP-glucose import). Palmitoylation indicates membrane association, tying these processes to membrane trafficking and protein turnover. The varied terms converge on a single functional theme of sorting, trafficking, and degradation inside the cell, despite some outliers.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018230","count":1},{"id":"GO:0042144","count":1},{"id":"GO:0048733","count":1},{"id":"GO:0006914","count":1},{"id":"GO:0032974","count":1}]},{"hash":"887767957210940762","title":"Autophagy\u2013Peroxisome Lipid Metabolism","description":"This cluster centers on autophagy-related processes (autophagosome maturation) and ER-dependent peroxisome organization, with supporting lipid biosynthesis (sphingolipids) and thyroid hormone metabolism, plus metal ion transport (iron and copper). The common thread appears to be cellular maintenance and metabolic regulation linking autophagy, peroxisomes, and lipid pathways, though several terms reflect broader metabolic activities. Confidence: Medium","confidence":"","size":25,"edges":254,"triangles":1427,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0032581","count":2},{"id":"GO:0097352","count":2},{"id":"GO:0030148","count":2},{"id":"GO:0010467","count":2},{"id":"GO:0098706","count":2}]},{"hash":"1530042366578829466","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":244,"triangles":1535,"max_degree":23,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":15},{"id":"GO:0042254","count":4},{"id":"GO:0006415","count":3},{"id":"GO:0045903","count":3},{"id":"GO:0046677","count":3}]},{"hash":"1560213953836746929","title":"Cell cycle and nucleotide biosynthesis","description":"The cluster shows strong representation of cell cycle and DNA replication initiation terms, along with multiple nucleotide metabolism processes (ADP, AMP salvage, GTP, CDP biosynthesis). This points to proteins involved in DNA synthesis and nucleotide supply during cell proliferation; tissue-specific development terms (liver, brain) may reflect context-dependent roles but do not define the main function of the cluster.","confidence":"High","size":24,"edges":19,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0006270","count":2},{"id":"GO:0015951","count":2},{"id":"GO:0001889","count":2},{"id":"GO:0006172","count":2}]},{"hash":"2305741578541386181","title":"Vertebrate organogenesis and neural development","description":"The GO terms cover diverse vertebrate organ and neural/sensory development processes (heart, forebrain, cerebellum, inner ear, thyroid, cranial skeleton, visual perception) and a developmental growth signal (insulin receptor pathway), suggesting a broad embryonic development theme rather than a single pathway.","confidence":"High","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007507","count":5},{"id":"GO:0008286","count":5},{"id":"GO:0008045","count":4},{"id":"GO:0048839","count":4},{"id":"GO:0030900","count":4}]},{"hash":"25721094198150361","title":"Vacuolar amino acid transporters","description":"The GO terms show multiple instances of transmembrane import of amino acids into the vacuole (histidine, serine, lysine) and proline transport, which points to a core function of vacuolar amino acid transport. Related terms about cellular responses to glucose and potassium starvation, plus a developmental term like root cap development, suggest a nutrient-stress and plant-specific context, but the dominant theme is vacuolar amino acid transport. Confidence: Medium","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":2},{"id":"GO:0071333","count":2},{"id":"GO:0031505","count":2},{"id":"GO:0090513","count":2},{"id":"GO:1901481","count":2}]},{"hash":"1692308268416667925","title":"Transcriptional Regulation and Cell Cycle Control","description":"The cluster's top GO terms are dominated by DNA-templated transcription and regulation of transcription by RNA polymerase II, along with G2/M transition and meiosis-related chromosome pairing, indicating a core focus on gene expression control and cell cycle progression. Additional terms such as angiogenesis and Wnt signaling regulation suggest broader developmental and signaling context, but the prevailing theme ties to transcriptional control coupled with cell division and genome maintenance.","confidence":"Medium","size":24,"edges":34,"triangles":13,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0045819","count":4},{"id":"GO:0097350","count":4},{"id":"GO:0090090","count":4},{"id":"GO:0000086","count":4}]},{"hash":"2303630549058654726","title":"Peptidoglycan turnover and UDP-GlcNAc biosynthesis","description":"This cluster features strong signals for peptidoglycan catabolic processes (N-acetylmuramic acid and related muropeptides), UDP-N-acetylglucosamine biosynthesis, and carbohydrate metabolism/transport, all pointing to bacterial cell wall remodeling and recycling. The DNA-templated transcription and translation terms likely reflect general housekeeping processes within the cluster rather than a distinct specialized function.","confidence":"Medium","size":24,"edges":14,"triangles":2,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006541","count":3},{"id":"GO:0050821","count":3},{"id":"GO:0006412","count":2},{"id":"GO:0006048","count":2}]},{"hash":"1498446349900087969","title":"Bacterial cell wall and envelope biosynthesis","description":"The top GO terms cluster around envelope-related biosynthesis: peptidoglycan, glycolipid, and lipoteichoic acid biosynthesis, dolichol-linked oligosaccharide biosynthetic processes, and cell wall organization, with accompanying cell division and cell cycle terms. This points to a group of proteins focused on bacterial cell envelope biogenesis and related division processes.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016999","count":1},{"id":"GO:0005975","count":1},{"id":"GO:0030259","count":1},{"id":"GO:0071555","count":1},{"id":"GO:0006488","count":1}]},{"hash":"467735572223178440","title":"Gene expression regulation and RNA processing","description":"The cluster is enriched for DNA-templated transcription, alternative mRNA splicing via spliceosome, and translation initiation/reinitiation terms, plus related transcriptional regulation. This points to a cohesive set of proteins involved in regulating gene expression at transcriptional and RNA-processing levels, with some links to translation initiation.","confidence":"Medium","size":24,"edges":8,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0000380","count":2},{"id":"GO:0035961","count":2}]},{"hash":"2212977445000068306","title":"Chromatin remodeling and transcription regulation","description":"Based on enriched GO terms, this cluster centers on chromatin dynamics and transcription control, including chromatin remodeling, nucleosome mobilization, rDNA heterochromatin formation, DNA-templated transcription, and negative regulation of transcription by RNA Pol II. Additional terms about transcription from Pol II promoters and protein localization to chromatin reinforce a cohesive chromatin-transcription regulatory module, with a separate stress-related term likely reflecting context-specific transcriptional responses. Overall, a chromatin remodeling/transcription regulation theme best fits the cluster.","confidence":"High","size":24,"edges":36,"triangles":7,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0000183","count":3},{"id":"GO:0043457","count":3},{"id":"GO:0042766","count":3},{"id":"GO:0043044","count":3}]},{"hash":"1085445387449271196","title":"Chromatin Regulation and Cell Cycle Control","description":"The top GO terms cluster around chromatin organization (heterochromatin formation, localization to chromatin), DNA replication, transcription by RNA polymerase II, centrosome cycle, and mitotic G2 DNA damage checkpoint signaling, which together point to chromatin state dynamics and cell cycle control. A few terms relate to development or immune responses, likely reflecting broader functional annotations in different contexts, but the core theme is chromatin regulation and replication/mitosis.","confidence":"Medium","size":24,"edges":46,"triangles":23,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0007098","count":2},{"id":"GO:0071169","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0030466","count":2},{"id":"GO:0006366","count":2}]},{"hash":"547855629355982139","title":"Cardiac muscle development and sarcomere organization with H2S signaling","description":"Most terms center on heart development and sarcomere structure (endocardial cushion development, cardiac muscle regeneration, sarcomere organization), indicating a cardiac muscle function cluster. Hydrogen sulfide biosynthesis and transsulfuration appear as metabolic supports linked to cardiovascular signaling, with a few other terms reflecting broader signaling and transcriptional activity. Overall, the cluster is best described as cardiac muscle development and structure with a metabolic/signaling component.","confidence":"Medium","size":24,"edges":6,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045943","count":3},{"id":"GO:0003197","count":2},{"id":"GO:0071353","count":2},{"id":"GO:0061026","count":2},{"id":"GO:0045214","count":2}]},{"hash":"1914182630344028128","title":"Ribosome biogenesis and mitochondrial translation","description":"The cluster is dominated by translation-related terms: translation, maturation of SSU-rRNA, ribosomal large subunit assembly, and mitochondrial translation, indicating a group enriched for ribosome biogenesis and protein synthesis machinery. Additional terms like brain development or immune responses are present but far less central to the core theme.","confidence":"High","size":23,"edges":96,"triangles":168,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0000462","count":4},{"id":"GO:0007420","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0007584","count":3}]},{"hash":"1692979683992937025","title":"DNA replication and cell cycle","description":"The strongest signals are cell division and DNA replication (GO:0051301 and GO:0006260), indicating a core role in genome duplication and cell-cycle progression. The presence of transcription elongation regulation by RNA Pol II suggests coordinated gene expression during replication. Additional terms point to proteostasis and trafficking in the secretory pathway (ER unfolded protein response, ERAD, ER-to-Golgi transport) and peroxisomal import, which may reflect linked quality-control processes during growth or stress, as well as chromatin dynamics. Overall, the cluster seems to integrate nuclear replication/division with protein folding, trafficking, and chromatin regulation.","confidence":"Medium","size":23,"edges":97,"triangles":163,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0032968","count":3},{"id":"GO:0030466","count":3},{"id":"GO:0016562","count":3},{"id":"GO:0030968","count":3}]},{"hash":"1305354919838187113","title":"N-linked glycosylation and GPI-anchor biosynthesis","description":"The cluster is enriched for glycosylation-related processes\u2014GPI anchor biosynthesis, dolichol-linked oligosaccharide biosynthesis, and N-linked glycosylation, plus ER quality-control (unfolded protein response regulation). This collectively reflects components of the secretory pathway and glycoprotein maturation. Some developmental terms (pollen tube guidance, outflow tract morphogenesis) may reflect broader roles but do not override the dominant glycosylation signal.","confidence":"High","size":23,"edges":141,"triangles":672,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":9},{"id":"GO:0006488","count":5},{"id":"GO:0010183","count":4},{"id":"GO:0031505","count":3},{"id":"GO:0006487","count":3}]},{"hash":"1827200722739427997","title":"RNA methylation and cofactor biosynthesis","description":"This cluster centers on RNA modification (rRNA N7-methylation, tRNA methylation, 7-methylguanosine capping, arginine methylation on proteins) and biosynthesis of essential cofactors and vitamins (biotin, ubiquinone, vitamin E). The convergence of methylation-related GO terms with several biosynthetic processes suggests a theme linking RNA modification machinery and metabolic/cofactor production. While there are a few outliers like xenobiotic response and aging, the dominant signal is RNA methylation together with cofactor biosynthesis.","confidence":"Medium","size":23,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0070476","count":3},{"id":"GO:0019919","count":3},{"id":"GO:0030488","count":3}]},{"hash":"2225723847744130050","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":136,"triangles":443,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006189","count":4},{"id":"GO:0006223","count":4},{"id":"GO:0006412","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0055114","count":3}]},{"hash":"643757639888306835","title":"Telomere maintenance and chromatin regulation","description":"The cluster centers on telomere and subtelomeric chromatin processes (telomere maintenance via recombination, subtelomeric heterochromatin formation) and DNA repair (break-induced replication), with related chromatin/regulatory activities such as imprinting at the mating-type locus and Pol II\u2013driven regulation of ribosomal protein gene transcription. Taken together, these terms point to genome stability and chromatin organization as the core theme, even though a few terms (embryonic development, NAD biosynthesis) are less directly connected. Confidence reflects the strongest signal around telomere/chromatin maintenance.","confidence":"Medium","size":23,"edges":67,"triangles":94,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0000733","count":2},{"id":"GO:0000727","count":2},{"id":"GO:0010688","count":2},{"id":"GO:0006348","count":2},{"id":"GO:0000722","count":2}]},{"hash":"1220019600027624062","title":"mRNA decay and translation regulation","description":"This cluster is enriched for mRNA processing and decay terms (deadenylation, decapping, processing body assembly) and translation regulation, pointing to a cohesive role in mRNA stability and control of protein synthesis. Some transcription elongation terms appear, but the dominant signal is mRNA decay/translation control.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010606","count":3},{"id":"GO:0000289","count":3},{"id":"GO:0000290","count":2},{"id":"GO:0017148","count":2},{"id":"GO:0000749","count":2}]},{"hash":"511631454772496461","title":"ER-Golgi Vesicle Trafficking and Endocytosis","description":"The top GO terms point strongly to proteins involved in intracellular membrane trafficking: vesicle transport between the ER and Golgi (both directions), targeting to the vacuole, and endocytosis. While DNA-templated transcription appears, it is not the dominant theme, suggesting the cluster mainly reflects endomembrane trafficking functions. Pigmentation and aging annotations seem less central or incidental. Overall, the cluster is best described by ER-Golgi vesicle trafficking and endocytosis.","confidence":"Medium","size":22,"edges":24,"triangles":6,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006623","count":2},{"id":"GO:0006897","count":2},{"id":"GO:0043473","count":2},{"id":"GO:0006888","count":2}]},{"hash":"1538901345183723098","title":"DNA Repair and Cell Cycle Regulation","description":"The top GO terms cluster around DNA damage response via homologous recombination, chromatin organization, and mitotic control (APC-dependent degradation, spindle checkpoint). This indicates a cohesive module coordinating DNA repair with cell division, with ribosome biogenesis/translation appearing as secondary growth-state signals. Confidence: High","confidence":"","size":22,"edges":205,"triangles":1100,"max_degree":21,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000724","count":7},{"id":"GO:0006351","count":6},{"id":"GO:0051301","count":6},{"id":"GO:0042254","count":5},{"id":"GO:0006412","count":4}]},{"hash":"108109241228641187","title":"DNA Replication and Stress Regulation","description":"The top GO terms center on DNA replication plus several stress- and quality-control processes (protein refolding, ER stress response, inhibition of apoptotic signaling, inclusion body assembly), suggesting a functional theme of coordinating genome maintenance with cellular stress responses and protein homeostasis. Some terms appear as outliers or legacy annotations, but the dominant pattern points to links between DNA maintenance and protective stress pathways.","confidence":"Medium","size":22,"edges":13,"triangles":7,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0070389","count":4},{"id":"GO:0061370","count":4},{"id":"GO:1903382","count":3},{"id":"GO:1903751","count":3}]},{"hash":"918022386177115215","title":"Flavin-dependent mitochondrial respiration and Complex II assembly","description":"The top terms point to mitochondrial metabolism and flavin cofactors: succinate metabolism, mitochondrial electron transport (complex II is highlighted), and protein flavinylation/FAD linkage, indicating a coherent group of flavin-dependent mitochondrial enzymes and respiratory chain assembly. Secondary terms like mitochondrial inheritance and stress fiber assembly are less central to this core theme, reinforcing a mitochondria-centric cluster.","confidence":"High","size":22,"edges":14,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000001","count":2},{"id":"GO:0043149","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0016311","count":2},{"id":"GO:0006121","count":1}]},{"hash":"2120736786797845873","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051084","count":1},{"id":"GO:0045041","count":1},{"id":"GO:0032543","count":1},{"id":"GO:0033617","count":1},{"id":"GO:0022417","count":1}]},{"hash":"2224092493618584095","title":"RNA polymerase II Transcription Regulation","description":"The top GO terms are dominated by regulation and initiation of transcription by RNA polymerase II (DNA-templated transcription, promoter-specific initiation, and regulation of transcription), indicating that this cluster principally represents proteins involved in transcriptional control rather than core transcription machinery. Some terms touch on stress responses and developmental processes, but their presence is secondary to the strong transcription-regulation signal. Thus, the cluster most likely groups factors that modulate gene expression at the RNA Pol II level, across various contexts.","confidence":"High","size":22,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0033138","count":3},{"id":"GO:0045944","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006367","count":2},{"id":"GO:0006355","count":2}]},{"hash":"482290204356240247","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042273","count":1},{"id":"GO:0006413","count":1},{"id":"GO:0000304","count":1},{"id":"GO:0006541","count":1},{"id":"GO:0008614","count":1}]},{"hash":"379282415825928631","title":"Cell Cycle and Stress Response","description":"The terms cluster around mitotic processes (mitotic cell cycle, cell division) and apoptosis, with supporting transcriptional activity, plus multiple stress- and nutrient-sensing pathways (unfolded protein response, amino acid starvation, cadmium response, TORC1 signaling). This suggests a cohesive theme of coordinating cell-cycle progression with cellular stress and metabolic signaling rather than a single, narrow function.","confidence":"Medium","size":22,"edges":7,"triangles":1,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0006915","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0006986","count":3}]},{"hash":"272905612042545123","title":"Actin cytoskeleton and GTPase-driven motility","description":"The majority of terms point to actin cytoskeleton organization and small GTPase\u2013mediated signaling, including processes involved in cell motility and neuronal migration. Although a few terms relate to endocrine pancreas development or pancreatic differentiation, the dominant theme is cytoskeleton dynamics governed by GTPase activity.","confidence":"Medium","size":22,"edges":12,"triangles":7,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0030036","count":2},{"id":"GO:0046626","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0007264","count":2},{"id":"GO:0021816","count":2}]},{"hash":"918538320224153712","title":"Unknown","description":"The top GO terms are highly heterogeneous, spanning peroxisome import, behavioral response, detoxification, plant-specific chlorophyll catabolism, ubiquitin-dependent proteolysis, dosage compensation, DNA repair, and immune system recombination. There is no single coherent biological function or pathway that ties these proteins together, so a meaningful concise label cannot be assigned.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016558","count":2},{"id":"GO:0001662","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0015996","count":2},{"id":"GO:0031146","count":1}]},{"hash":"1380065276114063580","title":"Rab-regulated vesicle trafficking","description":"Dominant GO terms center on Rab protein signal transduction and GTPase regulation, plus transport between cellular compartments (ER-Golgi, endosome, intracellular transport). This points to a cohesive theme of Rab/GTPase\u2013driven membrane trafficking and remodeling, with sporulation and morphogenesis terms reflecting broader membrane dynamics that fit this function. ","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032483","count":3},{"id":"GO:0045737","count":3},{"id":"GO:0032120","count":2},{"id":"GO:0045815","count":2},{"id":"GO:0043087","count":2}]},{"hash":"1745446147132878523","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":109,"triangles":268,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":9},{"id":"GO:0009097","count":5},{"id":"GO:0032869","count":3},{"id":"GO:0009089","count":3},{"id":"GO:0019878","count":3}]},{"hash":"855315019667737806","title":"Carbohydrate Metabolic Pathways","description":"The cluster is dominated by GO terms tied to sugar metabolism and energy production, including glycolysis, gluconeogenesis, the pentose phosphate shunt, fructose and lactose catabolism, and related carbohydrate biosynthesis. The presence of thiamine biosynthesis (a cofactor for many carbohydrate-processing enzymes) and other sugar-catabolic processes suggests a cohesive module of carbohydrate metabolism driving energy generation. The density of connections supports a defined metabolic cluster rather than disparate functions.","confidence":"High","size":22,"edges":230,"triangles":1520,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":6},{"id":"GO:0009228","count":5},{"id":"GO:0006000","count":4},{"id":"GO:0006098","count":4},{"id":"GO:0006096","count":4}]},{"hash":"1215629036890645494","title":"Transmembrane Sugar and Nutrient Transporters","description":"The GO terms are dominated by transmembrane transport of sugars and related nutrients (fructose, galactose, glucose, dehydroascorbic acid, urate) and conditions linked to glucose uptake or starvation, plus xenobiotic transport. This pattern strongly suggests a cluster of membrane transport proteins mediating nutrient uptake and substrate handling, with some peripheral signals related to metabolism. ","confidence":"Medium","size":22,"edges":9,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1990539","count":2},{"id":"GO:0015757","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0042908","count":2},{"id":"GO:0042149","count":2}]},{"hash":"1247798282954535441","title":"RNA Processing and mRNA Export Machinery","description":"The most represented terms center on RNA processing and nucleocytoplasmic transport: mRNA export from the nucleus and regulation of alternative splicing via the spliceosome, plus protein processing and Golgi retention suggesting coordinated protein maturation and trafficking. Additional terms reference cytoskeletal dynamics (microtubule depolymerization, cilium movement) and DNA replication/viral genome replication, which may reflect shared involvement in cell-cycle\u2013related machinery or multi-functional complexes linking gene expression with trafficking. Overall, the cluster seems to reflect RNA processing/export with protein maturation and trafficking components rather than a single enzymatic pathway.","confidence":"Medium","size":21,"edges":52,"triangles":34,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0019079","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0031117","count":3},{"id":"GO:0006406","count":3},{"id":"GO:0006260","count":3}]},{"hash":"2239787933335149127","title":"mRNA splicing and translation initiation","description":"The top GO terms point to mRNA processing (spliceosome-mediated splicing and polyadenylation) and multiple steps of translation initiation (preinitiation complex formation, initiation, reinitiation, and IRES-dependent initiation), with accompanying ribosome biogenesis. This suggests a cluster of proteins associated with both splicing and the translation initiation machinery, supporting a cohesive theme of mRNA processing linked to protein synthesis. High","confidence":"High","size":21,"edges":57,"triangles":42,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":4},{"id":"GO:0006446","count":4},{"id":"GO:0006378","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0002188","count":3}]},{"hash":"2088732785228502120","title":"Gene expression and cell proliferation","description":"The cluster centers on core processes that drive cell growth and division: transcription (DNA-templated transcription), translation readiness (tRNA aminoacylation), and protein assembly (protein homotetramerization), plus nucleotide biosynthesis (GTP/GMP) and metabolic responses (glucose starvation). The presence of mitotic regulation and lymphocyte proliferation further ties to cell-cycle\u2013driven proliferation. Together, these terms suggest a cohesive theme around gene expression machinery supporting cell growth and division.","confidence":"Medium","size":21,"edges":54,"triangles":54,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046651","count":5},{"id":"GO:0051289","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0006431","count":3},{"id":"GO:0006429","count":3}]},{"hash":"2091625772774900781","title":"Cholesterol homeostasis and lipoprotein metabolism","description":"The cluster's top GO terms center on cholesterol handling (homeostasis, storage, esterification) and lipoprotein biology (VLDL particle assembly, regulation of plasma lipoprotein levels), with supporting lipid biosynthesis and lipid modification processes. This points to a cohesive function in lipid/cholesterol metabolism and lipoprotein trafficking, hence this label.","confidence":"High","size":21,"edges":208,"triangles":1293,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0006655","count":4},{"id":"GO:0042121","count":3},{"id":"GO:0034379","count":3},{"id":"GO:0010742","count":3},{"id":"GO:0042632","count":3}]},{"hash":"1062374672828867424","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":7,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0045454","count":5},{"id":"GO:0001707","count":3},{"id":"GO:0006626","count":3},{"id":"GO:0071374","count":3},{"id":"GO:0006469","count":3}]},{"hash":"1333338280060080923","title":"DNA repair and antibody diversification","description":"It combines DNA repair processes (DSB repair, interstrand cross-link repair, recombination regulation, gene conversion) with immunoglobulin diversification (somatic hypermutation and IgA isotype switching), suggesting a B cell\u2013centric DNA damage response theme; embryonic development and oxidative phosphorylation appear ancillary.","confidence":"Medium","size":21,"edges":49,"triangles":52,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0001701","count":5},{"id":"GO:0006119","count":5},{"id":"GO:0045910","count":5},{"id":"GO:0006302","count":5},{"id":"GO:0048298","count":5}]},{"hash":"33285871999803235","title":"Unknown","description":"The top GO terms indicate cellular responses to freezing and to pheromone-triggered conjugation, representing two distinct biological processes (cold-stress response vs mating/conjugation signaling). There is no clear shared function or common pathway linking most proteins in this cluster, so a unifying label isn\u2019t well-supported.","confidence":"","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071497","count":1},{"id":"GO:0000749","count":1}]},{"hash":"649822164502714402","title":"Chromatin regulation and cell cycle control","description":"These proteins show enrichment for transcriptional regulation and cell-cycle\u2013related processes (DNA-templated transcription, cell division, mitotic cell cycle) and include a chromatin-modifying signal (histone H3 acetylation). Additional terms point to stress responses and development, suggesting a theme of chromatin-mediated transcriptional control coordinating proliferation with development and stress signals.","confidence":"Medium","size":21,"edges":174,"triangles":804,"max_degree":20,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0000278","count":4},{"id":"GO:0001403","count":4},{"id":"GO:0050830","count":3}]},{"hash":"1366559420477230736","title":"Cell Cycle Regulation and Chromatin Remodeling","description":"This cluster is dominated by GO terms centered on cell cycle stages and chromatin dynamics: mitotic cell cycle, G2/M transition, meiotic cell cycle, along with chromatin remodeling and nucleosome disassembly. These terms suggest proteins that coordinate cell division with changes in chromatin structure. Additional terms related to nutrient signaling and metabolism (insulin signaling, sucrose catabolism, glycogen regulation) may reflect growth-state cues that influence cell cycle progression, while chemotaxis signals a broader cellular response environment. Overall, the core theme appears to be regulation of the cell cycle in concert with chromatin remodeling.","confidence":"High","size":21,"edges":8,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0005987","count":2},{"id":"GO:0043044","count":2},{"id":"GO:0006337","count":2},{"id":"GO:2000219","count":2},{"id":"GO:0000086","count":2}]},{"hash":"1177300496512022534","title":"Mitotic cell cycle and transcription regulation","description":"Dominant GO terms cluster around cell division and G2/M transition of the mitotic cell cycle, as well as DNA-templated transcription and transcriptional regulation. This points to a cohesive group of proteins coordinating cell cycle progression with gene expression. Additional terms touch on signaling and autophagy-related assembly, but the primary theme remains cell-cycle control and transcription. ","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0000086","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0000122","count":1},{"id":"GO:0044321","count":1}]},{"hash":"1385199175413818082","title":"RNA metabolism and translation","description":"This cluster is dominated by GO terms related to mRNA processing (polyadenylation, deadenylation-dependent decay, mRNA localization) and translation (cytoplasmic translation, translational elongation). While there are a few immune or growth-factor related terms (B cell homeostasis, lymph node development, EGF response), the core theme centers on RNA metabolism and protein synthesis, suggesting shared involvement in mRNA turnover and ribosome-associated translation.","confidence":"Medium","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":1},{"id":"GO:1902172","count":1},{"id":"GO:0048535","count":1},{"id":"GO:0046782","count":1},{"id":"GO:0002181","count":1}]},{"hash":"2092484141551083437","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":65,"triangles":73,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0035948","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0000466","count":3},{"id":"GO:0000463","count":3}]},{"hash":"1161740110449840602","title":"Mitochondrial electron transport and respiration","description":"The cluster is dominated by GO terms tied to mitochondrial energy metabolism: aerobic respiration, mitochondrial electron transport (cytochrome c to oxygen), and assembly of the respiratory chain complex IV. Additional terms point to proton transmembrane transport and dihydrolipoamide metabolism, both central to mitochondrial ATP production. While there are a couple of peripheral terms (e.g., certain amino-acid catabolic processes), the overarching theme is mitochondrial respiration and energy generation.","confidence":"High","size":20,"edges":181,"triangles":990,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0006212","count":3},{"id":"GO:0042853","count":3},{"id":"GO:0006123","count":3},{"id":"GO:0009060","count":3},{"id":"GO:1902600","count":3}]},{"hash":"1491063738701945937","title":"Unknown","description":"The GO terms are highly heterogeneous (cell wall biogenesis, metal ion transport, peroxisome/autophagy processes, sphingolipid biosynthesis, and mRNA decay) with no clear unifying function, and there are no interactions among the proteins (Edges: 0). This makes it inappropriate to assign a specific cohesive label; Unknown is most suitable.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009272","count":2},{"id":"GO:0006827","count":1},{"id":"GO:0033215","count":1},{"id":"GO:1901684","count":1},{"id":"GO:0032581","count":1}]},{"hash":"39684349925813695","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":22,"triangles":11,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":4},{"id":"GO:0071031","count":3},{"id":"GO:0019076","count":2},{"id":"GO:0019068","count":2},{"id":"GO:0075713","count":2}]},{"hash":"1903080538824856085","title":"Membrane-Targeting and Transport","description":"This cluster is dominated by GO terms related to membrane localization and transfer of molecules: post-translational protein targeting to membranes and ER membranes, plasma membrane transport, and metabolite processing such as ethanol catabolism and nitrogen utilization. While a few terms (seed development, synaptonemal complex assembly, pheromone response) are more organism-specific or broader, the strongest and most recurrent theme is proteins involved in membrane targeting/localization and transport processes. This makes Membrane-Targeting and Transport a concise, representative label for the cluster.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019740","count":2},{"id":"GO:0034589","count":1},{"id":"GO:0006847","count":1},{"id":"GO:0006068","count":1},{"id":"GO:0071497","count":1}]},{"hash":"1500504631046991368","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070935","count":2},{"id":"GO:0033129","count":2},{"id":"GO:0010898","count":2},{"id":"GO:0071374","count":2},{"id":"GO:0000082","count":2}]},{"hash":"1323175576835770473","title":"COPI-Mediated ER-Golgi Trafficking","description":"The dominant GO terms describe ER-to-Golgi vesicle transport, COPI coating/budding, and Golgi ribbon formation, all central to COPI-mediated trafficking in the secretory pathway. While a few terms pertain to development or behavior, the core theme is ER\u2013Golgi transport and COPI vesicle formation, making this a concise, representative label.","confidence":"High","size":20,"edges":14,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":6},{"id":"GO:0048205","count":4},{"id":"GO:0035964","count":4},{"id":"GO:0002121","count":4},{"id":"GO:0090161","count":4}]},{"hash":"427880519549983582","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":189,"triangles":1122,"max_degree":19,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":12},{"id":"GO:0009432","count":10},{"id":"GO:0000463","count":9},{"id":"GO:1902626","count":9},{"id":"GO:0000466","count":9}]},{"hash":"905495181314167285","title":"Autophagy and nucleophagy pathways","description":"This cluster is dominated by GO terms related to autophagy and nuclear/nucleophagy processes: autophagosome assembly, Cvt pathway (cytoplasm to vacuole targeting), piecemeal microautophagy of the nucleus, and nucleophagy. These suggest the proteins function in autophagic degradation and nuclear turnover, with some immune signaling terms appearing as related, likely reflecting cross-talk between autophagy and immunity rather than a primary function. Overall, the common theme is autophagy-based cellular quality control and nuclear autophagy.","confidence":"High","size":20,"edges":12,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006348","count":3},{"id":"GO:0050853","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0035914","count":2}]},{"hash":"75069450914039927","title":"Transcriptional Regulation and Cell Cycle","description":"The cluster shows strong signals for transcription-related processes (DNA-templated transcription, RNA Pol II promoter regulation, nitrogen catabolite activation of transcription) and cell cycle control, with additional but weaker ties to RNA turnover and metabolic regulation. This suggests a cohesive module of proteins involved in governing gene expression and cell division, rather than a single metabolic pathway.","confidence":"Medium","size":20,"edges":14,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000288","count":3},{"id":"GO:0007049","count":3},{"id":"GO:0006351","count":2},{"id":"GO:1901717","count":2},{"id":"GO:1901714","count":2}]},{"hash":"1717622569842222211","title":"Yeast metabolic regulation and transcriptional control","description":"This cluster centers on regulatory processes across metabolism: regulation of cellular respiration, biosynthesis of nucleotides and amino acids, sterol-related pathways, and transcriptional control in response to carbon sources, all consistent with yeast metabolism regulation. The mix of positive regulation terms and carbon-source\u2013responsive transcription terms suggests a functional theme of coordinating metabolic gene expression in yeast, rather than a single enzymatic pathway.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043457","count":4},{"id":"GO:1904741","count":3},{"id":"GO:1900399","count":3},{"id":"GO:2001278","count":3},{"id":"GO:2001158","count":3}]},{"hash":"253356017720196403","title":"Sugar and Nutrient Membrane Transporters","description":"This cluster is dominated by transmembrane transport of sugars (fructose, galactose, glucose) and other nutrients, with supporting terms on glucose starvation response and related uptake processes. The shared theme is membrane transporter activity for carbohydrate and nutrient uptake, with some broader transport roles included.","confidence":"High","size":20,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1990539","count":6},{"id":"GO:0015757","count":6},{"id":"GO:0042128","count":6},{"id":"GO:0042908","count":6},{"id":"GO:0042149","count":6}]},{"hash":"308189967622961663","title":"Embryogenesis and organ morphogenesis","description":"The top GO terms span diverse developmental processes across multiple tissues (placental development, cartilage morphogenesis, endocrine system and pancreatic cell development, heart/EMT in endocardial cushion formation, left-right patterning, and lymph node development), indicating a cohesive theme of embryogenesis and organ morphogenesis rather than a single, narrow function.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060806","count":1},{"id":"GO:0060536","count":1},{"id":"GO:0035270","count":1},{"id":"GO:0003323","count":1},{"id":"GO:0003198","count":1}]},{"hash":"2286427047750604612","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":23,"triangles":17,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000032","count":4},{"id":"GO:0006493","count":4},{"id":"GO:0044845","count":4},{"id":"GO:0006491","count":4},{"id":"GO:0043710","count":4}]},{"hash":"1520062042305462117","title":"Mitochondrial Electron Transport and Proton Transport","description":"It is dominated by energy-production terms: mitochondrial electron transport, respiratory chain, and proton transmembrane transport, indicating a cluster of respiratory components. Some RNA splicing and intron-related terms appear ancillary to the core energy metabolism theme.","confidence":"High","size":19,"edges":55,"triangles":121,"max_degree":11,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:1902600","count":7},{"id":"GO:0006122","count":6},{"id":"GO:0015979","count":5},{"id":"GO:0022904","count":4},{"id":"GO:0090305","count":3}]},{"hash":"920486857423474519","title":"Mitotic cell cycle regulators","description":"The cluster is enriched for mitosis- and cell division-related GO terms (mitotic cell cycle, mitotic sister chromatid biorientation, cell division, exit from mitosis, meiotic cell cycle), suggesting proteins involved in mitotic progression and chromosome segregation. A subset of terms relating to stress signaling and immune response (innate immune response, JNK cascade regulation, cadmium response) may reflect broader regulatory roles or cross-talk but do not override the main mitotic theme. Confidence in this label is therefore Medium.","confidence":"Medium","size":19,"edges":17,"triangles":3,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:1990758","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0051291","count":3}]},{"hash":"81547585371381275","title":"ER-Golgi transport and ER organization","description":"This cluster is dominated by GO terms describing movement of cargo from the ER to the Golgi, COPI coats and vesicle budding, and ER morphology/organization (ER retention, inheritance, tubular networks, Golgi ribbon). These collectively indicate a cohesive module for the secretory pathway and ER architecture, with a few ancillary terms (like nuclear pore assembly or behavior) that are less central. Overall, the common theme is ER-to-Golgi trafficking and ER network organization.","confidence":"High","size":19,"edges":91,"triangles":176,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0006621","count":2},{"id":"GO:0048309","count":2},{"id":"GO:0051292","count":2},{"id":"GO:0071786","count":2}]},{"hash":"1106801589832373996","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":25,"triangles":10,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019835","count":5},{"id":"GO:0015856","count":5},{"id":"GO:1903088","count":5},{"id":"GO:0006209","count":5},{"id":"GO:1903791","count":5}]},{"hash":"1702819834621157392","title":"Neural and craniofacial development with DNA maintenance","description":"The cluster is dominated by neural and craniofacial development terms (neuron development; hippocampus development; embryonic cranial skeleton morphogenesis), indicating a developmental theme in neural and cranial structures. Supporting terms like DNA replication and DNA repair suggest proliferative DNA maintenance accompanying development, while neddylation and endocytosis terms may reflect general cellular processes active during tissue morphogenesis. Overall, the strongest, coherent signal is neural/craniofacial development with concurrent DNA maintenance activities.","confidence":"Medium","size":19,"edges":54,"triangles":61,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0032495","count":4},{"id":"GO:0006281","count":4},{"id":"GO:0045116","count":4},{"id":"GO:0048701","count":4}]},{"hash":"2246510285741383748","title":"Post-transcriptional RNA processing and translation regulation","description":"Proteins in this cluster are enriched for translation initiation/reinitiation and several mRNA processing steps (polyadenylation, stability, and splicing regulation), suggesting a cohesive role in post-transcriptional gene expression control rather than a single narrowly defined function.","confidence":"High","size":19,"edges":133,"triangles":496,"max_degree":18,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0001731","count":5},{"id":"GO:0002188","count":5},{"id":"GO:1903586","count":4},{"id":"GO:1905663","count":4},{"id":"GO:1900363","count":4}]},{"hash":"1474456978913178696","title":"Endocytic and secretory vesicle trafficking","description":"The top GO terms cluster around vesicle transport between the plasma membrane, endosomes, lysosomes, and the ER-Golgi secretory pathway, including endocytic recycling and endosome-to-recycling routes, pointing to a coherent role in intracellular vesicle trafficking and sorting, possibly involving receptor endocytosis and recycling.","confidence":"High","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048227","count":2},{"id":"GO:1902953","count":2},{"id":"GO:0051005","count":2},{"id":"GO:0014902","count":2},{"id":"GO:0048011","count":2}]},{"hash":"2116540831492585296","title":"Unknown","description":"No GO terms or network connections are provided, and the edges/triangles are zero, so there is no shared functional signal to define a label.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"913019940065617677","title":"Regulators of signaling and development","description":"The top GO terms point to broad regulation of signaling pathways (ERK cascade, T cell receptor signaling, phosphorylation, protein binding) along with developmental processes (nervous system and skeletal muscle development) and cellular fate (apoptosis, DNA repair). This suggests the proteins act as regulators across multiple signaling and developmental contexts rather than a single, cohesive function, hence a general label like this is appropriate.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0033138","count":2},{"id":"GO:0032092","count":2},{"id":"GO:0070374","count":2},{"id":"GO:0006915","count":2}]},{"hash":"1000726049774158959","title":"LPS and glycan biosynthesis","description":"The cluster is dominated by GO terms for O antigen biosynthesis, LPS core region biosynthesis, and sugar-related metabolism (galactose, GDP-mannose, ADP-L-glycero-beta-D-manno-heptose), pointing to assembly of bacterial cell envelope glycans and sugar-nucleotide metabolism. Some terms like ergosterol, sporopollenin, and phenylpropanoid biosynthesis are outliers, but the strongest signal ties to polysaccharide/glycan biosynthesis pathways. ","confidence":"High","size":19,"edges":17,"triangles":7,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009243","count":4},{"id":"GO:0006012","count":4},{"id":"GO:0019673","count":4},{"id":"GO:0008204","count":4},{"id":"GO:0055114","count":4}]},{"hash":"2034065301521117726","title":"Rho GTPase Signaling and Cell Adhesion","description":"The top GO terms point to regulation and activation of Rho family GTPases, indicating a core theme of Rho-mediated signal transduction driving cytoskeletal remodeling, adhesion, and related signaling. Contextual terms like EGFR response and platelet secretion fit within broader signaling networks that involve GTPase activity, but the strongest, recurring pattern centers on Rho GTPase regulation.","confidence":"Medium","size":19,"edges":6,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0090630","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0071364","count":2},{"id":"GO:1904693","count":2}]},{"hash":"1781636235363652716","title":"Secretory Pathway Vesicle Trafficking","description":"The terms point strongly to vesicle transport and secretory processes (ER-to-Golgi transport, COPI-coated Golgi vesicles, lipoprotein assembly), suggesting a cohesive theme of secretory pathway function; a few terms are off-theme but do not override the main signal.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071497","count":3},{"id":"GO:0000749","count":2},{"id":"GO:0061000","count":1},{"id":"GO:0030037","count":1},{"id":"GO:1902953","count":1}]},{"hash":"876287118524416688","title":"mRNA processing and translation regulation","description":"The top GO terms cluster around mRNA maturation and handling\u2014nonsense-mediated decay, spliceosome-mediated splicing and mRNA export\u2014along with regulation of translational initiation and reinitiation, indicating a cohesive group involved in mRNA processing and translation control (with TORC1 signaling and cell division as related processes).","confidence":"High","size":18,"edges":47,"triangles":52,"max_degree":16,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000184","count":4},{"id":"GO:1900363","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0006406","count":3}]},{"hash":"916228716822512234","title":"DNA Damage Repair and Chemical Stress Response","description":"The cluster centers on genome maintenance with nucleotide-excision repair and DNA alkylation repair, plus DNA damage checkpoint signaling and apoptotic regulation, suggesting a cohesive DNA-damage response module. Additional terms for cadmium, xenobiotic, estradiol, and folic acid responses indicate broader chemical stress signaling that accompanies DNA repair functions.","confidence":"High","size":18,"edges":65,"triangles":102,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0071276","count":3},{"id":"GO:0007568","count":3},{"id":"GO:0006289","count":2},{"id":"GO:0032355","count":2},{"id":"GO:0006307","count":2}]},{"hash":"1586476680107718541","title":"Ribosome biogenesis and Translation Initiation","description":"The cluster is dominated by GO terms related to ribosome assembly and translation, including translation, ribosome biogenesis, maturation of SSU-rRNA, and formation of the translation preinitiation complex, with multiple terms showing equal emphasis. This points to components involved in producing and initiating new ribosomes for protein synthesis. A few other terms like mitotic cell cycle and cell morphogenesis appear, but the strongest signal centers on ribosome formation and translation control.","confidence":"High","size":18,"edges":57,"triangles":82,"max_degree":11,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0000462","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0002188","count":3}]},{"hash":"883346707718412872","title":"Cerebellar neuron development and Purkinje cell maturation","description":"This cluster is dominated by GO terms tied to cerebellar development, especially Purkinje cell layer maturation, radial glia\u2013guided Purkinje cell migration, and granule cell precursor proliferation, along with general neuron and nervous system development terms. These cohesive cerebellar-focused processes suggest a single functional theme centered on cerebellar neuron formation and maturation; ancillary terms like DNA repair or insulin signaling may be less central.","confidence":"High","size":18,"edges":10,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0021691","count":2},{"id":"GO:0008286","count":2},{"id":"GO:0021942","count":2},{"id":"GO:0048755","count":2},{"id":"GO:1902499","count":2}]},{"hash":"2103929246482922024","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":151,"triangles":785,"max_degree":17,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000462","count":9},{"id":"GO:0000472","count":8},{"id":"GO:0000480","count":8},{"id":"GO:0000463","count":6},{"id":"GO:0042273","count":6}]},{"hash":"2134179037198281764","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000472","count":7},{"id":"GO:0051301","count":7},{"id":"GO:0000480","count":7},{"id":"GO:0001731","count":6},{"id":"GO:0000462","count":6}]},{"hash":"1538873970226548690","title":"Unknown","description":"The terms point to diverse regulatory and metabolic roles, with a mix of plant-specific growth and stress responses and some unrelated mammalian processes, giving no single unifying function for the cluster.","confidence":"","size":18,"edges":19,"triangles":3,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0010520","count":2},{"id":"GO:0010082","count":2},{"id":"GO:0009650","count":2},{"id":"GO:0009410","count":2},{"id":"GO:0006013","count":2}]},{"hash":"1591175000100819414","title":"Unknown","description":"There are no GO terms provided and the network has no connections or enriched terms to suggest a shared function, so no meaningful label can be inferred.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"783200137883845941","title":"Hippo/Wnt-driven development and differentiation","description":"The top GO terms center on developmental signaling and differentiation, notably hippo signaling and positive regulation of canonical Wnt signaling, plus forebrain development and keratinocyte differentiation. The presence of mitotic cell cycle and apoptotic process suggests regulation of proliferation and cell fate during development. Innate immune response and cadmium ion response appear as ancillary stress-related terms but do not define the main theme. Overall, this cluster seems to group proteins involved in growth control, tissue morphogenesis, and differentiation via Hippo/Wnt pathways.","confidence":"Medium","size":18,"edges":4,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":9},{"id":"GO:0045087","count":9},{"id":"GO:0071276","count":8},{"id":"GO:0000902","count":8},{"id":"GO:0035329","count":7}]},{"hash":"2042475956486063956","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":8,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0061481","count":1},{"id":"GO:2000627","count":1},{"id":"GO:0042254","count":1},{"id":"GO:1901254","count":1},{"id":"GO:0010610","count":1}]},{"hash":"2103138253247207779","title":"Yeast stress-response transcription and mating","description":"The cluster centers on stress-related GO terms (endoplasmic reticulum stress, freezing response) and transcriptional regulation (DNA-templated transcription, regulation of DNA binding, negative regulation of transcription by RNA Pol II), with yeast-specific processes like mating/conjugation and cell polarity maintenance. This suggests a yeast-oriented module where stress signals interface with transcriptional control and mating-related development, possibly coordinating environmental response with cellular differentiation.","confidence":"Medium","size":18,"edges":6,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0034976","count":3},{"id":"GO:1903206","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0071497","count":2},{"id":"GO:0000749","count":2}]},{"hash":"2090044189095687489","title":"Unknown","description":"These terms cover disparate cellular processes\u2014from DNA replication and transcription to metabolism and various protein-processing/trafficking events, plus ER-stress\u2013related apoptosis. There isn't a single unifying function that ties all proteins together, so an Unknown label with None confidence is most appropriate.","confidence":"","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042220","count":2},{"id":"GO:0018013","count":2},{"id":"GO:0018107","count":2},{"id":"GO:0006006","count":2},{"id":"GO:0070059","count":2}]},{"hash":"1057781273730041837","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0044205","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0071375","count":2},{"id":"GO:0006696","count":2},{"id":"GO:0030722","count":1}]},{"hash":"227403413910974410","title":"Unknown","description":"The Top Terms include mitochondrial complex IV assembly and aerobic respiration alongside ER-to-Golgi transport, RNA folding, and intron processing. This mix of mitochondrial, vesicular transport, and RNA-processing functions does not point to a single cohesive theme, so a specific, representative label is not reliably assignable.","confidence":"","size":17,"edges":9,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0034337","count":1},{"id":"GO:0006314","count":1},{"id":"GO:0000372","count":1}]},{"hash":"518482552537532317","title":"Genome maintenance and cell-cycle progression","description":"The cluster is enriched for cell division (DNA replication, mitotic DNA replication checkpoint signaling) and DNA repair processes, with transcription-related activity. Additional terms for ER unfolded protein response and proteasome regulatory particle assembly reflect concurrent protein quality control and stress responses that accompany genome maintenance. Overall, the proteins appear to function together to preserve genome integrity during replication and division.","confidence":"High","size":17,"edges":51,"triangles":47,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0006260","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0030968","count":3},{"id":"GO:0070914","count":3}]},{"hash":"473665483329509458","title":"Nuclear transport and RNA export","description":"The top GO terms are dominated by nuclear transport and RNA processing/export activities, including NLS-bearing protein import into the nucleus, tRNA and poly(A)+ mRNA export, and nuclear pore organization, as well as localization to the nuclear inner membrane. Some terms related to metabolic or hormonal responses appear but do not define the core function; overall, the cluster centers on macromolecule trafficking across the nuclear envelope and RNA export. This suggests the proteins belong to the nuclear transport/RNA export machinery.","confidence":"Medium","size":17,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010269","count":3},{"id":"GO:0019563","count":3},{"id":"GO:0006607","count":2},{"id":"GO:0036228","count":2},{"id":"GO:0006409","count":2}]},{"hash":"194112854683722456","title":"Mitochondrial transport and membrane dynamics","description":"The GO terms cluster around mitochondrial functions: transport of ions and metabolites into and across mitochondrial membranes (pyrimidine nucleotides, citrate, magnesium), regulation of membrane permeability, and mitochondrial membrane fission, suggesting a cohesive theme of mitochondrial transport/metabolism and membrane remodeling. Some unrelated terms (vacuolar sorting, pregnancy) appear as noise. ","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043328","count":1},{"id":"GO:0006828","count":1},{"id":"GO:0046902","count":1},{"id":"GO:0007565","count":1},{"id":"GO:1990519","count":1}]},{"hash":"782999784511619295","title":"Signaling and chromatin regulation in development","description":"This cluster includes GO terms for canonical Wnt signaling (both activation and inhibition), T cell receptor signaling, and developmental processes like embryonic cranial skeleton morphogenesis, alongside nuclear functions such as DNA replication, chromatin remodeling, and RNA polymerase II promoter clearance. The common thread is signaling events coupled with chromatin/transcriptional regulation during development and cell-cycle-related processes, suggesting a cohesive role in signal-driven regulation of gene expression in a developmental context.","confidence":"Medium","size":17,"edges":47,"triangles":37,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0090263","count":4},{"id":"GO:0050852","count":4},{"id":"GO:0006260","count":3},{"id":"GO:0090090","count":3},{"id":"GO:0051436","count":3}]},{"hash":"2133564475620160646","title":"Regulation of Translation Initiation","description":"The strongest signals in this cluster are terms related to translation initiation: formation of the translation preinitiation complex, IRES-dependent translational initiation, and regulation of translational initiation. While there are some additional terms (post-translational modification and cell cycle processes), the core pattern points to control of translation initiation as the main theme.","confidence":"Medium","size":17,"edges":8,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0048140","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0075522","count":2},{"id":"GO:0006446","count":2}]},{"hash":"876668083737769536","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":116,"triangles":478,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":4},{"id":"GO:0031124","count":3},{"id":"GO:0016584","count":3},{"id":"GO:0006367","count":3},{"id":"GO:0000472","count":3}]},{"hash":"1507705429214958661","title":"Embryogenesis and tissue differentiation","description":"Dominant signal is embryonic development and tissue specification: placenta, cartilage, endocrine organogenesis, pancreatic cells, EMT in heart cushion, and left-right patterning. A few terms relate to general cellular processes (transcription initiation, nuclear membrane reassembly) seen during development, but they do not override the developmental theme.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060806","count":2},{"id":"GO:0060536","count":2},{"id":"GO:0035270","count":2},{"id":"GO:0003323","count":2},{"id":"GO:0003198","count":2}]},{"hash":"723034963130701558","title":"Developmental Transcriptional Regulation","description":"This cluster groups proteins tied to broad developmental processes (brain, retina, heart, gonad, multicellular organism development) and a central regulatory term (negative regulation of transcription by RNA polymerase II), indicating transcriptional control during development across multiple tissues rather than a single pathway.","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0008584","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0007275","count":2}]},{"hash":"1351031304996063603","title":"Neural development and signaling","description":"The cluster shows enrichment for nervous system development, dendrite morphogenesis, and multiple neural signaling pathways (dopamine response, ephrin receptor signaling, Wnt); accompanied by actin cytoskeleton regulation and protein stability terms, suggesting proteins that coordinate neural differentiation and synaptic signaling.","confidence":"High","size":17,"edges":35,"triangles":25,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031532","count":4},{"id":"GO:1990758","count":3},{"id":"GO:0046330","count":3},{"id":"GO:0007399","count":3},{"id":"GO:1903351","count":3}]},{"hash":"654565540264692195","title":"Endomembrane trafficking and organelle localization","description":"Most GO terms converge on endomembrane transport and organization, including endosomal transport, Golgi to lysosome transport, endosomal vesicle fusion, and overall endomembrane system organization, with additional support from vacuole inheritance and oskar mRNA localization/polarity cues during development. A couple of general terms for transcription and cell division are present but do not override the core trafficking/localization theme.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0048227","count":1},{"id":"GO:0090160","count":1},{"id":"GO:0016197","count":1}]},{"hash":"1286849327293607170","title":"Autophagosome Biogenesis","description":"The cluster shows multiple autophagy-related GO terms (macroautophagy, autophagosome assembly, autophagosome membrane docking) and related membrane-trafficking activity (SNARE complex assembly), suggesting these proteins share a role in autophagosome formation and vesicle fusion. The other GO terms appear incidental and less representative of the primary function. Overall, the dominant autophagy-related terms indicate autophagosome biogenesis as the central theme.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030846","count":2},{"id":"GO:0035493","count":1},{"id":"GO:0007098","count":1},{"id":"GO:0016236","count":1},{"id":"GO:0000045","count":1}]},{"hash":"1743555593225717962","title":"Transcriptional Regulation of Metabolic Pathways","description":"This cluster is dominated by GO terms about DNA-templated transcription and regulation of transcription from RNA Pol II promoter, with several entries tied to metabolic cues (carbon source, respiration, amino acid biosynthesis). The common theme appears to be modulation of metabolic-gene expression in response to nutrient/energy states, rather than a single enzymatic pathway.","confidence":"Medium","size":17,"edges":84,"triangles":183,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0035961","count":2},{"id":"GO:1904741","count":2},{"id":"GO:0061415","count":2},{"id":"GO:2001196","count":2}]},{"hash":"179655886377480554","title":"Neurodevelopment and interneuron differentiation","description":"This cluster is driven by terms tied to neural development and interneuron differentiation (cerebral cortex GABAergic interneuron, olfactory bulb interneuron, subpallium neuron fate, spinal cord oligodendrocyte fate), with supporting signals from neural crest migration and broad embryonic organogenesis. The presence of placenta, pancreas, and bronchiole development terms suggests broader developmental programs, but the strongest common theme centers on neurodevelopment and interneuron specification, making the label a good representation overall. ","confidence":"Medium","size":17,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0021892","count":2},{"id":"GO:0031018","count":2},{"id":"GO:0001755","count":2},{"id":"GO:0021889","count":2},{"id":"GO:0060435","count":2}]},{"hash":"560883811464590010","title":"Placental and cardiac development with vascular signaling","description":"The terms include heart development, maternal placenta development, labyrinthine layer blood vessel development, and fibroblast migration, with supporting signals such as prostaglandin response, JNK cascade regulation, and peptidyl-threonine phosphorylation. Together they point to developmental programs governing placenta and heart formation, vascular remodeling, and related signaling pathways; apoptosis appears but is not the dominant theme.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":4},{"id":"GO:0007121","count":3},{"id":"GO:2001275","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0001893","count":3}]},{"hash":"878230607810101634","title":"Autophagy and organelle trafficking","description":"These proteins appear linked to autophagy-related pathways (pexophagy, phagophore assembly, and the Cvt pathway) as well as intracellular transport between ER, cytosol, and vacuole/ER exit sites. The combination suggests a coherent theme of autophagy-associated vesicle trafficking, with ancillary calcium signaling context. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030242","count":1},{"id":"GO:0034497","count":1},{"id":"GO:0032258","count":1},{"id":"GO:0051561","count":1},{"id":"GO:0032471","count":1}]},{"hash":"279262775427621577","title":"DNA Metabolism and Oxidative Stress Response","description":"This cluster centers on DNA metabolism (DNA-templated transcription, DNA replication, deoxyribonucleotide biosynthesis) and oxidative stress/detoxification responses, suggesting a coordinated group involved in nucleotide metabolism with redox defense. Some metabolic terms appear broader context, but the dominant signal is DNA-related processes linked to stress response.","confidence":"Medium","size":16,"edges":5,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0034599","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0006094","count":2},{"id":"GO:0009236","count":2}]},{"hash":"455357615463326494","title":"Ascomycete ascospore formation and cell wall biosynthesis","description":"The dominant GO terms center on ascospore wall beta-glucan biosynthesis and assembly, plus fungal-type cell wall synthesis, which together indicate a sporulation-related cell wall construction program in fungi; accompanying terms like filamentous growth and division septum assembly reflect related developmental processes, while calcium signaling and cyclic nucleotide biosynthesis suggest regulatory coordination.","confidence":"High","size":16,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070509","count":2},{"id":"GO:0009190","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0034412","count":2},{"id":"GO:0071970","count":2}]},{"hash":"1152044047436552219","title":"Ubiquitin-mediated proteolysis and cell cycle control","description":"This cluster is dominated by terms related to protein turnover and quality control (SCF-dependent ubiquitination, proteasomal degradation, protein polyubiquitination, glycoprotein catabolism) alongside cell cycle processes (mitotic cell cycle, cell division) and ER stress response (unfolded protein response), suggesting a theme of proteostasis coordinating cell proliferation. Some terms are peripheral (methylmercury response, histone demethylation), but the core signals proteolysis and cell cycle regulation.","confidence":"Medium","size":16,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046626","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0030968","count":2},{"id":"GO:0031146","count":1}]},{"hash":"1029846305062881588","title":"Telomere Chromatin Silencing and Cell Cycle Regulation","description":"This cluster is dominated by terms for subtelomeric heterochromatin formation and telomere-specific chromatin silencing, indicating roles in maintaining telomere structure. It also includes terms related to the mitotic cell cycle and general cell cycle processes, along with SCF-dependent ubiquitin-proteasomal protein catabolic processes and apoptosis. The combination suggests proteins that connect chromatin state at telomeres with cell division and proteostasis, forming a coherent theme around telomere chromatin maintenance coupled to cell cycle control.","confidence":"High","size":16,"edges":85,"triangles":233,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006348","count":9},{"id":"GO:0031939","count":8},{"id":"GO:0030466","count":8},{"id":"GO:0030433","count":6},{"id":"GO:0051301","count":6}]},{"hash":"405005984007454124","title":"Ribosome Biogenesis and Translation","description":"This cluster's strongest GO terms center on cytoplasmic translation and ribosomal large subunit assembly/biogenesis, indicating involvement in ribosome production and protein synthesis. Additional terms regarding protein stabilization and targeting align with ribosome-associated quality control and post-translational regulation, but the dominant theme is ribosome biogenesis and translation.","confidence":"High","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":11},{"id":"GO:0000027","count":6},{"id":"GO:0032092","count":2},{"id":"GO:0050821","count":2},{"id":"GO:0042273","count":2}]},{"hash":"1382932193673214963","title":"RNA Processing and Translational Initiation Regulation","description":"These proteins cluster around translation initiation, including formation of the preinitiation complex, IRES-dependent and reinitiation events, and regulation of translational initiation, suggesting a module focused on controlling protein synthesis at initiation. The presence of regulatory ncRNA-mediated gene silencing and spliceosome-associated regulation of splicing hints at broader RNA-processing roles that modulate translation. A few terms (e.g., obsolete polyadenylation, transcription-coupled repair) are peripheral to the core theme. Overall, the cluster appears to couple RNA processing with initiation-level translation control.","confidence":"Medium","size":16,"edges":67,"triangles":135,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0002188","count":2}]},{"hash":"764440270881965690","title":"Ribosome biogenesis and translation","description":"This cluster is dominated by GO terms for translation and ribosome biogenesis, with multiple terms pointing to LSU-rRNA maturation, rRNA/pseudouridine synthesis, and box C/D snoRNP assembly\u2014key steps in building and modifying ribosomes. A few regulatory terms related to MAPK signaling appear, but the core signal clearly reflects ribosome production and function. Confidence: High","confidence":"","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":12},{"id":"GO:0042254","count":4},{"id":"GO:0000027","count":4},{"id":"GO:1900745","count":2},{"id":"GO:0000185","count":2}]},{"hash":"1415297974350485136","title":"Mitochondrial protein import and mitophagy","description":"The top GO terms point to mitochondrial maintenance: protein import into the mitochondrial matrix, calcium import into mitochondria, and regulation of mitophagy, plus ROS regulation. This suggests a core theme of mitochondrial quality control and function, with some neuronal terms reflecting mitochondria\u2019s role in synaptic activity and learning. Overall, the cluster appears centered on mitochondrial import, calcium handling, and turnover. ","confidence":"High","size":16,"edges":60,"triangles":116,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0030150","count":4},{"id":"GO:0007270","count":3},{"id":"GO:0007612","count":3},{"id":"GO:0006820","count":3},{"id":"GO:0036444","count":3}]},{"hash":"1375036482769212772","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0006369","count":4},{"id":"GO:0042273","count":4},{"id":"GO:0030490","count":4},{"id":"GO:0045292","count":4}]},{"hash":"365477182496668000","title":"Developmental growth and cell cycle","description":"This cluster is dominated by GO terms related to development (brain development, male gonad development, single fertilization, osteoblast differentiation, multicellular organism growth) and cell division/chromatin assembly (mitotic cell cycle, CENP-A containing chromatin assembly), suggesting a core theme around developmental programs and cell proliferation. A defense response to Gram-positive bacteria appears among the top terms but is less aligned with the main developmental/cell cycle signals, possibly representing annotation overlap or incidental associations. Overall, the label captures the prevailing functional orientation of the cluster.","confidence":"Medium","size":16,"edges":68,"triangles":135,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0050830","count":7},{"id":"GO:0008584","count":6},{"id":"GO:0007420","count":6},{"id":"GO:0071276","count":6},{"id":"GO:0007338","count":6}]},{"hash":"1059062858417560691","title":"Regulated translation initiation and TORC1 signaling","description":"This cluster is dominated by translation initiation and its regulation, including preinitiation complex formation, reinitiation, IRES- and viral-associated initiation, and TORC1 signaling with mRNA stabilization and ncRNA-mediated gene silencing as supportive regulatory factors; a spinal cord development term is an outlier. The overall theme is translational control.","confidence":"High","size":16,"edges":48,"triangles":50,"max_degree":10,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0001731","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0021510","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0038202","count":4}]},{"hash":"547725996258928897","title":"Cell Cycle and Chromosome Segregation","description":"The cluster\u2019s strongest signals are mitosis-related: sister chromatid cohesion, chromosome segregation, and general cell division, with additional hints of transcriptional regulation and translation initiation, suggesting a module coordinating chromosome management during the cell cycle.","confidence":"High","size":16,"edges":47,"triangles":55,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0030433","count":3},{"id":"GO:0007064","count":2},{"id":"GO:0045143","count":2},{"id":"GO:0043966","count":2}]},{"hash":"487378353973896446","title":"Unknown","description":"The terms include mitochondrial translation, nucleotide and phosphate transport, and proteasome assembly, with no single shared function across the proteins; this appears to be a mixed or misclustered set, so a single cohesive label cannot be assigned.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032543","count":1},{"id":"GO:0015862","count":1},{"id":"GO:0035364","count":1},{"id":"GO:0006817","count":1},{"id":"GO:0043248","count":1}]},{"hash":"674732917036675664","title":"Mitotic progression and APC/C ubiquitination","description":"The cluster is dominated by terms tied to mitosis and cell-cycle control, notably mitotic cell cycle, anaphase-promoting complex-dependent catabolic process, and mitotic spindle assembly, along with K11-linked ubiquitination linked to APC/C regulation. Additional terms related to protein transport and nuclear pore localization fit the broader reorganization of cellular machinery during cell division. This combination strongly points to mitotic machinery and ubiquitin-mediated regulation as the core theme. ","confidence":"High","size":16,"edges":118,"triangles":533,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070979","count":6},{"id":"GO:0051301","count":6},{"id":"GO:0031145","count":6},{"id":"GO:0000278","count":5},{"id":"GO:0030433","count":4}]},{"hash":"64629318149343223","title":"Developmental signaling and transcription","description":"The cluster combines terms related to morphogenesis and differentiation (cell morphogenesis, mast cell differentiation, estrogen response) with signaling pathways (MAPK-related activity, long-term synaptic potentiation, calcium-dependent exocytosis) and core gene expression processes (DNA replication, DNA-templated transcription). This suggests a cohesive theme around developmentally regulated signaling and gene expression, including neuronal plasticity and hormonal responses, rather than a single specialized process.","confidence":"Medium","size":16,"edges":12,"triangles":2,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000902","count":6},{"id":"GO:0006260","count":6},{"id":"GO:0006351","count":4},{"id":"GO:0034198","count":4},{"id":"GO:0035994","count":4}]},{"hash":"2253712568029657085","title":"Phosphate Transport and Homeostasis","description":"The top GO terms are dominated by phosphate-related processes: transmembrane transport of phosphate ions, intracellular phosphate ion homeostasis, and responses to phosphate starvation, indicating a coherent cluster of proteins involved in phosphate handling and balance. A few terms like cell division and B cell receptor signaling are less central, but do not override the phosphate-centric theme, suggesting some multifunctional members. ","confidence":"High","size":16,"edges":23,"triangles":13,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0050859","count":2},{"id":"GO:2000769","count":2},{"id":"GO:0016036","count":2}]},{"hash":"252208464898730010","title":"Transcription Regulation and Endocytic Trafficking","description":"The cluster shows enrichment for transcription-related processes (DNA-templated transcription; negative regulation of transcription by RNA polymerase II) alongside vesicle trafficking terms (clathrin-dependent endocytosis; endosome to lysosome transport; CvT pathway) and related signaling (cellular response to EGF) plus redox-related terms. This combination suggests two related functional themes: regulation of gene expression and intracellular transport/signaling via endocytic pathways, making the label representative though not exclusively unified. ","confidence":"Medium","size":16,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0045988","count":3},{"id":"GO:0072583","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0007289","count":2}]},{"hash":"981059201709387473","title":"Transcriptional Regulation and RNA Processing","description":"Most represented terms point to regulation of gene expression, especially transcriptional control (GO:0006355, GO:0007249) and RNA processing (GO:0035196). A few terms hint at signaling roles (neurotransmitter secretion, voltage-gated sodium channel regulation) but are less frequent, so the core theme remains transcriptional regulation and RNA processing.","confidence":"Medium","size":16,"edges":25,"triangles":9,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007269","count":2},{"id":"GO:1904378","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0000289","count":2}]},{"hash":"1757564723204935770","title":"Lipid metabolism and xenobiotic catabolism","description":"This cluster is dominated by metabolic and detoxification processes: triglyceride catabolism, regulation of endocannabinoid signaling (lipid signaling), several xenobiotic/aromatic compound catabolic pathways (1,2-dichloroethane, 3-phenylpropionate, beta-ketoadipate), cellular oxidant detoxification, and biotin biosynthesis. A single term about secondary shoot formation is an outlier, but the overall theme centers on lipid-related signaling and broad metabolic/catabolic functions.","confidence":"Medium","size":16,"edges":26,"triangles":22,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":11},{"id":"GO:2000124","count":11},{"id":"GO:0019260","count":9},{"id":"GO:0010223","count":9},{"id":"GO:0042952","count":9}]},{"hash":"628830088622832015","title":"Muscle Development and Regeneration","description":"Based on the strongest GO signals within the cluster (heart development, cardiac muscle hypertrophy in response to stress, and skeletal muscle satellite cell maintenance for regeneration), the dominant theme appears to be muscle development and regeneration. The other terms (seed development, placenta morphogenesis, T cell differentiation, transcription regulation) are more divergent and may reflect broader developmental roles or annotation noise, but the muscle-related terms provide the clearest tying thread. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":2},{"id":"GO:0014898","count":2},{"id":"GO:0048316","count":1},{"id":"GO:0033082","count":1},{"id":"GO:0090309","count":1}]},{"hash":"2106224399016015759","title":"Mitochondrial metabolism and cristae formation","description":"The cluster is dominated by mitochondrial functions: pyruvate import and acetyl-CoA biosynthesis, translation in mitochondria and membrane protein insertion, and cristae formation, all of which tie to energy production and insulin secretion in glucose-stimulated cells. Ion homeostasis and transport (potassium) further support mitochondrial energetics, while occasional unrelated terms (sporulation, 6-sulfoquinovose catabolism) may reflect annotation noise.","confidence":"High","size":15,"edges":52,"triangles":77,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0035774","count":3},{"id":"GO:0061732","count":3},{"id":"GO:1902361","count":3},{"id":"GO:0051204","count":2},{"id":"GO:0070131","count":2}]},{"hash":"806653419579557335","title":"Hypusine-dependent translation regulation","description":"The top GO terms cluster around core protein synthesis processes: translation, initiation, and termination, plus regulation of translational fidelity and elongation. Notably, peptidyl-hypusine biosynthetic process points to hypusination of eIF5A, a key driver of translation elongation, especially over polyproline stretches, which also aligns with positive regulation of translational elongation and, in some contexts, frameshifting. A few terms about defense-related programmed cell death or vacuole inheritance appear secondary to the dominant translation-focused signal. Overall, this cluster seems to reflect components of the translation machinery and its regulation via hypusine modification.","confidence":"High","size":15,"edges":36,"triangles":25,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0006353","count":2},{"id":"GO:0006450","count":2},{"id":"GO:0034050","count":2},{"id":"GO:0045905","count":2}]},{"hash":"1834330707898045138","title":"SRP/Sec-Dependent Targeting to Membrane","description":"This cluster is dominated by GO terms for targeting nascent proteins to membranes via SRP and Sec pathways, including cotranslational and post-translational translocation and secretion, indicating a membrane protein targeting/secretion module. Other terms like lipid biosynthesis and cell cycle are present but peripheral.","confidence":"High","size":15,"edges":89,"triangles":341,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":2},{"id":"GO:0006605","count":1},{"id":"GO:0043952","count":1},{"id":"GO:0031204","count":1},{"id":"GO:0009306","count":1}]},{"hash":"589869101038225015","title":"Quinone and tetrapyrrole cofactor biosynthesis","description":"Based on the GO terms, the proteins are enriched for biosynthesis of several quinones (menaquinone, plastoquinone, phylloquinone) and vitamin K, as well as heme O and chlorophyll, all of which are cofactors or pigments derived from tetrapyrroles or quinone pathways. This points to a common theme of producing electron carriers and photosynthetic pigments rather than a single, narrow function. Some terms (e.g., placenta development, cardiac differentiation) appear to be outliers or annotation noise, not central to the cluster\u2019s function.","confidence":"High","size":15,"edges":30,"triangles":37,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0001893","count":2},{"id":"GO:2000727","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0015995","count":2},{"id":"GO:0048034","count":2}]},{"hash":"1795475462655220615","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":61,"triangles":105,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":7},{"id":"GO:0006888","count":7},{"id":"GO:0030433","count":6},{"id":"GO:0000472","count":6},{"id":"GO:0051260","count":6}]},{"hash":"952715072964583805","title":"Lipid and Steroid Metabolism","description":"The proteins are enriched for retinoid metabolism (retinol, retinal), sphingolipid-related processes (IPC metabolic process), sebaceous gland differentiation, and CNS myelin maintenance, along with steroid biosynthesis (testosterone and estrogen). This points to a unifying theme of lipid- and steroid-mediated metabolism across tissues, with retinoid and sphingolipid pathways as central connectors. Some terms (e.g., propylene catabolic process, BH4 biosynthesis) are less directly tied but do not outweigh the lipid/steroid pattern.","confidence":"Medium","size":15,"edges":17,"triangles":4,"max_degree":4,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0042572","count":5},{"id":"GO:0042574","count":5},{"id":"GO:0001949","count":3},{"id":"GO:0032286","count":3},{"id":"GO:0006675","count":3}]},{"hash":"2103677921395254842","title":"Cell Division and Vesicle Trafficking","description":"Connections among GO terms point to ongoing cell proliferation and division (cell division; mitotic spindle assembly; mitotic cell cycle; cell population proliferation) while also highlighting intracellular trafficking and protein processing (COPII-coated vesicle budding; retrograde Golgi-ER transport; ribosomal large subunit export). Ubiquitination likely modulates these processes during the cell cycle. The combination suggests a functional module centered on cell division with coordinated vesicle trafficking and protein turnover.","confidence":"High","size":15,"edges":26,"triangles":19,"max_degree":9,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0016567","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0035690","count":4},{"id":"GO:0000055","count":4},{"id":"GO:0006890","count":4}]},{"hash":"1364882997672621334","title":"RNA processing and Fe-S cluster biosynthesis","description":"The GO terms show a strong emphasis on RNA metabolism (adenosine-to-inosine editing, snoRNA catabolic process, translation) alongside iron-sulfur cluster assembly/maturation, suggesting a functional cluster around RNA processing enzymes that require Fe-S cofactors. Other terms (DNA repair, prenylation-related biosynthesis) are secondary, making the primary theme RNA processing with Fe-S cluster involvement. ","confidence":"Medium","size":15,"edges":54,"triangles":89,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0097428","count":2},{"id":"GO:0016226","count":2},{"id":"GO:0006382","count":1},{"id":"GO:0045337","count":1}]},{"hash":"1989088754413956642","title":"Ribosome biogenesis and translation","description":"The top GO terms cluster around translation, ribosome assembly, and rRNA maturation (e.g., translation, ribosome assembly, maturation of SSU-rRNA, and mitochondrial translation), which strongly indicates a theme focused on the protein synthesis machinery. The development-related terms (heart development, angiogenesis, sperm capacitation) likely reflect broader roles of these components in multicellular contexts rather than a separate function of the cluster. Overall, the core signal is ribosome biogenesis and translation with ancillary developmental associations.","confidence":"High","size":15,"edges":75,"triangles":222,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0007275","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0000462","count":2},{"id":"GO:0070131","count":2}]},{"hash":"760531541454625179","title":"Methylation and RNA modification","description":"Several top GO terms point to methylation, including rRNA methylation, tRNA methylation, peptidyl-arginine methylation (ADMA), peptidyl-glutamine methylation, and general rRNA modification. While a few terms relate to lipid biosynthesis and growth, the dominant signal is diverse methylation activities affecting RNA and proteins, suggesting a cluster of methyltransferases or modification enzymes.","confidence":"High","size":15,"edges":18,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0001300","count":2},{"id":"GO:0006656","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0018364","count":1},{"id":"GO:0006972","count":1}]},{"hash":"1231089604121749951","title":"Nuclear transport and ribosome biogenesis","description":"This cluster centers on nuclear import/export and ribosome assembly processes, including proteins involved in import into the nucleus, export of the ribosomal large subunit, ribosomal protein import, nuclear pore complex assembly, and rRNA maturation. The presence of GO terms for GTPase regulation also aligns with Ran-family\u2013mediated transport. A minor term about intraciliary transport is noted but does not override the dominant nuclear\u2013ribosome theme.","confidence":"Medium","size":15,"edges":60,"triangles":122,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0000055","count":3},{"id":"GO:0006607","count":3},{"id":"GO:0042176","count":3},{"id":"GO:0060188","count":3}]},{"hash":"1033665959839580728","title":"Ribosome Biogenesis and Protein Synthesis with Cell Cycle","description":"The GO terms cluster around ribosome biogenesis (ribosomal subunit biogenesis, export from nucleus), cytoplasmic translation, and ribosome-associated processes, together with DNA-templated transcription and cell cycle. This points to a coherent theme of ribosome assembly and function tightly linked to cell growth and division, with translation regulation also touching on nutrient/stress responses. ","confidence":"High","size":15,"edges":8,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1903833","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006400","count":1},{"id":"GO:1901001","count":1}]},{"hash":"138078546130636808","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":104,"triangles":442,"max_degree":14,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000472","count":5},{"id":"GO:0000184","count":5},{"id":"GO:0000398","count":5},{"id":"GO:0000480","count":5},{"id":"GO:0048568","count":5}]},{"hash":"1191215636555153801","title":"Retinoid and steroid metabolism","description":"The top GO terms center on retinol and retinal metabolic processes and on testosterone/androgen biosynthesis, suggesting a shared theme of retinoid and steroid hormone metabolism. Some bacterial biosynthetic terms appear less related and may reflect broader biosynthetic activity or annotation noise, but the dominant pattern supports a retinoid-steroid metabolic cluster.","confidence":"Medium","size":15,"edges":24,"triangles":11,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0042572","count":4},{"id":"GO:0061370","count":4},{"id":"GO:0042574","count":4},{"id":"GO:0008209","count":4}]},{"hash":"1734697694715758878","title":"Cell Cycle and Mitosis","description":"Dominant GO terms point to cell division and mitosis, including cell cycle, exit from mitosis, and nuclear membrane reassembly, indicating this cluster mainly concerns mitotic progression and cytokinesis. Some non-central terms appear incidental and do not change the overall theme.","confidence":"High","size":15,"edges":19,"triangles":17,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0006915","count":5},{"id":"GO:0010458","count":5},{"id":"GO:0007049","count":5},{"id":"GO:0031468","count":4}]},{"hash":"963883766662984976","title":"Lipopolysaccharide and O-antigen Biosynthesis","description":"The GO terms point strongly to lipopolysaccharide and O-antigen biosynthesis (LPS, O-antigen, UDP-GlcNAc, GDP-mannose) and related cell wall organization, suggesting these proteins function together in LPS and cell wall production; a few transcription and nucleotide catabolism terms appear incidental to the core theme.","confidence":"High","size":15,"edges":15,"triangles":3,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009103","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0009243","count":3},{"id":"GO:0006048","count":3},{"id":"GO:0071555","count":3}]},{"hash":"1736668257328077231","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":58,"triangles":131,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0000467","count":4},{"id":"GO:0071042","count":3},{"id":"GO:0016973","count":3},{"id":"GO:0071035","count":3},{"id":"GO:0006397","count":3}]},{"hash":"1700313186939287923","title":"Ubiquitin-regulated Transcription in Development","description":"Exploration of top GO terms shows a combination of protein polyubiquitination and transcriptional regulation (DNA-templated transcription; negative regulation of Pol II transcription), plus developmental processes (brain development; seminiferous tubule development). This points to a theme of ubiquitin-dependent control of gene expression active in development.","confidence":"Medium","size":15,"edges":28,"triangles":16,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0032208","count":2},{"id":"GO:0072520","count":2}]},{"hash":"128233084250985437","title":"Unknown","description":"The top GO terms are highly diverse and only loosely related, spanning chromatin/ transcription regulation, cell division, development, stress responses, and germline differentiation. There is no clear, cohesive function or pathway that ties these proteins together, and several terms are obsolete, so a single representative label cannot be confidently assigned.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006348","count":2},{"id":"GO:2000575","count":1},{"id":"GO:0000022","count":1},{"id":"GO:0071406","count":1},{"id":"GO:0016479","count":1}]},{"hash":"501731763904391059","title":"mRNA Decapping and P-body Regulation","description":"The cluster is characterized by GO terms centered on mRNA decapping (both deadenylation-dependent and -independent), negative regulation of translation, and positive/processing body assembly, which together define a set of proteins involved in mRNA turnover and translational control (P-body\u2013related). While a few metabolic biosynthesis terms appear, the predominance of RNA metabolism terms supports this theme.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0042619","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0000290","count":1},{"id":"GO:0017148","count":1}]},{"hash":"1603443592362455867","title":"Transmembrane Transporters for Ions and Metabolites","description":"The top GO terms point to transport across membranes for diverse ions and metabolites (K+, phosphate, nitrate, galactose, fucose, sialic acid, vitamins) and include neurotransmitter loading into synaptic vesicles, indicating a unifying theme of membrane transport without a single substrate. This justifies a label of broad transmembrane transporters.","confidence":"High","size":15,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":6},{"id":"GO:0035435","count":6},{"id":"GO:0098700","count":5},{"id":"GO:0006855","count":5},{"id":"GO:0015706","count":5}]},{"hash":"563934486481793691","title":"Transmembrane transport and vacuolar trafficking","description":"This cluster is dominated by GO terms related to membrane transport and vacuolar sorting, including transmembrane transport, xenobiotic transport, calcium export, amino acid export, and trafficking to vacuoles via multivesicular body pathways, as well as auxin transport. A few terms like palmitoylation and sebaceous gland development are less directly related, but the core signal points to membrane transport and vacuolar trafficking functions.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018230","count":2},{"id":"GO:0042144","count":2},{"id":"GO:0048733","count":2},{"id":"GO:0006855","count":2},{"id":"GO:1990034","count":2}]},{"hash":"2121772591440212122","title":"Fungal Vacuolar and Endosomal Trafficking","description":"Top GO terms indicate a core role in vacuolar transport via the multivesicular body pathway, endosome localization, and ER exit, with additional membrane transport and chitin biosynthesis signals suggesting fungal development. This combination points to a cohesive function in intracellular trafficking and membrane transport in fungi, including vacuole/endosome sorting and related processes.","confidence":"High","size":15,"edges":24,"triangles":29,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0043328","count":8},{"id":"GO:0030435","count":1},{"id":"GO:0010570","count":1},{"id":"GO:0006855","count":1},{"id":"GO:0045332","count":1}]},{"hash":"123928696593726446","title":"Diverse Transmembrane Transport","description":"The cluster is dominated by GO terms for transport across membranes of a wide variety of substrates (nitrate, arabinose, galactose, fucose, sialic acid, vitamins, xenobiotics, potassium ions) and even vesicle-associated neurotransmitter loading, indicating a coherent theme of membrane transport rather than a single substrate or process. Although nitrate assimilation is a metabolic term, the overall pattern supports a broad transmembrane transport function. ","confidence":"High","size":15,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":9},{"id":"GO:0098700","count":8},{"id":"GO:0015751","count":8},{"id":"GO:0006855","count":8},{"id":"GO:0015706","count":8}]},{"hash":"2267464186880213526","title":"Developmental gene regulation and cytoskeleton remodeling","description":"The terms cluster around embryonic development (spinal cord development, gastrulation, multicellular organism development) alongside transcriptional control (DNA-templated transcription) and RNA processing (RNA guanine-N7 methylation), plus actin filament remodeling. Although some terms are obsolete, the dominant signal points to developmental gene expression and cytoskeletal changes during morphogenesis.","confidence":"Medium","size":14,"edges":50,"triangles":84,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0009097","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0007584","count":3},{"id":"GO:0036265","count":3}]},{"hash":"178172211485680707","title":"Mitochondrial translation and ribosome biogenesis","description":"This cluster centers on mitochondrial protein synthesis and ribosome assembly, reflected by GO terms for translation, mitochondrial translation termination, ribosome biogenesis, and protein insertion into the mitochondrial inner membrane.","confidence":"High","size":14,"edges":40,"triangles":49,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0070126","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0019284","count":1},{"id":"GO:0016310","count":1}]},{"hash":"1976861911948235220","title":"Mitochondrial assembly and oxidative stress","description":"The cluster\u2019s strongest terms center on mitochondrial complexity and assembly (mitochondrial respiratory chain complex IV assembly) as well as redox-related responses (cellular response to hydrogen peroxide, obsolete oxidation-reduction process), which together point to a core theme of mitochondrial function and oxidative stress handling. Some terms related to reproductive development (prostate gland development, male sex differentiation) and cell cycle are present but appear less central, likely reflecting multifunctional proteins or annotation spillover. Overall, a concise label focusing on mitochondrial assembly and oxidative stress best captures the dominant signal.","confidence":"Medium","size":14,"edges":13,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":2},{"id":"GO:0061179","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006463","count":2},{"id":"GO:0046661","count":2}]},{"hash":"597098257331162811","title":"Ribosome Biogenesis and rRNA Processing","description":"Most GO terms point to ribosome production and maturation: ribosome biogenesis, maturation/processing of 5.8S and LSU rRNA, ITS1 cleavage, and translation, with related protein import and spliceosome-associated remodeling. The dominant theme is assembly of ribosomes and their translation function, with a few auxiliary nuclear processes. ","confidence":"High","size":14,"edges":89,"triangles":341,"max_degree":13,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":6},{"id":"GO:0000464","count":5},{"id":"GO:0002181","count":4},{"id":"GO:0000466","count":4},{"id":"GO:0000463","count":4}]},{"hash":"194662576637153925","title":"Mitochondrial Transport and Metabolic Signaling","description":"This cluster centers on mitochondrial processes: transport of ions (manganese, magnesium), metabolites like citrate and nucleotides into mitochondria, membrane permeability and fission, and signaling related to insulin/IGF responses, pointing to core mitochondrial metabolism and regulation. The pregnancy term appears ancillary/noise rather than a defining theme.","confidence":"High","size":14,"edges":29,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":8},{"id":"GO:0006828","count":7},{"id":"GO:0046902","count":7},{"id":"GO:0007565","count":7},{"id":"GO:1990519","count":7}]},{"hash":"631916636155299009","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":16,"triangles":10,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009408","count":6},{"id":"GO:0006986","count":6},{"id":"GO:0006260","count":6},{"id":"GO:0001707","count":5},{"id":"GO:0006626","count":5}]},{"hash":"2244951543074569289","title":"ER glycosylation and protein targeting","description":"The top terms show N- and O-linked glycosylation and post-translational targeting to the ER membrane, plus Sec-dependent transport and ERAD-related quality control, pointing to ER-based protein maturation and trafficking. A few terms like development and magnesium transport are less central.","confidence":"High","size":14,"edges":63,"triangles":140,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0018279","count":4},{"id":"GO:0035269","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0015693","count":2},{"id":"GO:0006620","count":2}]},{"hash":"1521271693365453452","title":"Oxidative Stress Response and Redox Homeostasis","description":"GO terms converge on oxidative stress management, including detoxification of oxidants and redox balance via deglutathionylation, indicating a cohesive redox-regulation theme.","confidence":"High","size":14,"edges":26,"triangles":38,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1903026","count":7},{"id":"GO:0098869","count":7},{"id":"GO:0055114","count":7},{"id":"GO:0080058","count":7},{"id":"GO:0034599","count":7}]},{"hash":"2122961881897240168","title":"Developmental Epigenetic Regulation","description":"The cluster centers on chromatin-based transcriptional control (histone demethylation, chromatin binding, transcription regulation) and includes development processes such as blastocyst formation and morphogenesis, implying an epigenetic module governing developmental gene expression.","confidence":"Medium","size":14,"edges":21,"triangles":8,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0061188","count":3},{"id":"GO:0035563","count":3},{"id":"GO:0001825","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0006351","count":3}]},{"hash":"2066291193652566956","title":"Developmental Gene Regulation and Signaling","description":"The cluster is enriched for transcription-related terms (DNA-templated transcription, alternative mRNA splicing) and development-associated processes (heart development, cerebral cortex development, hippocampus development), with supporting signals from insulin receptor signaling and cell size regulation. This points to a group of proteins involved in controlling gene expression during development and related signaling pathways.","confidence":"Medium","size":14,"edges":10,"triangles":1,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0043433","count":4},{"id":"GO:0000380","count":3},{"id":"GO:0007095","count":3},{"id":"GO:0008286","count":3}]},{"hash":"530524898536496827","title":"Stress-Responsive Protein Folding and Ubiquitination","description":"This cluster's GO terms point to protein folding (GO:0006457) and peptidyl-prolyl isomerization (GO:0000413), along with K11-linked ubiquitination (GO:0070979) and oxidative stress response (GO:0070301). Together these indicate a theme of protein quality control and cellular stress responses. Peripheral signals like lipid droplet organization and viral process terms may reflect context-specific roles or annotation noise, rather than core cluster function.","confidence":"Medium","size":14,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0070979","count":1},{"id":"GO:0070301","count":1},{"id":"GO:1901407","count":1},{"id":"GO:0034389","count":1},{"id":"GO:0019064","count":1}]},{"hash":"517198881386803426","title":"ER stress response and cell-cycle coordination","description":"The top GO terms point to ER-associated processes (unfolded protein response and ER-Golgi transport) alongside core gene expression and cell-cycle activities (DNA replication, G1/S transition, RNA polymerase III\u2013related transcription/translation). This suggests a cluster of proteins that bridge ER stress management with transcription/translation and progression through the cell cycle, rather than a single narrow pathway. Confidence: Medium","confidence":"","size":14,"edges":13,"triangles":4,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0030968","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1637187082194533961","title":"Unknown","description":"Top GO terms span diverse processes (cell wall organization, dephosphorylation, response to testosterone, copper and zinc ion transport, various carbohydrate-related metabolism and catabolic/biosynthetic pathways). With no edges connecting the proteins, there isn\u2019t a single coherent function linking them. Therefore, I cannot assign a meaningful specific label beyond Unknown, with no confidence.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":2},{"id":"GO:0016311","count":2},{"id":"GO:0033574","count":2},{"id":"GO:0006825","count":2},{"id":"GO:0006045","count":2}]},{"hash":"2190178118966289483","title":"Embryonic Development and Tissue Morphogenesis","description":"The top GO terms cluster around placental/trophoblast differentiation, cartilage morphogenesis, endocrine and pancreatic development, and left-right patterning, indicating a cohesive theme of embryonic development and tissue morphogenesis; a couple of more general processes appear at low frequency.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060806","count":4},{"id":"GO:0060536","count":4},{"id":"GO:0035270","count":4},{"id":"GO:0003323","count":4},{"id":"GO:0003198","count":4}]},{"hash":"274311348161296902","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":23,"triangles":19,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006782","count":4},{"id":"GO:0017000","count":3},{"id":"GO:0055129","count":3},{"id":"GO:0009089","count":3},{"id":"GO:0009102","count":3}]},{"hash":"2182928691759390185","title":"Unknown","description":"The top GO terms span highly diverse processes (DNA replication, transcription, metabolism, signaling, neuron axon fasciculation, immune signaling, pain response, pollen recognition, and nuclear export), with only a single edge connecting proteins. This lacks a cohesive theme or shared pathway, suggesting the cluster does not reflect a single biological function. ","confidence":"","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0006006","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0000189","count":4},{"id":"GO:0097156","count":4}]},{"hash":"19225911192517727","title":"Cell Cycle and Innate Immune Signaling","description":"This cluster centers on cell cycle regulation (DNA replication initiation, G2/M transition) alongside stress- and immune-related pathways (ER stress\u2013induced apoptosis, amino acid starvation response, innate immune defense, and Gram-positive bacteria defense). The presence of microtubule localization and developmental terms suggests integration with cytoskeletal dynamics during division and signaling. Overall, a cohesive theme is the coupling of cell cycle control with stress and immune responses.","confidence":"Medium","size":14,"edges":11,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0032298","count":4},{"id":"GO:0050830","count":3},{"id":"GO:0051092","count":3},{"id":"GO:0000086","count":3},{"id":"GO:0034198","count":3}]},{"hash":"1055842172894780482","title":"Stress-Activated Signaling and Apoptosis","description":"The top terms cluster around apoptotic processes and stress-responsive signaling (JNK cascade, osmosensory signaling, cadmium/arsenite responses), with support from transcriptional regulation and exocytosis. This suggests a coherent theme of cellular stress signaling leading to apoptosis, even though some terms are broader (e.g., cell migration, transcription). ","confidence":"Medium","size":14,"edges":6,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":3},{"id":"GO:0016477","count":2},{"id":"GO:0045956","count":2},{"id":"GO:2001033","count":2},{"id":"GO:0071276","count":2}]},{"hash":"391597244846732538","title":"Fungal cell wall biogenesis and GPI-anchored protein trafficking","description":"The top GO terms cluster around synthesis of fungal-type cell wall components, attachment of GPI anchors to proteins, and trafficking of such proteins to the vacuole via multivesicular body sorting, which together point to fungal cell wall assembly and surface protein processing. The other terms (nucleotide metabolism and unrelated processes) appear more incidental and do not define the core theme. ","confidence":"Medium","size":14,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009272","count":3},{"id":"GO:0043328","count":1},{"id":"GO:0016255","count":1},{"id":"GO:0051402","count":1},{"id":"GO:0002100","count":1}]},{"hash":"800338269797351234","title":"Golgi trafficking and SNARE-mediated protein localization","description":"The dominant GO terms center on Golgi apparatus processes (Golgi ribbon formation, ER-to-Golgi transport, regulation of Golgi organization, Golgi-to-vacuole transport) and SNARE complex assembly, plus terms related to protein localization to cell surfaces and plasma membranes. This points to a cohesive function group of proteins involved in Golgi-based vesicular trafficking and membrane targeting, with SNAREs facilitating fusion. There are also hints of specialized secretory roles (cornified envelope, acrosome reaction) that fit membrane trafficking contexts.","confidence":"High","size":14,"edges":14,"triangles":10,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0090161","count":4},{"id":"GO:0006888","count":4},{"id":"GO:1903358","count":3},{"id":"GO:0006896","count":3},{"id":"GO:0035493","count":2}]},{"hash":"1589772469010697111","title":"Sterol and Fatty Acid Biosynthesis","description":"The GO terms overwhelmingly point to lipid metabolism, especially sterol biosynthesis (ergosterol and cholesterol via lathosterol, 4-alpha-methyl-delta7-sterol oxidation, and regulation of ergosterol biosynthesis) and fatty acid/ether lipid synthesis, suggesting a cohesive lipid biosynthesis module. A few terms related to immune or skin differentiation appear as potential noise. ","confidence":"High","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046485","count":1},{"id":"GO:0000001","count":1},{"id":"GO:0080065","count":1},{"id":"GO:0032443","count":1},{"id":"GO:0006636","count":1}]},{"hash":"889117935827348489","title":"Multisystem Signaling and Stress Responses","description":"The cluster\u2019s GO terms span immune signaling (T cell receptor signaling, beta selection, ephrin receptor signaling), neural development and dopamine response, as well as metabolic and stress-related processes (xenobiotic response, glucose starvation, glucose homeostasis, JNK cascade), suggesting a broad theme of signaling and stress responses across different systems rather than a single, narrow function.","confidence":"Medium","size":13,"edges":20,"triangles":4,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035690","count":3},{"id":"GO:0042149","count":3},{"id":"GO:0050852","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0042593","count":2}]},{"hash":"1391361092896897830","title":"Antioxidant detox and PI3K/AKT signaling in neurons","description":"The top GO terms point to detoxification of cellular oxidants and hydrogen peroxide catabolism, indicating an oxidative stress response. Additionally, there are terms related to activation and positive regulation of PI3K/AKT signaling and serine phosphorylation, suggesting coordinated signaling events. The dopaminergic synaptic transmission term hints at a neuronal context, while transcription and nuclear regulation terms may reflect downstream responses; overall the cluster appears to combine antioxidant processes with AKT pathway signaling in a neural setting.","confidence":"Medium","size":13,"edges":7,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0098869","count":5},{"id":"GO:0042744","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0032148","count":3},{"id":"GO:0033138","count":3}]},{"hash":"21903778072712624","title":"Mitochondrial energy metabolism and proton transport","description":"This cluster is dominated by GO terms tied to mitochondrial ATP synthesis driven by the proton motive force, proton transmembrane transport, and organellar acidification (vacuolar). These reflect a common theme of energy production and maintenance of proton gradients across membranes. Some other terms (lipid metabolism, lysine homeostasis, transcription regulation, angiogenesis, etc.) appear peripheral or broader in scope, but do not override the central energy/gradient theme.","confidence":"Medium","size":13,"edges":59,"triangles":151,"max_degree":11,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006626","count":4},{"id":"GO:0042776","count":4},{"id":"GO:1902906","count":3},{"id":"GO:0090463","count":3},{"id":"GO:0006629","count":3}]},{"hash":"233234390821684470","title":"Aldehyde and Alcohol Metabolism with Stress Response","description":"This cluster is enriched for aldehyde/alcohol metabolism (formaldehyde, furaldehyde, ethanol, retinol, fatty acids) and stress response processes (nitrosative stress, copper ion response, nitrosylation), suggesting a cohesive theme of detoxification and metabolic processing of aldehydes/alcohols coupled with stress signaling.","confidence":"High","size":13,"edges":44,"triangles":76,"max_degree":11,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0046294","count":10},{"id":"GO:0042572","count":10},{"id":"GO:0051409","count":10},{"id":"GO:0010430","count":10},{"id":"GO:0046688","count":10}]},{"hash":"514561802615719699","title":"Unknown","description":"This cluster has no interactions (Edges: 0, Triangles: 0, Max Degree: 0) and no GO terms shown. With 13 proteins and no shared functional signals, there is no clear common function to label. The data provides no basis to connect their roles, so the appropriate label is Unknown.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2059456323616000223","title":"RNA processing and post-transcriptional regulation","description":"The terms cluster around post-transcriptional control of mRNA: mRNA splicing by the spliceosome, mRNA polyadenylation and regulation, mRNA stability, and miRNA-mediated silencing of translation. This points to a cohesive group of proteins involved in RNA maturation and regulation after transcription.","confidence":"High","size":13,"edges":22,"triangles":35,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0035278","count":7},{"id":"GO:0045292","count":7},{"id":"GO:1903586","count":6},{"id":"GO:1905663","count":6},{"id":"GO:1900363","count":6}]},{"hash":"792968431467353058","title":"Diverse Signaling and Stimulus Responses","description":"This cluster includes GO terms across GPCR signaling regulation, cellular responses to prostaglandin E and glucagon, pheromone signaling, photoreceptor development, auxin transport, and related signaling contexts. The unifying theme is broad signal transduction and responses to various stimuli rather than a single, cohesive pathway, making a high-level label like \u201cDiverse Signaling and Stimulus Responses\u201d appropriate.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008277","count":1},{"id":"GO:0003380","count":1},{"id":"GO:0071380","count":1},{"id":"GO:0007637","count":1},{"id":"GO:0042462","count":1}]},{"hash":"895970171322845977","title":"Regulated vesicle trafficking and vacuole fusion","description":"The top GO terms cluster around intracellular transport, vesicle tethering, endosome-to-lysosome transport, and regulation of SNARE complex assembly and vacuole/vacuolar fusion, with some Rap-mediated GTPase signaling. This pattern points to a cohesive module coordinating vesicle trafficking and membrane fusion, particularly in the vacuole/endosome system.","confidence":"High","size":13,"edges":29,"triangles":27,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0032889","count":3},{"id":"GO:0032486","count":2},{"id":"GO:0090630","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0042144","count":2}]},{"hash":"1238438719157580607","title":"Amino acid and cofactor biosynthesis cluster","description":"Most of the top GO terms describe biosynthetic processes for amino acids (histidine, phenylalanine, alanine, aspartate) and cofactors (biotin, heme), with additional terms touching on lipid biosynthesis (sphingomyelin) and regulatory signaling (positive regulation of TORC2 signaling) as well as fruit ripening. This suggests a broader metabolic biosynthesis theme rather than a single tightly connected function, so the label reflects the central pattern while acknowledging variability. ","confidence":"Medium","size":13,"edges":24,"triangles":19,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1904515","count":2},{"id":"GO:0000105","count":2},{"id":"GO:0034276","count":2},{"id":"GO:0033585","count":2},{"id":"GO:0009102","count":2}]},{"hash":"146438564551294480","title":"Mitochondrial Transport and Membrane Dynamics","description":"Most terms converge on mitochondrial function: transport of ions, import/export of nucleotides and metabolites, and regulation of membrane permeability and fission; several terms touch on metabolic signaling pathways (insulin/IGF). The cluster thus represents mitochondrial transport and membrane dynamics with metabolic signaling relevance.","confidence":"High","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006828","count":13},{"id":"GO:0046902","count":13},{"id":"GO:0007565","count":13},{"id":"GO:1990519","count":13},{"id":"GO:0090149","count":13}]},{"hash":"1877489872144383687","title":"ER-Golgi and endosomal vesicle transport","description":"This cluster is dominated by terms describing vesicle trafficking between the ER and Golgi (anterograde and retrograde) and endosomal transport (early to late endosomes, endosome to Golgi), indicating a core theme of intracellular transport. The presence of positive regulation of GTPase activity points to small GTPases (e.g., Rab proteins) as key regulators of these trafficking steps. While mitotic cell cycle and cell division appear, the central signal remains vesicle trafficking and membrane transport pathways, with some autophagy-related CVT pathway involvement, supporting a cohesive transport-centric cluster.","confidence":"Medium","size":12,"edges":44,"triangles":77,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0000278","count":4},{"id":"GO:0006888","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0051301","count":3}]},{"hash":"960386618804628980","title":"Unknown","description":"The top terms span mitochondrial protein import and chaperone activity, cell division, proteolysis, RNA processing, stress responses, reproduction-related binding, and even plant cell wall polysaccharide catabolism, indicating no single cohesive function dominates this cluster.","confidence":"","size":12,"edges":26,"triangles":24,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0051131","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0045041","count":4},{"id":"GO:0030245","count":3},{"id":"GO:0045493","count":2}]},{"hash":"2197404413155319782","title":"Redox metabolism and oxidative stress detoxification","description":"This cluster centers on redox-related functions: oxidative stress response, cellular oxidant detoxification, and F420-dependent metabolism, plus a TNT degradation path, all pointing to redox-based detoxification and pollutant metabolism. Some outliers (thyroid hormone generation, vacuolar acidification, uracil catabolism) exist, but the dominant theme is redox biology and detoxification.","confidence":"Medium","size":12,"edges":15,"triangles":7,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0034599","count":3},{"id":"GO:0052645","count":2},{"id":"GO:0046256","count":2},{"id":"GO:0006590","count":2}]},{"hash":"219432609387055437","title":"Iron-sulfur cluster assembly and maturation","description":"Prominent terms point to [2Fe-2S] cluster assembly and transfer, and maturation of Fe-S proteins (GO:0044571, GO:0097428), indicating these proteins participate in the biogenesis and maturation of iron-sulfur cofactors. Additional terms related to RNA processing and cell-cycle regulation may reflect broader cellular roles or downstream effects, but the Fe-S biogenesis axis is the most coherent unifying theme for this cluster.","confidence":"Medium","size":12,"edges":26,"triangles":19,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:1903026","count":2},{"id":"GO:0006406","count":2},{"id":"GO:0034396","count":1},{"id":"GO:0044571","count":1},{"id":"GO:0036086","count":1}]},{"hash":"2109824995692303429","title":"Osmotic Stress and Carbohydrate Biosynthesis","description":"The cluster\u2019s top GO terms center on osmotic protection and carbohydrate metabolism (response to sorbitol, mannitol, water deprivation; biosynthesis of glycogen, starch, sucrose), with supporting links to mycothiol and bacillithiol biosynthesis. This suggests proteins involved in producing osmoprotectants and storing energy as carbohydrates, common in bacteria under osmotic stress. Confidence in this theme is High.","confidence":"High","size":12,"edges":15,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0072708","count":3},{"id":"GO:0008654","count":3},{"id":"GO:0005978","count":3},{"id":"GO:0009414","count":3},{"id":"GO:0019252","count":3}]},{"hash":"171045278245375719","title":"Sugar and nutrient transporters under osmotic stress","description":"The terms show diverse transport activities for sugars (fructose, galactose, glucose), along with nitrate, urate, dehydroascorbic acid, and xenobiotics, plus a cellular response to osmotic stress. This points to a transporter-centric cluster whose common function is moving diverse substrates across membranes in response to osmotic/nutrient stress.","confidence":"High","size":12,"edges":22,"triangles":12,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006970","count":5},{"id":"GO:1990539","count":4},{"id":"GO:0015757","count":4},{"id":"GO:0042128","count":4},{"id":"GO:0042908","count":4}]},{"hash":"1412468723971528549","title":"Unknown","description":"The top GO terms span multiple unrelated processes (cerebral cortex development, T cell receptor signaling, Wnt signaling, apoptosis, DNA replication, splicing, sperm capacitation) plus noise (obsolete oxidation-reduction term), with no clear, single functional theme linking the cluster. This diversity suggests there isn\u2019t a cohesive function to label succinctly.","confidence":"","size":12,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045793","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0021987","count":2},{"id":"GO:0048240","count":2}]},{"hash":"250643204476111345","title":"ER-Golgi Vesicle Transport","description":"Dominated by ER\u2013Golgi and retrograde vesicle transport terms, plus general intracellular transport, with a few entries on protein isomerization and lipid transport; together they point to vesicular trafficking in the secretory pathway.","confidence":"High","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0006886","count":2},{"id":"GO:1903071","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0000413","count":2}]},{"hash":"556308063034138513","title":"Mitochondrial transport and dynamics in metabolic signaling","description":"The top GO terms concentrate on mitochondria-related processes: ion transport (manganese, magnesium), regulation of membrane permeability, mitochondrial fission, nucleotide import, and citrate transport, plus genome maintenance. Also, signals related to insulin/IGF and pregnancy point to metabolic regulation linked to mitochondrial function. Together, they suggest a cluster of proteins involved in mitochondrial transport and dynamics tied to metabolic signaling.","confidence":"High","size":12,"edges":65,"triangles":210,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0061179","count":11},{"id":"GO:0006828","count":10},{"id":"GO:0046902","count":10},{"id":"GO:0007565","count":10},{"id":"GO:1990519","count":10}]},{"hash":"270704179514137583","title":"Ribosome biogenesis and translation machinery","description":"The cluster is dominated by GO terms related to protein synthesis and ribosome function\u2014translation, ribosome biogenesis, initiation, elongation, and termination, plus selenocysteine incorporation and cytoplasmic translation regulation. This points to a cohesive group of proteins involved in ribosome assembly and the translation process, with a few outliers like glial proliferation and antibiotic response that are less central to the core theme. Overall, the functions cohere around the machinery and regulation of translation.","confidence":"High","size":12,"edges":50,"triangles":124,"max_degree":11,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0042254","count":6},{"id":"GO:0014009","count":5},{"id":"GO:0000288","count":5},{"id":"GO:0006415","count":5}]},{"hash":"855521622080626049","title":"Ribosome biogenesis and translation","description":"The cluster is enriched for preribosome assembly, large subunit biogenesis, LSU-rRNA maturation, ribosome biogenesis, and translation, pointing to a shared function in ribosome formation and protein synthesis. Minor terms about respiration and lipid biosynthesis are outliers.","confidence":"High","size":12,"edges":19,"triangles":13,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:1902626","count":3},{"id":"GO:0042273","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0006412","count":2}]},{"hash":"228536127603878323","title":"Peroxisomal Lipid Metabolism and Spermatogenesis","description":"The cluster\u2019s GO terms cluster around peroxisomal functions, including very long-chain fatty acid metabolism, protein import into the peroxisome matrix, and peroxisome\u2013chloroplast associations, with several spermatogenesis/meiosis terms (primary spermatocyte growth, spermatocyte division, male meiosis cytokinesis) suggesting a germ-cell development angle. While there are some plant-related terms that seem out of place, the dominant signal ties peroxisomal lipid processing to germ-cell meiosis processes, justifying the label. ","confidence":"Medium","size":12,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048147","count":1},{"id":"GO:0007285","count":1},{"id":"GO:0000038","count":1},{"id":"GO:0009640","count":1},{"id":"GO:0007112","count":1}]},{"hash":"1031615902586527946","title":"Unknown","description":"The GO terms are highly diverse and span cell cycle, RNA processing, neural development, metabolism, transcription, vesicle transport, and immune response, with no clear, single functional theme tying the proteins together; therefore a cohesive, intuitive label cannot be assigned.","confidence":"","size":12,"edges":8,"triangles":3,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0009236","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0042220","count":2},{"id":"GO:0000447","count":2}]},{"hash":"282842238345637886","title":"Cofactor biosynthesis and sulfur metabolism","description":"The top GO terms cluster around biosynthetic pathways for essential cofactors and sulfur-related metabolism: siroheme biosynthesis, cobalamin biosynthesis, sulfate assimilation, methionine biosynthesis, and methylation. A few obsolete terms and a single potassium transport term are less informative. Taken together, this cluster seems to group proteins involved in assembling cofactors and processing sulfur-containing compounds rather than a single transport or signaling function.","confidence":"High","size":12,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019354","count":1},{"id":"GO:0009086","count":1},{"id":"GO:0000103","count":1},{"id":"GO:0032259","count":1},{"id":"GO:0009236","count":1}]},{"hash":"1991187131087883673","title":"Cardiac development and mitosis regulation","description":"The cluster includes heart development terms (endocardial cushion development, cardiac muscle tissue regeneration) alongside cell cycle/mitosis terms (mitotic spindle organization, mitotic sister chromatid biorientation, microtubule polymerization, kinetochore attachment) and transcription regulation (DNA-templated transcription and its regulation). This suggests a module integrating cardiac development signals with cell division machinery and transcription control, rather than a single metabolic process. Confidence: Medium","confidence":"","size":12,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0009236","count":2},{"id":"GO:0003197","count":2},{"id":"GO:0061026","count":2},{"id":"GO:0006355","count":2}]},{"hash":"1325575970158789957","title":"Protein quality control and degradation","description":"Most prominent GO terms describe proteostasis processes, including ubiquitin-dependent ERAD, proteasome regulatory particle assembly, and endosomal microautophagy, along with protein processing. Additional terms touch on vesicle transport and heat response, suggesting involvement in stress-related protein turnover. While some terms (e.g., transcription or viral replication) appear unrelated or obsolete, the core pattern points to protein quality control and turnover. Confidence: Medium","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0016485","count":1},{"id":"GO:0003341","count":1},{"id":"GO:0061738","count":1}]},{"hash":"1427087506014724073","title":"DNA Replication and Chromosome Maintenance","description":"The terms cluster around core genome maintenance activities: DNA replication, double-strand break repair by homologous recombination, and chromosomal condensation/cohesion during mitosis and meiosis, including rDNA chromatin organization. This points to a cohesive module governing DNA replication/repair and higher-order chromatin dynamics across cell division and meiotic processes.","confidence":"High","size":12,"edges":64,"triangles":201,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0000733","count":4},{"id":"GO:0009432","count":4},{"id":"GO:0000724","count":4},{"id":"GO:0007076","count":3}]},{"hash":"2027815774125415225","title":"Oxidative and ER Stress Response","description":"The terms mainly reflect redox and protein-folding stress: cellular oxidant detoxification, response to oxidative stress, and endoplasmic reticulum stress responses, plus protein deglutathionylation and redox-related regulation. A few terms about transcriptional regulation of RNA Pol II appear secondary, suggesting transcriptional adjustment under stress, while unrelated terms like viral process or endothelial proliferation may be incidental. Overall the cluster seems to represent cellular stress response with emphasis on redox balance and ER stress.","confidence":"Medium","size":12,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":1},{"id":"GO:1903026","count":1},{"id":"GO:0098869","count":1},{"id":"GO:0033158","count":1},{"id":"GO:0055114","count":1}]},{"hash":"1901067625330266967","title":"Nuclear transcription and RNA processing","description":"Enriched GO terms include nucleolus organization, RNA splicing, mRNA processing, and regulation of DNA-templated transcription, indicating a core role in nuclear gene expression and RNA maturation. A few terms about translation initiation factor assembly and other cellular processes appear, but the dominant signature is transcription and RNA processing in the nucleus.","confidence":"High","size":12,"edges":27,"triangles":21,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0007000","count":2},{"id":"GO:0008380","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1256343568015958532","title":"ER-Golgi Trafficking and MHC II Presentation","description":"The top GO terms point to a core role in the secretory pathway (ER-to-Golgi transport, COPII vesicle loading, intracellular transport) with an additional association to antigen processing and presentation via MHC class II, suggesting these proteins function together in protein trafficking and immune antigen processing. Some DNA replication/repair and development terms appear, but they are less central to the cluster\u2019s main theme. Overall, the strongest, cohesive signal is ER-Golgi trafficking linked to antigen presentation.","confidence":"Medium","size":12,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0051534","count":2},{"id":"GO:0090110","count":2}]},{"hash":"566997118180762119","title":"ERK/MAPK signaling and apoptotic regulation","description":"The top GO terms show an emphasis on ERK1/ERK2 cascade regulation, apoptosis, and stress responses, with additional mentions of transcription and signaling initiation. This points to a coherent module of signaling pathways (notably MAPK/ERK) that regulate gene expression and cell fate decisions, occasionally intersecting with cell cycle-related signaling. Confidence in this theme is Medium due to some divergent terms (e.g., visual perception, septation signaling) that broaden the functional scope but do not override the central MAPK/apoptosis signal cluster.","confidence":"Medium","size":12,"edges":15,"triangles":2,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0031028","count":2},{"id":"GO:0033138","count":2},{"id":"GO:0032092","count":2},{"id":"GO:0070374","count":2},{"id":"GO:0006915","count":2}]},{"hash":"919806324899389136","title":"Adaptive immune signaling and actin remodeling","description":"The cluster prominently features adaptive immune signaling terms (T cell receptor signaling, NK T cell differentiation, B cell affinity maturation) alongside actin cytoskeleton remodeling terms (lamellipodium assembly, actin filament binding), suggesting proteins that coordinate immune activation with cytoskeletal dynamics. Some other terms hint at broader trafficking or development roles, but the core theme is immune signaling linked to actin remodeling.","confidence":"High","size":12,"edges":38,"triangles":73,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0045056","count":5},{"id":"GO:0001865","count":5},{"id":"GO:1904531","count":5},{"id":"GO:0060444","count":5},{"id":"GO:0010954","count":5}]},{"hash":"1491879523280634750","title":"Actin Cytoskeleton Remodeling and Cell Polarity","description":"This cluster is dominated by GO terms tied to actin dynamics and cell shape: barbed-end capping, actin polymerization, lamellipodium and ruffle formation, and dendritic spine morphogenesis, all pointing to actin-driven remodeling of the cytoskeleton. Additional terms reflect cell polarity, endothelial barrier aspects, and immune signaling (T cell receptor) as downstream contexts where actin remodeling is crucial. Taken together, the proteins likely participate in coordinated actin cytoskeleton rearrangements that govern cell motility, shape, and junctional integrity across diverse cell types.","confidence":"High","size":12,"edges":33,"triangles":38,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0051016","count":4},{"id":"GO:0071963","count":3},{"id":"GO:1902237","count":3},{"id":"GO:0030041","count":3},{"id":"GO:1903753","count":3}]},{"hash":"1247782992521168233","title":"Mitochondrial translation and oxidative phosphorylation","description":"This cluster combines protein synthesis machinery with mitochondrial energy-generation processes. The dominant translation and ribosome biogenesis terms co-occur with mitochondrial cristae formation, electron transport, ATP synthase complex assembly, and proton motive force-driven ATP production, pointing to a cohesive module of mitochondrially targeted protein synthesis linked to respiration.","confidence":"High","size":11,"edges":30,"triangles":34,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0015966","count":2},{"id":"GO:0042407","count":1},{"id":"GO:0006122","count":1},{"id":"GO:0033615","count":1}]},{"hash":"2129273712983782477","title":"Mitochondrial energy production and copper homeostasis","description":"The cluster\u2019s GO terms cluster around mitochondrial function: proton motive force\u2013driven ATP synthesis and respiratory chain complex IV assembly point to oxidative phosphorylation; cristae formation and protein complex oligomerization reflect inner-membrane structure and multi-subunit complex assembly; mitochondrial translation is indicated by the translation term, and copper ion transport/homeostasis (including intracellular copper) aligns with cytochrome c oxidase metal cofactors and redox balance. An oocyte construction term seems less central but may reflect maternal mitochondrial components. Overall, the protein set appears to represent mitochondrial energy metabolism and copper handling.","confidence":"High","size":11,"edges":53,"triangles":148,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0015986","count":3},{"id":"GO:0035786","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0042407","count":1},{"id":"GO:0099132","count":1}]},{"hash":"721991565813864318","title":"RNA methylation and translation","description":"This cluster centers on translation and diverse RNA methylation/modification processes, including rRNA and tRNA methylation, guanine-N7 methylation, and mRNA capping, suggesting a core role in RNA processing and ribosome-associated modification. Some other terms (biotin/ubiquinone biosynthesis, hyperosmotic response) are peripheral noise relative to the dominant RNA-centric theme. ","confidence":"Medium","size":11,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0018364","count":1},{"id":"GO:0006972","count":1},{"id":"GO:0070476","count":1},{"id":"GO:0019919","count":1}]},{"hash":"2101770783978004009","title":"Golgi-vacuole vesicle trafficking and autophagosome docking","description":"This cluster is dominated by GO terms for vesicle transport between the Golgi, vacuoles/lysosomes, and autophagic compartments: SNARE complex assembly, intra-Golgi vesicle transport, vesicle fusion with Golgi, vacuole fusion, Golgi ribbon formation, and autophagosome membrane docking. Eosinophil degranulation reflects secretory vesicle activity, supporting a trafficking/exocytosis theme. The TCA cycle term appears as an outlier; overall, the pattern reflects vesicle trafficking and autophagy-related processes.","confidence":"High","size":11,"edges":51,"triangles":135,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006099","count":2},{"id":"GO:0035493","count":1},{"id":"GO:0043308","count":1},{"id":"GO:0042144","count":1}]},{"hash":"2042198583805206994","title":"Diverse Small-Molecule Biosynthesis","description":"A mix of GO terms centers on biosynthesis of various small molecules: antibiotics, poly-hydroxybutyrate, retinol/retinal vitamins, sex steroids, and alkaloids, plus a developmental cue (lung development) that can relate to retinoid signaling. This suggests the cluster groups proteins involved in multiple biosynthetic pathways rather than a single, coherent function, hence a broad \u201cdiverse biosynthesis\u201d label.","confidence":"Medium","size":11,"edges":5,"triangles":1,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0017000","count":5},{"id":"GO:0042619","count":5},{"id":"GO:0042572","count":3},{"id":"GO:0061370","count":3}]},{"hash":"125540973068828243","title":"Metabolic Stress Response and DNA Repair","description":"The top GO terms include metabolic processes (fructose metabolism, carbohydrate phosphorylation), oxidative stress response and protein quality control, plus genome maintenance activities (nucleotide-excision repair) and cell cycle-related terms. This mix points to a cluster balancing metabolism with stress response and DNA repair, rather than a single specialized function.","confidence":"Medium","size":11,"edges":10,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006000","count":2},{"id":"GO:0046835","count":2},{"id":"GO:0032024","count":2},{"id":"GO:0006515","count":1},{"id":"GO:0034599","count":1}]},{"hash":"1709413425657829701","title":"Post-transcriptional mRNA Processing and Regulation","description":"These proteins cluster around RNA processing and post-transcriptional regulation. The top GO terms emphasize mRNA splicing via the spliceosome, mRNA polyadenylation, regulation of mRNA stability under stress, mRNA stabilization, alternative splicing regulation, and miRNA-mediated translational silencing, all pointing to coordinated control of mRNA fate after transcription. Obsolete terms do not negate the core theme. ","confidence":"High","size":11,"edges":16,"triangles":10,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":3},{"id":"GO:1903586","count":2},{"id":"GO:1905663","count":2},{"id":"GO:1900363","count":2},{"id":"GO:0006378","count":2}]},{"hash":"1921552284451255690","title":"Chromosome regulation and cell cycle","description":"Proteins in this cluster show a convergence on chromosome biology and cell division: dosage compensation, DNA-templated transcription, DNA replication, G1/S transition, meiotic cell cycle, and kinetochore localization. Some terms relate to neural or immune contexts, but the core signal is regulation of chromosomal processes and cell cycle events.","confidence":"Medium","size":11,"edges":30,"triangles":32,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009048","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0043029","count":3},{"id":"GO:0060079","count":3},{"id":"GO:0014044","count":3}]},{"hash":"67226378269026408","title":"Aldehyde and Redox Metabolism with Stress Signaling","description":"This cluster centers on metabolism of small aldehydes and related compounds (formaldehyde, furaldehyde, retinol, omega-oxidation of fatty acids, and non-phosphorylated glucose catabolism, plus pyruvate fermentation), and is supplemented by redox- and metal-stress responses (nitrosative stress, copper ion response, S-nitrosylation) and extracellular signaling regulation. The combination suggests roles in aldehyde metabolism and redox signaling under stress rather than a single canonical pathway.","confidence":"Medium","size":11,"edges":45,"triangles":120,"max_degree":9,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0042572","count":11},{"id":"GO:0046294","count":9},{"id":"GO:0051409","count":9},{"id":"GO:0010430","count":9},{"id":"GO:0046688","count":9}]},{"hash":"2168850473270096118","title":"Proteostasis and organelle quality control","description":"This cluster centers on maintaining protein homeostasis through processing, degradation, and stress-related dynamics (stress granule disassembly, proteasome assembly, autophagy-related endosomal pathways), along with trafficking and retention of proteins in organelles (Golgi, peroxisomes) and heat/aging-related responses, suggesting a cohesive theme of proteostasis and organelle quality control under stress.","confidence":"Medium","size":11,"edges":47,"triangles":105,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0035617","count":4},{"id":"GO:0045053","count":4},{"id":"GO:0016485","count":3},{"id":"GO:0061738","count":3},{"id":"GO:0070682","count":3}]},{"hash":"1168582794007323593","title":"Neuronal polarity and receptor trafficking","description":"This cluster centers on cell polarity and actin cytoskeleton organization with involvement in endocytosis and transport of neurotransmitter receptors to the postsynaptic membrane, supporting neuronal development and synaptic signaling (e.g., substantia nigra development, receptor trafficking). While some terms (e.g., T cell signaling, androgen receptor signaling) are broader signaling pathways, the dominant pattern links polarity, cytoskeleton dynamics, and synaptic receptor trafficking in neurons. Confidence: Medium","confidence":"","size":11,"edges":18,"triangles":8,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0071963","count":3},{"id":"GO:0090263","count":2},{"id":"GO:0030521","count":2},{"id":"GO:0000001","count":2},{"id":"GO:0098887","count":2}]},{"hash":"1221352726666707874","title":"Amino acid biosynthesis and related metabolism","description":"Top GO terms indicate a cluster centered on amino acid biosynthesis and related metabolism (serine, tryptophan, pyruvate pathways, transsulfuration, and coenzyme M). Some detox- or stress-related terms (cadmium response, morphine response) may reflect broader regulatory or stress-associated co-expression rather than a single shared function.","confidence":"Medium","size":11,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043278","count":3},{"id":"GO:0000162","count":3},{"id":"GO:0042866","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0019499","count":2}]},{"hash":"1454242839988541761","title":"DNA repair and proteostasis in neurons","description":"The cluster combines DNA replication and repair processes (DNA replication; nucleotide-excision repair; meiotic double-strand break repair) with protein quality control and trafficking pathways (ER-to-Golgi transport; ubiquitin-dependent ERAD; aggresome assembly), plus neuronal context signals (substantia nigra development; excitatory synaptic potential). This suggests a thematic linkage between genome maintenance and proteostasis within neuronal cells, potentially affecting development and synaptic function. ","confidence":"Medium","size":10,"edges":43,"triangles":105,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0021762","count":5},{"id":"GO:1990918","count":5},{"id":"GO:0006888","count":5},{"id":"GO:0043588","count":4}]},{"hash":"45167495592215814","title":"RNA Processing and Translation Machinery","description":"This cluster is dominated by GO terms for translation (cytosolic and mitochondrial), translational termination, and translational fidelity, along with mRNA decay and spliceosomal tri-snRNP complex assembly, plus a diphthamide modification of a translation factor. Taken together, these points suggest a cohesive theme centered on protein synthesis and RNA processing rather than a single differentiation program. Differentiation terms appear as contextual associations rather than core functions.","confidence":"Medium","size":10,"edges":30,"triangles":35,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0032543","count":3},{"id":"GO:0000244","count":2},{"id":"GO:0035914","count":2},{"id":"GO:0014009","count":2}]},{"hash":"2062906572711126731","title":"Golgi-to-vacuole trafficking","description":"The top GO terms cluster around Golgi apparatus functions and targeting to the vacuole (Golgi localization, Golgi to vacuole transport, protein targeting to vacuole, Golgi inheritance) with support from endocytosis. This suggests a cohesive module of proteins involved in Golgi-mediated trafficking to vacuoles and related Golgi maintenance, rather than unrelated processes. A few unrelated terms (e.g., Purkinje cell maturation, pigmentation) appear incidental and do not define the core function of the cluster.","confidence":"High","size":10,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006896","count":2},{"id":"GO:0006623","count":2},{"id":"GO:0009615","count":1},{"id":"GO:0051645","count":1},{"id":"GO:1901998","count":1}]},{"hash":"238046037074056766","title":"Proteostasis and Innate Immune Signaling","description":"The cluster shows strong signals for proteasome-dependent protein catabolism and its regulation, ERAD-related pathways, and translation, indicating a focus on protein quality control and turnover; it also includes stress and metal-response elements (cadmium ion) and innate immune signaling (MyD88-TLR, type II interferon pathways), suggesting crosstalk between proteostasis and immune stress responses.","confidence":"Medium","size":10,"edges":22,"triangles":18,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0032436","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0006412","count":4},{"id":"GO:0043433","count":4},{"id":"GO:0034126","count":3}]},{"hash":"1576361148546605020","title":"ER-Golgi vesicle trafficking and COPII regulation","description":"The GO terms cluster around transport between the endoplasmic reticulum and Golgi, including ER-to-Golgi and retrograde Golgi-ER transport, COPII vesicle coating regulation, and general protein transport, with related regulation of GTPase activity. This points to intracellular trafficking within the early secretory pathway, centered on ER-Golgi vesicle flow and COPII\u2013mediated processes. ","confidence":"High","size":10,"edges":7,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0090316","count":3},{"id":"GO:0071806","count":3},{"id":"GO:0000060","count":3},{"id":"GO:0006890","count":3}]},{"hash":"2198286161220090689","title":"Mitochondrial translation and energy metabolism","description":"The set of GO terms centers on mitochondria: mitochondrial translation and initiation, general translation, and proton motive force-driven ATP synthesis, with supporting links to ubiquinone biosynthesis/regulation and lipid homeostasis in mitochondrial membranes. There are some non-mitochondrial annotations in the list (e.g., Purkinje cell morphogenesis, protein secretion) that likely reflect annotation noise, but the core terms strongly point to mitochondrial protein synthesis and energy production.","confidence":"Medium","size":10,"edges":9,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0070124","count":1},{"id":"GO:0015986","count":1},{"id":"GO:0099132","count":1},{"id":"GO:1901006","count":1}]},{"hash":"881847237396508041","title":"Mitochondrial protein import and mitophagy regulation","description":"The top GO terms cluster around mitochondrial inner membrane protein insertion and targeting to mitochondrion, together with negative regulation of mitophagy, implying a module focused on mitochondrial membrane maintenance and quality control. Additional signals of membrane remodeling (cholesterol homeostasis) and apoptotic membrane changes (phosphatidylserine exposure) support a broader theme of mitochondrial membrane stress responses. This suggests a coherent, though not exclusively tied, mitochondria-centric function.","confidence":"Medium","size":10,"edges":14,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0045039","count":3},{"id":"GO:0072321","count":2},{"id":"GO:0006626","count":2},{"id":"GO:0071222","count":1},{"id":"GO:0042632","count":1}]},{"hash":"379567937779147825","title":"Tubulin Assembly and Microtubule Organization","description":"Dominant GO terms point to tubulin complex assembly and cortical microtubule organization, indicating a core function in assembling and organizing microtubules. Supporting terms for chaperone-mediated protein complex assembly, protein folding, and cytoplasmic protein quality control by the ubiquitin-proteasome system suggest a proteostasis environment that assists tubulin biogenesis. Incidental nucleotide metabolism terms are present but likely less informative for the primary function.","confidence":"Medium","size":10,"edges":17,"triangles":12,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007021","count":2},{"id":"GO:0009220","count":1},{"id":"GO:0046081","count":1},{"id":"GO:0006229","count":1},{"id":"GO:0035863","count":1}]},{"hash":"1140583516064420348","title":"ER-Driven Protein Processing and Autophagy Under Stress","description":"GO terms cluster around endoplasmic reticulum (ER) activities (ER tubular network organization, ER-to-Golgi transport, ER-dependent peroxisome organization, vacuolar protein processing) and autophagy (autophagosome maturation), with oxidative-stress\u2013induced apoptotic signaling affecting mitochondrial membrane potential. This suggests an ER-centric stress response coordinating protein processing and autophagy, with related ER-associated metabolism like cholesterol synthesis. ","confidence":"Medium","size":10,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006624","count":1},{"id":"GO:0002037","count":1},{"id":"GO:0008631","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0010917","count":1}]},{"hash":"391348623837914957","title":"DNA replication and repair with SOS response","description":"The cluster is dominated by core genome maintenance processes: DNA-templated replication, nucleotide-excision repair, DNA recombination, and the SOS response, with supporting signals of cell division. Some ancillary terms (iron transport, tRNA modification) are present but do not define the core theme. This makes genome maintenance and stress response the best representative concept for the cluster.","confidence":"High","size":10,"edges":8,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0039657","count":1},{"id":"GO:0006289","count":1},{"id":"GO:0006261","count":1},{"id":"GO:0006310","count":1}]},{"hash":"878722655263644480","title":"Core cellular processes","description":"The top GO terms span diverse fundamental processes: cytoskeletal assembly (tubulin complex), membrane organization and trafficking (eisosome and multivesicular body assembly), cell division machinery (spindle pole body remodeling and cell cycle), chromatin organization (subtelomeric heterochromatin formation), protein folding, transcription elongation, and autophagy regulation. This broad mix points to general housekeeping roles rather than a single specialized pathway, so the label \"Core cellular processes\" is representative, with medium confidence. ","confidence":"Medium","size":10,"edges":16,"triangles":11,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007021","count":3},{"id":"GO:0006469","count":2},{"id":"GO:0031322","count":2},{"id":"GO:0070941","count":2},{"id":"GO:0006348","count":2}]},{"hash":"668627585675767759","title":"Methionine and One-Carbon Metabolism","description":"The GO terms clustered here point to methionine salvage and methyl-donor pathways: L-methionine salvage, betaine/choline catabolism feeding methyl groups, S-methylmethionine cycle, and related pteridine-containing metabolism. Together these suggest a cohesive theme around methionine turnover and one-carbon/methyl donor metabolism, even though individual annotations are few. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050666","count":1},{"id":"GO:0006579","count":1},{"id":"GO:0042426","count":1},{"id":"GO:0071267","count":1},{"id":"GO:0042558","count":1}]},{"hash":"1025398997382555566","title":"Unknown","description":"The GO terms cover host\u2013pathogen interactions (symbiont entry into host cell, viral process) as well as proteolysis and protein turnover (protein catabolic process, negative regulation of proteolysis, protein oligomerization/heterooligomerization) and some metabolism-related terms (insulin/bradykinin catabolism, PQQ biosynthesis), with no single cohesive function tying the cluster together.","confidence":"","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046718","count":1},{"id":"GO:0032461","count":1},{"id":"GO:0045861","count":1},{"id":"GO:0044257","count":1},{"id":"GO:0018189","count":1}]},{"hash":"2183611130767845946","title":"Plant meiosis and Fe-S cluster assembly","description":"The terms point to a plant-specific meiotic and DNA repair program (reciprocal meiotic recombination, double-strand break repair, cell division) and, separately, plant reproductive development (embryo sac and pollen development). The presence of [2Fe-2S] cluster assembly strongly suggests iron-sulfur cluster biogenesis, tying the theme to Fe-S biology in meiosis/dna repair contexts. Obsolete transcription-in-response-to-iron terms are minor remnants and do not override the core theme.","confidence":"Medium","size":10,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0009553","count":1},{"id":"GO:0009555","count":1},{"id":"GO:0006302","count":1},{"id":"GO:0007131","count":1}]},{"hash":"920751645466049649","title":"Notch-Driven Developmental Signaling","description":"These proteins show enrichment for Notch signaling, cell-cell signaling, and developmental processes such as angiogenesis and multicellular organism development, pointing to a developmental signaling theme. The presence of adaptive immune response and some metabolic terms suggests additional multifunctionality or cross-talk, but Notch- and development-centric terms are the strongest signal.","confidence":"Medium","size":10,"edges":8,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0002250","count":2},{"id":"GO:0042853","count":2},{"id":"GO:0007219","count":2},{"id":"GO:0097053","count":2}]},{"hash":"228635630422709326","title":"Unknown","description":"The GO terms are highly diverse, spanning nuclear DNA processes (DNA-templated transcription, DNA strand elongation) and host-invasion terms (symbiont/viral entry into host cells and nucleus), plus developmental and anti-apoptotic processes (meristem maintenance, hair cycle, negative regulation of senescence). There is no clear single function or theme tying these proteins together, so a concise, representative label cannot be assigned beyond Unknown.","confidence":"","size":10,"edges":42,"triangles":99,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0046718","count":1},{"id":"GO:0010073","count":1},{"id":"GO:0075732","count":1},{"id":"GO:2000773","count":1}]},{"hash":"1560789687722682544","title":"Central Metabolism: TCA Cycle and Amino Acid Biosynthesis","description":"This cluster is dominated by the tricarboxylic acid cycle term with related metabolic processes (2-oxoglutarate, leucine biosynthesis), pointing to a cohesive central metabolism module. A few terms about glial cell regulation and female gonad development are present but appear peripheral or annotation noise, so the main theme is metabolism.","confidence":"Medium","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":7},{"id":"GO:0019878","count":5},{"id":"GO:1903976","count":4},{"id":"GO:0008585","count":4},{"id":"GO:0060253","count":4}]},{"hash":"882888025608355263","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042594","count":2},{"id":"GO:0014850","count":2},{"id":"GO:0006531","count":2},{"id":"GO:0044208","count":2},{"id":"GO:0006106","count":1}]},{"hash":"1611784378681175628","title":"SNARE-driven vesicle trafficking and Golgi transport","description":"The proteins cluster around vesicle trafficking and Golgi-associated processes, with GO terms for SNARE complex assembly, vesicle fusion with Golgi, endosome transport, and protein localization to the plasma membrane, plus exocytic functions like acrosome reaction and cornified envelope assembly, all pointing to a secretory pathway/golgi-centric role.","confidence":"High","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035493","count":3},{"id":"GO:1903575","count":3},{"id":"GO:0007340","count":3},{"id":"GO:0045022","count":3},{"id":"GO:2000010","count":3}]},{"hash":"133698785244633694","title":"Transmembrane amino acid and ion transporters","description":"The top GO terms cluster around transmembrane transport of amino acids and small ions (GABA, leucine, ornithine, D-serine, ammonium, polyamines, carnitine, rubidium) and related cell volume homeostasis, indicating proteins that function as membrane transporters moving diverse substrates across biological membranes. This label captures the shared function without tying to a single substrate.","confidence":"High","size":10,"edges":39,"triangles":80,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0015812","count":10},{"id":"GO:0098713","count":10},{"id":"GO:0070634","count":10},{"id":"GO:0071477","count":10},{"id":"GO:1902274","count":10}]},{"hash":"2185466402999317929","title":"Cell polarity and cytoskeleton remodeling","description":"Top GO terms cluster around centrosome cycle, polarity establishment, cytoskeletal dynamics (ruffle and focal adhesion assembly), and membrane trafficking/localization, suggesting a shared theme of polarity-driven cytoskeletal remodeling and cell migration. Some terms are more specialized (megakaryocyte development, axis specification) but still align with polarity and adhesion contexts, supporting a cohesive label of polarity-guided cytoskeletal organization.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007098","count":2},{"id":"GO:0007121","count":2},{"id":"GO:0035855","count":1},{"id":"GO:0010761","count":1},{"id":"GO:0042070","count":1}]},{"hash":"2070180986074912295","title":"Cell cycle regulation and stress-induced apoptosis","description":"The cluster is dominated by cell cycle-related terms (G2/M transition; mitotic cell cycle; cell division; mitotic G1 DNA damage checkpoint signaling) and apoptotic pathways (intrinsic ER-stress\u2013driven apoptosis; general apoptotic process), with supporting signals from stress-activated pathways (JNK cascade; NF-kappaB signaling). A few immune signaling terms (T cell receptor signaling) may reflect broader signaling cross-talk, but the core theme ties mitotic control to apoptosis under cellular stress. Confidence: High","confidence":"","size":9,"edges":29,"triangles":43,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0007254","count":4},{"id":"GO:0050852","count":4},{"id":"GO:0051092","count":4},{"id":"GO:0070059","count":4}]},{"hash":"146180715253548638","title":"tRNA wobble modification and ion transport","description":"The cluster shows explicit GO terms for tRNA wobble base modifications (lysidine biosynthesis and uridine thiolation) alongside ion transport/homeostasis (potassium and sodium export, intracellular potassium homeostasis, vacuolar acidification). Additional terms hint at stress responses (methylglyoxal) and urmylation, which can accompany cellular stress contexts. Overall, the strongest coherent themes are tRNA wobble modification and ion transport/homeostasis, with supporting stress-related terms, yielding a moderate confidence in the label.","confidence":"Medium","size":9,"edges":15,"triangles":6,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0032447","count":1},{"id":"GO:0010098","count":1},{"id":"GO:0002136","count":1},{"id":"GO:0002143","count":1}]},{"hash":"865249007460723256","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":18,"triangles":13,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:1905639","count":3},{"id":"GO:0016554","count":3},{"id":"GO:0009793","count":3},{"id":"GO:1900865","count":3},{"id":"GO:0080156","count":3}]},{"hash":"1094294661582402019","title":"ER-Golgi vesicle trafficking","description":"The top GO terms cluster around transport between the endoplasmic reticulum and Golgi, including Golgi-to-ER retrograde transport and Golgi-to-lysosome pathways, with additional related vesicle trafficking and complex assembly terms. This points to a cohesive function in the secretory/vesicular transport system rather than unrelated processes, making ER-Golgi vesicle trafficking a concise and representative label for this cluster.","confidence":"High","size":9,"edges":19,"triangles":14,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0006890","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0042144","count":2},{"id":"GO:0060291","count":2}]},{"hash":"2031025143605936826","title":"Protein Folding and Degradation Machinery","description":"The cluster is dominated by GO terms for chaperone-mediated protein complex assembly and proteasome assembly, which together point to protein quality control via folding and degradation. The presence of several membrane transport terms is likely secondary or reflective of broader cellular contexts rather than a single cohesive transport theme. Overall, the core function appears to be protein handling by chaperones and proteasomes.","confidence":"Medium","size":9,"edges":11,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":2},{"id":"GO:0051131","count":2},{"id":"GO:0043248","count":2},{"id":"GO:1990539","count":1},{"id":"GO:0015757","count":1}]},{"hash":"1414588057613797815","title":"Ribosome biogenesis and protein quality control","description":"The cluster is dominated by ribosome-related processes: ribosome biogenesis, ribosomal small subunit assembly, and translation, indicating a focus on ribosome production and function. Supporting this, chaperone-mediated protein complex assembly and proteasome regulatory particle assembly point to a coordinated protein folding and degradation system ensuring ribosome assembly quality, with autophagy-related turnover also fitting into this protein homeostasis network. Some terms (transcription elongation regulation and proton transport) are more peripheral but do not negate the core ribosome/protein quality theme.","confidence":"Medium","size":9,"edges":15,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051131","count":2},{"id":"GO:0032968","count":2},{"id":"GO:1902600","count":2},{"id":"GO:0006412","count":1},{"id":"GO:0006407","count":1}]},{"hash":"2048189896916963463","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":2},{"id":"GO:0071421","count":1},{"id":"GO:0006880","count":1},{"id":"GO:0071369","count":1},{"id":"GO:0071281","count":1}]},{"hash":"1211730175082535689","title":"Ribosome biogenesis and rRNA processing","description":"GO terms cluster around ribosome biogenesis and rRNA maturation (LSU/SSU/5.8S), plus ribosomal large subunit biogenesis, supporting a nucleolar ribosome assembly theme; other terms (splicing, ubiquitination) appear but are less dominant.","confidence":"High","size":9,"edges":23,"triangles":32,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0000463","count":5},{"id":"GO:0042273","count":5},{"id":"GO:0000466","count":5},{"id":"GO:0000209","count":4}]},{"hash":"2296134798649634815","title":"Translation and Proton Transport","description":"The cluster centers on translation-related processes (tRNA metabolism and regulation of translational fidelity) and proton-driven activities (proton transmembrane transport, proton motive force-driven ATP synthesis, and vacuolar acidification). A couple of terms refer to development in zebrafish, which may be incidental or context-specific, but the core pattern ties together protein synthesis machinery with membrane proton energetics. Medium","confidence":"","size":9,"edges":12,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1900832","count":1},{"id":"GO:0006399","count":1},{"id":"GO:0006450","count":1},{"id":"GO:1900829","count":1},{"id":"GO:0042777","count":1}]},{"hash":"2006984062326512378","title":"Fungal cell wall biosynthesis and sphingolipid metabolism","description":"This cluster\u2019s strongest, coherent theme centers on fungal-type cell wall biogenesis, cell wall repair, and sphingolipid biosynthesis, with an accompanying osmoregulatory signal (hypotonic response) and related lipid transport. While there are a few RNA processing and mitochondrial terms present as outliers, the dominant pattern ties to fungal cell wall construction and membrane remodeling in response to stress.","confidence":"Medium","size":9,"edges":11,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009272","count":2},{"id":"GO:0071433","count":2},{"id":"GO:0015883","count":2},{"id":"GO:0061454","count":2},{"id":"GO:0030148","count":2}]},{"hash":"446107151310237426","title":"Nuclear Import and Replication Initiation","description":"Top terms cluster around nuclear localization and transport (NLS-bearing import, ribosomal protein import, nuclear pore assembly) and assembly of the pre-replicative complex for DNA replication. A secondary theme involves transcription regulation and xenobiotic response, but nuclear transport/replication initiation is the dominant shared function.","confidence":"Medium","size":9,"edges":29,"triangles":56,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0042176","count":3},{"id":"GO:0006607","count":2},{"id":"GO:0060188","count":2},{"id":"GO:0051292","count":2},{"id":"GO:0043547","count":2}]},{"hash":"490491114390838003","title":"Nuclear RNA processing and ribosome biogenesis","description":"This cluster is enriched for RNA-centric processes: maturation of SSU-rRNA, spliceosomal snRNP assembly, histone mRNA metabolism, and P-body assembly, with supporting signals for nuclear import and broader RNA regulation. Together these point to a cohesive theme of RNA processing and ribosome biogenesis in the nucleus, with some links to RNA turnover and chromatin-related regulation.","confidence":"Medium","size":9,"edges":26,"triangles":45,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0030490","count":2},{"id":"GO:0070317","count":2},{"id":"GO:1990141","count":1},{"id":"GO:0000387","count":1},{"id":"GO:0060965","count":1}]},{"hash":"1117610848382784042","title":"RNA processing and post-transcriptional regulation","description":"Top terms point to mRNA polyadenylation, spliceosome-mediated splicing, mRNA stabilization, and miRNA-mediated translational silencing, suggesting a core role in post-transcriptional gene regulation; calcium response appears ancillary.","confidence":"Medium","size":9,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0071277","count":3},{"id":"GO:1903586","count":2},{"id":"GO:1905663","count":2},{"id":"GO:1900363","count":2},{"id":"GO:0006378","count":2}]},{"hash":"1664683179727421706","title":"Mitophagy and Energy Metabolism","description":"This cluster mixes autophagy/mitophagy-related terms with core metabolic processes (glycolysis, gluconeogenesis, carbohydrate phosphorylation, fructose metabolism) and dephosphorylation, suggesting a theme around mitochondrial quality control coupled to energy metabolism. Some terms (cobalt ion response, respiratory gas exchange) are less directly connected, but the autophagy/metabolism linkage is the strongest cohesive thread.","confidence":"Medium","size":9,"edges":12,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0016311","count":2},{"id":"GO:0010666","count":2},{"id":"GO:0071279","count":2},{"id":"GO:0007585","count":2},{"id":"GO:0006094","count":2}]},{"hash":"930779368079535273","title":"Cellular stress response and proteostasis","description":"The top GO terms point to responses against heat, mechanical stimulus, and thermoception, i.e., cellular stress sensing, alongside processes that maintain protein and RNA homeostasis (ubiquitination, proteasome assembly, regulation of translational fidelity, mRNA stability). The presence of NOD2 signaling and NF-kappaB-related regulation suggests interplay with innate immune pathways commonly activated under stress. Together, these terms indicate a cohesive theme of stress detection and proteome/gene-expression maintenance, justifying the label.","confidence":"Medium","size":9,"edges":6,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":3},{"id":"GO:0071260","count":3},{"id":"GO:0043488","count":3},{"id":"GO:0070431","count":3},{"id":"GO:0016567","count":3}]},{"hash":"770508071540974296","title":"Germinal center B cell differentiation and humoral immunity","description":"This cluster is dominated by B cell\u2013 and germinal center\u2013associated terms (germinal center formation, marginal zone B cell differentiation, follicular dendritic cell differentiation, humoral immune response) with regulation of IL-10 production, indicating a core theme of B cell maturation and antibody-mediated immunity. A few metabolic terms are present but appear secondary to the dominant immune-related functions.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002268","count":1},{"id":"GO:0002455","count":1},{"id":"GO:0002467","count":1},{"id":"GO:0033617","count":1},{"id":"GO:0002315","count":1}]},{"hash":"947247126242443474","title":"Signaling and Gene Regulation Network","description":"The cluster includes GO terms spanning signaling pathways (NF-kappaB signaling, Rap signaling, regulation of voltage-gated channels, integrin activation), transcription/RNA processing (miRNA processing, regulation of transcription in G2/M), and context-specific processes (cholangiocyte proliferation, Purkinje cell layer organization). This mix suggests proteins participate in broader signaling and gene-expression regulation rather than a single, cohesive pathway, justifying a general \u201csignaling and gene regulation\u201d label.","confidence":"Medium","size":9,"edges":11,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009190","count":4},{"id":"GO:0090282","count":3},{"id":"GO:1990705","count":3},{"id":"GO:1905150","count":3},{"id":"GO:0007249","count":3}]},{"hash":"490199705951175313","title":"Carbohydrate and Metabolite Membrane Transporters","description":"The cluster shows strong representation of transmembrane transport GO terms for multiple sugars (fructose, galactose, glucose) and related metabolites (dehydroascorbic acid, urate), along with xenobiotic and nitrate-related transport and a glucose starvation response. This points to a cohesive group of membrane transport proteins specializing in carbohydrate and metabolite uptake, with broader substrate diversity. ","confidence":"High","size":9,"edges":10,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1990539","count":4},{"id":"GO:0015757","count":4},{"id":"GO:0042128","count":4},{"id":"GO:0042908","count":4},{"id":"GO:0042149","count":4}]},{"hash":"843975706280968441","title":"Transmembrane ion transport and membrane potential regulation","description":"Top GO terms point to diverse transmembrane transport processes (sulfate, L-aspartate, chloride, bicarbonate, fructose) and to regulation of membrane potential and intracellular pH, with gastric acid secretion also indicating proton transport. Together they suggest a cluster of membrane transporters and channels that maintain ion and nutrient homeostasis and electrical potential, with possible links to pH-dependent signaling like in sperm capacitation. Unknown outliers such as sensory perception of sound appear less central to core function. ","confidence":"Medium","size":9,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0048240","count":3},{"id":"GO:1902358","count":3},{"id":"GO:0089712","count":3},{"id":"GO:0042391","count":3},{"id":"GO:0007605","count":3}]},{"hash":"2135142598038833439","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":15,"triangles":11,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":4},{"id":"GO:0006526","count":3},{"id":"GO:0070814","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0019240","count":2}]},{"hash":"346234888313561718","title":"Unknown","description":"The GO terms span fungal meiosis and sporulation, sphingolipid metabolism, and various animal cell\u2013junction, barrier, and signaling processes, with no clear single function tying all proteins together. Therefore a coherent, specific label cannot be assigned.","confidence":"","size":9,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0007127","count":2},{"id":"GO:0030437","count":2},{"id":"GO:0006673","count":1},{"id":"GO:0035208","count":1},{"id":"GO:0061028","count":1}]},{"hash":"1604515150123800914","title":"Meiosis: recombination and repair","description":"The top GO terms center on meiotic recombination, meiotic mismatch repair, chromosome segregation, spindle midzone assembly, and heteroduplex formation, with additional signals from somatic hypermutation-related repair and general protein quality control. This points to a cohesive theme of meiosis and its DNA repair/recombination pathways, rather than unrelated functions.","confidence":"High","size":8,"edges":18,"triangles":16,"max_degree":7,"top_function":"protein folding","top_go_terms":[{"id":"GO:0006457","count":3},{"id":"GO:0006298","count":3},{"id":"GO:0006508","count":2},{"id":"GO:0007131","count":2},{"id":"GO:0016446","count":2}]},{"hash":"1802412582555754278","title":"DNA damage response and cell cycle control","description":"These proteins cluster around genome maintenance and cell division, with GO terms for DNA-templated transcription, DNA replication, mitotic cell cycle, and cellular response to ionizing radiation, plus apoptosis regulation. Some hormone-related terms appear as secondary associations, but the core theme is DNA damage response and cell cycle regulation.","confidence":"Medium","size":8,"edges":5,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0019858","count":2},{"id":"GO:0071479","count":2},{"id":"GO:0008584","count":2},{"id":"GO:0060374","count":2}]},{"hash":"1764147505265705538","title":"DNA Replication and Telomere Maintenance","description":"This cluster is dominated by GO terms tied to genome stability: DNA replication, DNA repair, sister chromatid cohesion, and telomere maintenance (via recombination and capping), plus replication fork processing and maintenance of repetitive DNA. These together point to a core function in ensuring accurate DNA duplication and telomere integrity during cell division. Minor terms related to ubiquitination and RNA processing may reflect supporting regulatory processes, but the primary theme remains replication and telomere maintenance.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0007064","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0000722","count":2},{"id":"GO:0016233","count":2}]},{"hash":"1785954257740826118","title":"Mitochondrial apoptosis and lipid transport","description":"The top GO terms cluster around mitochondrial targeting, regulation of intrinsic apoptotic signaling via p53, and regulation of cytochrome c release, along with phospholipid translocation/transport and mitochondrial respiratory chain assembly. This suggests a cohesive theme of mitochondrial membrane integrity and apoptotic signaling, with a few additional glycosylation/ER-related terms likely reflecting annotation noise rather than core function.","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006626","count":1},{"id":"GO:1902166","count":1},{"id":"GO:0030330","count":1},{"id":"GO:0045332","count":1},{"id":"GO:0090201","count":1}]},{"hash":"2023771856206134805","title":"Mitochondrial lipid metabolism and energy production","description":"This cluster is driven by lipid biosynthesis and remodeling processes (platelet activating factor biosynthesis, cardiolipin remodeling, ether lipid biosynthesis, phosphatidylcholine biosynthesis, CDP-diacylglycerol biosynthesis) and by mitochondrial ATP synthesis, pointing to a cohesive theme of mitochondrial lipid metabolism coupled to energy production. Immune-related terms (IL-2 production, regulation of T cell activation-induced cell death) may reflect roles of mitochondria in immune cell signaling but are less central to the main theme. Developmental terms like cerebellum morphogenesis and glandular epithelial maturation appear peripheral to the core lipid/mitochondrial signal. Overall, the cluster aligns best with mitochondrial lipid metabolism and energy generation.","confidence":"Medium","size":8,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006663","count":3},{"id":"GO:0021587","count":3},{"id":"GO:0070236","count":3},{"id":"GO:2001246","count":3},{"id":"GO:0035965","count":3}]},{"hash":"96590329103349680","title":"Secretory trafficking and lipid homeostasis","description":"The top GO terms point to processes in the secretory pathway (ER-to-Golgi vesicle transport; V-type ATPase complex assembly involved in vesicle acidification) and lipid handling (lipoprotein particle assembly; cholesterol homeostasis), suggesting a theme around vesicle trafficking coupled with lipid metabolism. While there are some metabolic terms (cysteine biosynthesis, sulfate assimilation) that are less directly linked, the strongest signal centers on secretory pathway functions and lipid processing, which inspires the concise label.","confidence":"Medium","size":8,"edges":24,"triangles":36,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0019344","count":1},{"id":"GO:0000103","count":1},{"id":"GO:1902358","count":1},{"id":"GO:0070072","count":1}]},{"hash":"1699963119508586592","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":19,"triangles":17,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0008033","count":2},{"id":"GO:0034473","count":1},{"id":"GO:0000958","count":1},{"id":"GO:0071035","count":1}]},{"hash":"1246094760902226910","title":"Neural development and cell cycle regulation","description":"This cluster is dominated by neural development terms (forebrain development, neural tube closure) and broader multicellular development, along with DNA-templated transcription and cell cycle processes (cell division, mitotic cell cycle). A few stress/immune terms are present, but the core theme centers on neural development tied to transcriptional activity and proliferation.","confidence":"Medium","size":8,"edges":5,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0050830","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0008584","count":2},{"id":"GO:0051301","count":2}]},{"hash":"1639035842870825206","title":"Mitochondrial Import and Complex Assembly","description":"The top GO terms cluster around mitochondrial protein handling: import into the mitochondrial matrix, outer membrane translocase assembly, tRNA import into mitochondrion, and assembly of the respiratory chain complex IV, with supporting links to mitochondrial translation and stress response. A few terms like toluene catabolic process, sodium ion transport, and cholesterol biosynthesis are less central, but the dominant theme points to mitochondrial biogenesis and protein sorting.","confidence":"Medium","size":8,"edges":14,"triangles":9,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0002181","count":2},{"id":"GO:0006605","count":1},{"id":"GO:0030150","count":1},{"id":"GO:0070096","count":1},{"id":"GO:0016031","count":1}]},{"hash":"1579592219633417245","title":"RNA Processing and Decay","description":"The top terms are centered on RNA metabolism, including rRNA processing, RNA catabolic process, and exonucleolytic RNA hydrolysis, suggesting a coherent theme of RNA processing/degradation. The presence of several unrelated biosynthetic terms (retinol/retinal/estrogen/testosterone pathways) is likely noise or cross-annotation, but the dominant signal remains RNA metabolism.","confidence":"Medium","size":8,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0006364","count":2},{"id":"GO:0090503","count":2},{"id":"GO:0006401","count":2},{"id":"GO:0042572","count":2}]},{"hash":"2130637090838652922","title":"Unknown","description":"The top terms span brain development, synaptic function, metabolism, and general cellular processes, with several obsolete terms and even sporulation, showing no single coherent theme. Because there isn\u2019t a dominant function tying these proteins together, a clear, representative label cannot be assigned.","confidence":"","size":8,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0090394","count":2},{"id":"GO:0021762","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0030435","count":2}]},{"hash":"1604175856106665872","title":"Unknown","description":"There isn\u2019t a single cohesive function tying the listed metabolism (glutamine/glutamate and phenylalanine biosynthesis, TCA) terms with DNA replication and spliceosome-related processes; the presence of obsolete GO terms and mixed functions suggests a heterogeneous cluster rather than a clear, unified role.","confidence":"","size":8,"edges":8,"triangles":1,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0006541","count":2},{"id":"GO:0072350","count":2},{"id":"GO:0006537","count":2},{"id":"GO:0019551","count":2}]},{"hash":"2075200642696967967","title":"Wnt Regulation and Angiogenesis","description":"This cluster is driven by terms for canonical Wnt signaling regulation (both positive and negative) and angiogenesis, suggesting a core theme of Wnt-mediated vascular processes. The presence of related immune signaling (T cell receptor signaling) and stress response terms (cadmium and hydrogen peroxide) may reflect broader signaling context, but the strongest pattern centers on modulation of Wnt pathways and angiogenesis.","confidence":"Medium","size":8,"edges":7,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071276","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0090263","count":2},{"id":"GO:0050852","count":2},{"id":"GO:0090090","count":2}]},{"hash":"1232367483555856364","title":"Organelle-specific autophagy","description":"This cluster centers on autophagy-related processes across organelles: nucleophagy, mitophagy, glycophagy, autophagosome assembly, and the Cvt pathway, with some lipidation aspects tied to autophagic machinery. These terms point to a cohesive theme of cargo-specific degradation within cells, making organelle-directed autophagy the most representative label. There are a few peripheral terms, but they do not dominate the set.","confidence":"High","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0044805","count":2},{"id":"GO:0000045","count":2},{"id":"GO:0034727","count":2},{"id":"GO:0006501","count":2},{"id":"GO:0000422","count":2}]},{"hash":"1291089132958641775","title":"Endocytic trafficking and lysosome targeting","description":"The GO terms cluster around vesicle transport between the plasma membrane, endosomes, and lysosomes, including ER-to-Golgi transport and endocytic recycling, plus a signaling link via neurotrophin receptor pathways; these collectively indicate a coherent group of proteins involved in intracellular vesicle trafficking and lysosome-related processes, with some involvement in membrane remodeling during differentiation. ","confidence":"High","size":8,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0048227","count":2},{"id":"GO:1902953","count":2},{"id":"GO:0051005","count":2},{"id":"GO:0014902","count":2},{"id":"GO:0048011","count":2}]},{"hash":"672134524088510595","title":"Dendritic spine morphogenesis and neuronal signaling","description":"The cluster centers on dendritic spine morphogenesis and neural signaling pathways, including ephrin receptor signaling, neurotrophin TRK signaling, and Wnt signaling, plus actin regulation. These terms together point to neuronal development and synaptic structure/function, with growth-factor related pathways reinforcing signaling roles. A heart development term appears as a peripheral association but does not define the main theme here; the dominant pattern is neuronal spine formation and signaling.","confidence":"High","size":8,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1904531","count":4},{"id":"GO:0010954","count":4},{"id":"GO:0007507","count":4},{"id":"GO:0048013","count":4},{"id":"GO:0060997","count":4}]},{"hash":"1823240899629597681","title":"Vesicle trafficking in mitosis","description":"The cluster shows a cohesive set of GO terms for vesicle transport between ER and Golgi, endosome-to-melanosome and multivesicular body pathways, vacuole targeting, and autophagosome regulation, all linked to cell cycle processes such as mitotic exit and cell division. This points to a functional module where vesicle trafficking and organelle sorting intersect with mitotic regulation. Hence, the label captures the core theme of endomembrane trafficking in the context of mitosis.","confidence":"High","size":8,"edges":18,"triangles":19,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006890","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0035646","count":4},{"id":"GO:1902902","count":3},{"id":"GO:0007049","count":3}]},{"hash":"2108387047924007261","title":"Amino acid and ion transmembrane transport","description":"The top GO terms all point to moving diverse substrates across membranes, including amino acids (GABA, ornithine, serine, lysine), ions (potassium), ammonium, and xenobiotics, indicating membrane transporter activity with broad substrate specificity. This cohesive pattern supports labeling the cluster as a transporter-focused group rather than a single-substrate pathway.","confidence":"High","size":8,"edges":7,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0015812","count":2},{"id":"GO:0098713","count":2},{"id":"GO:0070634","count":2}]},{"hash":"508921514975947661","title":"Lipid and hormone metabolism with oxidative stress response","description":"The top GO terms point to lipid- and hormone-related metabolism (retinol, bile acids, testosterone) and xenobiotic processing (naphthalene catabolic), along with cellular responses to oxidative stress (hydrogen peroxide) and stimulus signals (jasmonic acid). A cohesive interpretation is that this cluster centers on metabolism of lipids/hormones and detoxification with stress-response signaling, rather than a single narrowly defined pathway. Negative regulation of apoptotic process also fits a cell-survival context amid stress. ","confidence":"Medium","size":8,"edges":22,"triangles":35,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:1900053","count":6},{"id":"GO:0042572","count":6},{"id":"GO:0006699","count":6},{"id":"GO:0018931","count":6}]},{"hash":"1333130553121117293","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":10,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0019878","count":3},{"id":"GO:0033512","count":3},{"id":"GO:0070814","count":3},{"id":"GO:0009097","count":2},{"id":"GO:0042853","count":2}]},{"hash":"848210013142551057","title":"Gonad and Reproductive Development","description":"The top GO terms point to development of reproductive organs, including male gonad development, seminiferous tubule development, and follicle cell development in the egg chamber, suggesting a cohesive theme around gonad and gamete-related formation. Other terms like protein ubiquitination and cadmium response appear ancillary but may reflect broader regulatory or stress-response roles in these developmental processes. Overall, the cluster seems best described as proteins involved in gonad and reproductive tissue development.","confidence":"High","size":7,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0008584","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0072520","count":1}]},{"hash":"1239944725401455722","title":"Amino acid biosynthesis and energy metabolism","description":"The top GO terms cluster around amino acid biosynthesis (valine, branched-chain amino acids), pyruvate catabolism, and the electron transport chain, pointing to a metabolic module focused on amino acid production and energy generation. Occasional terms like DNA replication/repair and response to cocaine are less directly connected, possibly reflecting broader housekeeping roles or pleiotropy within the cluster.","confidence":"Medium","size":7,"edges":10,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009099","count":3},{"id":"GO:0009097","count":3},{"id":"GO:0006281","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0042220","count":2}]},{"hash":"420991898238584061","title":"Metabolic and Growth Factor Signaling","description":"The top terms cluster around insulin receptor signaling and insulin signaling, as well as growth hormone receptor signaling, indicating a theme of metabolic and endocrine signaling. Positive regulation of GTPase activity supports downstream modulation of signaling. Though there are also terms related to transcription, kinetochore localization, and even viral processes, the dominant signal is regulation of hormonal signaling pathways.","confidence":"Medium","size":7,"edges":9,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0046626","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0060396","count":2},{"id":"GO:2001241","count":2},{"id":"GO:0016032","count":2}]},{"hash":"986379637378251981","title":"RNA transcription machinery and ribosome biogenesis","description":"Dominant GO terms center on transcription by RNA polymerases I\u2013III (including elongation, termination, and RNA-templated transcription, plus tRNA transcription) and on ribosome biogenesis, pointing to a cluster of proteins involved in nuclear transcription processes and ribosome assembly. A couple of outlier terms related to cell morphogenesis and neuron axon fasciculation are present but do not define the cluster. ","confidence":"Medium","size":7,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000902","count":2},{"id":"GO:0006385","count":1},{"id":"GO:0006366","count":1},{"id":"GO:0006360","count":1},{"id":"GO:0042254","count":1}]},{"hash":"1908488483507844615","title":"DNA repair and genome maintenance","description":"The proteins show enrichment for DNA replication, nucleotide-excision repair, gene conversion at the mating-type locus, and chromosomal cohesion and spindle assembly checkpoint regulation, all pointing to a cohesive theme of genome integrity and recombination during replication/segregation. The isotype switching term appears as a potential outlier. ","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0045190","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0070651","count":2},{"id":"GO:0006289","count":1},{"id":"GO:0031292","count":1}]},{"hash":"1246661050344327641","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0048478","count":2},{"id":"GO:0006296","count":2},{"id":"GO:0006366","count":2},{"id":"GO:0070816","count":2},{"id":"GO:0006370","count":2}]},{"hash":"1905267704616853666","title":"Negative regulation of canonical Wnt signaling","description":"Several top terms point to negative regulation of the canonical Wnt signaling pathway, suggesting the proteins in this cluster act to dampen Wnt signaling. Additional terms related to heparan sulfate proteoglycan biosynthesis, transcriptional/ubiquitination regulation, and developmental processes (e.g., medulla oblongata development) fit a broader theme in which Wnt activity is modulated during development. While some terms are peripheral (mitotic cytokinesis, vacuole inheritance), the dominant pattern centers on suppressing or tuning Wnt signaling.","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0010909","count":3},{"id":"GO:0090090","count":3},{"id":"GO:0044336","count":3},{"id":"GO:0044334","count":3},{"id":"GO:0043547","count":3}]},{"hash":"458554996263396800","title":"Transcription machinery and cell cycle regulation","description":"This cluster is dominated by GO terms for RNA polymerase II/I transcription initiation and elongation, as well as DNA replication and cell cycle checkpoints, indicating a core theme of transcriptional machinery combined with cell cycle control. A few terms touch on neural development and synaptic activity, but the dominant signal is transcriptional regulation and DNA replication/cell cycle processes, justifying this label.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0051123","count":2},{"id":"GO:0042790","count":2},{"id":"GO:0006367","count":2},{"id":"GO:0032968","count":2},{"id":"GO:0060079","count":2}]},{"hash":"2025901401014830666","title":"Ribosome Biogenesis and Protein Synthesis","description":"These proteins are linked by GO terms centered on assembling and operating ribosomes (tRNA modification, cytoplasmic translation, ribosome and subunit biogenesis, nuclear export of ribosomal subunits). The strong presence of translation-related terms with ribosome assembly indicates a cohesive ribosome-focused cluster; mentions of cell cycle and stress response likely reflect broader growth regulation but do not override the core ribosome theme.","confidence":"High","size":7,"edges":9,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006400","count":2},{"id":"GO:1901001","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0002181","count":2},{"id":"GO:1903833","count":2}]},{"hash":"333378435829174623","title":"Dendritic Spine Remodeling","description":"The cluster centers on synaptic and dendritic spine biology, highlighted by positive regulation of synaptic plasticity and dendritic spine development, and includes regulation of actin nucleation via Arp2/3, pointing to actin cytoskeleton remodeling at synapses. Trafficking terms (Golgi to plasma membrane) also support spine maturation processes. While some terms reflect general cellular growth, the strongest signal is spine formation and synaptic remodeling.","confidence":"Medium","size":7,"edges":9,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0031915","count":2},{"id":"GO:0034316","count":2},{"id":"GO:0060999","count":2},{"id":"GO:0043001","count":2}]},{"hash":"856403592915370133","title":"mRNA Decay and P-Body Assembly","description":"This cluster is dominated by GO terms for deadenylation-dependent mRNA decay, decapping, and P-body assembly, along with miRNA-mediated post-transcriptional silencing, indicating a core role in mRNA turnover and post-transcriptional regulation. The presence of ubiquitin-proteasome-related terms may reflect broader coupling to protein turnover, but the primary signal is RNA decay and post-transcriptional control.","confidence":"High","size":7,"edges":13,"triangles":9,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0031145","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0035195","count":1},{"id":"GO:0000290","count":1},{"id":"GO:0033962","count":1}]},{"hash":"1642673458149490486","title":"Brain endothelial tight junction and BBB development","description":"The top terms center on tight junction assembly and the establishment of the endothelial blood-brain barrier, along with brain development and epithelial polarization, pointing to a cluster focused on BBB formation by brain endothelium. Some terms (kidney development, metabolic signaling) are supportive or ancillary but do not override the central theme of BBB/brain endothelial function.","confidence":"High","size":7,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0070830","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0001822","count":3},{"id":"GO:0007124","count":3},{"id":"GO:0001302","count":3}]},{"hash":"737444883960932092","title":"Oxidative Stress\u2013Driven Transcription Regulation","description":"This cluster centers on transcriptional regulation (DNA-templated transcription; RNA Pol II regulation) and stress responses, particularly oxidative stress (response to hydrogen peroxide) and ER stress. While a couple of terms (ephrin signaling, protein export from nucleus) are less directly tied to this theme, the convergence on transcription control under cellular stress suggests a cohesive role in adjusting gene expression in response to redox and ER challenges.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0034976","count":3},{"id":"GO:1903206","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0046826","count":3}]},{"hash":"1972037922854879451","title":"Unknown","description":"The terms span multiple, unrelated biological processes\u2014from lipid metabolism and secondary metabolite biosynthesis to metal ion homeostasis and protein processing/localization\u2014yet there are no connecting edges among the proteins, so there is no coherent shared function to define a meaningful cluster name. Therefore this cluster is best labeled Unknown with no confidence.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001561","count":1},{"id":"GO:0019491","count":1},{"id":"GO:1902181","count":1},{"id":"GO:0042400","count":1},{"id":"GO:0097089","count":1}]},{"hash":"775160803203056547","title":"Secretory and endolysosomal vesicle transport","description":"This cluster is dominated by GO terms for vesicle docking, tethering, and fusion, and for trafficking from Golgi to endosome and from endosome to lysosome, plus vesicle maturation and membrane docking. Collectively they indicate a core function in secretory and endolysosomal vesicle transport, with peripheral associations to immune granule function and synaptic vesicle dynamics.","confidence":"High","size":7,"edges":15,"triangles":9,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006904","count":3},{"id":"GO:0099022","count":3},{"id":"GO:0006895","count":3},{"id":"GO:0051469","count":3},{"id":"GO:0008333","count":3}]},{"hash":"598610014245165631","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034396","count":1},{"id":"GO:0035551","count":1},{"id":"GO:0034724","count":1},{"id":"GO:0070527","count":1},{"id":"GO:0030574","count":1}]},{"hash":"1723979306811140854","title":"Mitotic spindle assembly and cytokinesis","description":"The dominant GO terms cluster around cell division and cytoskeleton dynamics\u2014cell cycle, microtubule nucleation/organization, and spindle midzone assembly, plus FtsZ-dependent cytokinesis\u2014indicating a cohesive theme of mitotic spindle function and cytokinesis. Some terms (e.g., translation regulation, IL-4 response) appear as less central outliers but do not disrupt the core pattern. ","confidence":"High","size":6,"edges":7,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2000767","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0007020","count":2},{"id":"GO:0051258","count":2},{"id":"GO:0043093","count":2}]},{"hash":"131283766634373670","title":"Ubiquitin-dependent proteolysis and signaling","description":"The cluster is dominated by ubiquitin-related processes: APC/C- and SCF-dependent proteolysis, deubiquitination, and ERAD pathways, pointing to a core function in ubiquitin-mediated protein turnover. The inclusion of non-canonical NF-kappaB signaling, and both positive and negative regulation of canonical Wnt signaling, plus T cell receptor signaling, suggests these proteins modulate key signaling pathways via ubiquitin-mediated regulation. Supporting terms like zinc response and mRNA stability are less central but compatible with broader cellular regulation. ","confidence":"High","size":6,"edges":10,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0031145","count":3},{"id":"GO:0031146","count":3},{"id":"GO:0016579","count":3},{"id":"GO:0030433","count":2},{"id":"GO:0010043","count":2}]},{"hash":"395128912486447366","title":"Central Carbon Metabolism and Lipid Biosynthesis","description":"These proteins show enrichment for glycolysis, gluconeogenesis, pyruvate decarboxylation to acetyl-CoA, 2-oxoglutarate metabolism, and long-chain fatty acid biosynthesis, pointing to central carbon metabolism feeding energy production and lipid biosynthesis. Some other terms (DNA replication, sodium transport) appear incidental to the dominant metabolic theme.","confidence":"High","size":6,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0006213","count":1},{"id":"GO:0000002","count":1},{"id":"GO:0006814","count":1},{"id":"GO:0006096","count":1}]},{"hash":"579902228787905320","title":"Unknown","description":"The top GO terms indicate a mix of signaling, metabolism, transport, chromatin regulation, RNA silencing localization, and development, with no single unifying function. This makes the cluster heterogeneous and difficult to assign a representative, specific biological theme.","confidence":"","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":2},{"id":"GO:0015986","count":1},{"id":"GO:0099132","count":1},{"id":"GO:0034630","count":1},{"id":"GO:0070544","count":1}]},{"hash":"204799137459262579","title":"Amino acid and vitamin biosynthesis with aromatic catabolism","description":"The top GO terms point to biosynthetic processes for amino acids and vitamins (thiamine and histidine) and catabolic pathways for aromatic compounds (benzoate, 3-phenylpropionate), suggesting a metabolic cluster oriented around amino acid/vitamin production and aromatic compound degradation. A few terms (ethanol response, toxic substance response) may reflect general stress responses but do not override the metabolic theme.","confidence":"Medium","size":6,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045471","count":2},{"id":"GO:0043046","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0009228","count":2},{"id":"GO:0001701","count":2}]},{"hash":"770995225814185190","title":"ER-Golgi trafficking and GTPase regulation","description":"The cluster centers on intracellular membrane trafficking, especially ER-to-Golgi vesicle transport and targeting to the ER, plus endosome-to-Golgi transport and regulation of GTPase activity, which points to small GTPases driving vesicle dynamics. Viral process and autophagy terms reflect trafficking-related roles; skeletal/dendrite terms appear ancillary. Overall, the core theme is vesicle trafficking in the early secretory pathway, modulated by GTPases.","confidence":"Medium","size":6,"edges":7,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0006888","count":2},{"id":"GO:0016032","count":2},{"id":"GO:0006465","count":1},{"id":"GO:0045047","count":1}]},{"hash":"1187620837911282516","title":"Developmental Vesicle Trafficking and Autophagy","description":"This cluster centers on processes tied to intracellular trafficking (ER-Golgi, endosome-Golgi transport) and autophagy, with additional links to dendrite and skeletal development, and regulation of GTPase activity. The combination suggests a theme of cellular logistics during development, including neuronal and skeletal contexts, rather than a single narrowly defined pathway.","confidence":"Medium","size":6,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":1},{"id":"GO:0006914","count":1},{"id":"GO:0045212","count":1},{"id":"GO:0001501","count":1},{"id":"GO:0016358","count":1}]},{"hash":"1015866680126383732","title":"Developmental growth and metabolic biosynthesis","description":"The terms cluster around organismal development (somite development, compound eye morphogenesis, multicellular growth) and core biosynthetic/metabolic processes (NAD+ biosynthesis, polyamine biosynthesis, oxaloacetate metabolism), with some stress-response annotations; this points to a broad growth/metabolism theme rather than a single pathway.","confidence":"Medium","size":6,"edges":8,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0072756","count":1},{"id":"GO:0035264","count":1},{"id":"GO:0006378","count":1},{"id":"GO:0098789","count":1},{"id":"GO:0035736","count":1}]},{"hash":"215168268437745540","title":"Unknown","description":"The top GO terms are highly diverse, spanning DNA replication, developmental morphogenesis, neuron axon fasciculation, immune signaling, nociception, ion transport, pollen recognition, nuclear export, and lung mesenchyme development. There is no clear, shared biological process or pathway linking these proteins, so a single cohesive cluster label cannot be assigned.","confidence":"","size":6,"edges":4,"triangles":0,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0048701","count":3},{"id":"GO:0000189","count":2},{"id":"GO:0097156","count":2},{"id":"GO:0038110","count":2}]},{"hash":"207852145552136400","title":"Neural and glial development with transcriptional control","description":"The cluster's top GO terms center on neural development, including forebrain radial glial cell differentiation and enteric nervous system development, plus glial cell proliferation. Transcriptional regulation terms (DNA-templated transcription and its negative regulation) suggest that this cluster represents neural/glial differentiation with transcription control, despite a few more general or unrelated terms (bile duct development, mitochondrial chromosome packaging).","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0021861","count":2},{"id":"GO:0032258","count":2},{"id":"GO:0035622","count":1},{"id":"GO:0048484","count":1}]},{"hash":"301821893004786321","title":"Hormone-responsive transcription and phosphorylation regulation","description":"The cluster includes GO terms pointing to regulation of transcription (by RNA Pol I/III and DNA binding), and regulation of protein kinase activity with phosphorylation of serine/threonine residues, alongside hormone-related contexts (response to testosterone) and liver-associated processes (liver regeneration, adiponectin signaling). This suggests a cohesive role in hormone-driven signaling that modulates transcription through phosphorylation-based regulation, rather than a single, narrowly defined function.","confidence":"Medium","size":6,"edges":10,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0045859","count":1},{"id":"GO:0006356","count":1},{"id":"GO:0033574","count":1},{"id":"GO:0097421","count":1},{"id":"GO:0018105","count":1}]},{"hash":"97517077550720297","title":"Mitotic Regulation and Chromatin Organization","description":"The cluster centers on cell division and mitotic control, including G2/M transition, APC/C-dependent degradation, and spindle checkpoint-related processes, with supporting roles in chromatin organization and nuclear transport. Ubiquitination (K11-linked) and ERAD-related terms suggest a coordinated system of protein turnover during mitosis, linking cell cycle progression to chromatin regulation.","confidence":"Medium","size":6,"edges":9,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0000086","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0070979","count":2},{"id":"GO:0030433","count":2}]},{"hash":"1715299851349253307","title":"Innate Immune Response","description":"The cluster shows multiple GO terms tied to defense against pathogens and innate immunity (defense response to Gram-positive bacterium, defense response to virus, innate immune response), suggesting proteins involved in early immune defense. Other terms (redox homeostasis, transcription, pigmentation) are less central, so the core theme remains innate immune activity.","confidence":"Medium","size":6,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0050830","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0042552","count":2},{"id":"GO:0051607","count":2}]},{"hash":"1424357751393414074","title":"Meiosis recombination and DNA damage response","description":"This cluster prominently features meiotic processes (synaptonemal complex assembly and reciprocal meiotic recombination) along with DNA damage recognition and repair (gamma radiation response, replication-born DSB repair via sister chromatid exchange) and chromatin regulation hints, suggesting proteins involved in meiosis and DNA repair pathways.","confidence":"High","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007130","count":2},{"id":"GO:0071480","count":2},{"id":"GO:0043971","count":1},{"id":"GO:0070868","count":1},{"id":"GO:0043970","count":1}]},{"hash":"934319970621817978","title":"Sterol and lipid biosynthesis","description":"This cluster is dominated by GO terms related to sterol and lipid metabolism, including cholesterol biosynthetic pathways via lathosterol, ergosterol biosynthesis, fatty acid biosynthesis, ether lipid metabolism, and sphingolipid turnover. The inclusion of sebaceous gland differentiation and CNS myelin maintenance aligns with lipid-rich tissues, supporting a cohesive lipid/sterol biosynthesis theme, while a single term like B cell chemotaxis appears as noise. Overall, the terms point to sterol and lipid biosynthesis pathways as the core function of this group.","confidence":"High","size":6,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1901799","count":1},{"id":"GO:0046485","count":1},{"id":"GO:0080065","count":1},{"id":"GO:0033490","count":1},{"id":"GO:0035754","count":1}]},{"hash":"2269306489192011477","title":"Zinc ion transport and homeostasis","description":"The top terms cluster around zinc handling: multiple entries for zinc import across membranes, zinc ion homeostasis, detoxification of zinc, and cellular response to zinc starvation, plus cadmium transport. This points to a cohesive theme of zinc transporters and metal homeostasis. The limb development term appears incidental and does not override the zinc-centric pattern. ","confidence":"High","size":6,"edges":12,"triangles":9,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1903615","count":4},{"id":"GO:0060173","count":4},{"id":"GO:0006831","count":4},{"id":"GO:0006882","count":4},{"id":"GO:0010312","count":4}]},{"hash":"264058363094175914","title":"Fungal Cell Wall Biosynthesis and Glycosylation","description":"The top GO terms point to fungal-type cell wall biogenesis, mannoprotein biosynthesis, and various glycosylation and polysaccharide biosynthesis processes, including cell budding and division septum assembly, which collectively suggest a cluster of proteins involved in constructing and modifying the fungal cell wall. A few terms like purine metabolism are generic background signals, but the dominant pattern aligns with fungal cell wall formation and glycosylation.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006144","count":2},{"id":"GO:0009272","count":1},{"id":"GO:0000032","count":1},{"id":"GO:0007114","count":1},{"id":"GO:0042125","count":1}]},{"hash":"1883305132737022548","title":"Isoprenoid and carbohydrate metabolism","description":"This cluster shows strong association with isoprenoid biosynthesis, via the mevalonate and MEP pathways, and cholesterol production, suggesting lipid/isoprenoid metabolism. It also includes several carbohydrate-related processes (galactose/glycolysis, galacturonate, GDP-L-fucose salvage) and a glycolytic/amino-sugar salvage angle, indicating a broader metabolic module focused on lipid precursors and sugar metabolism rather than a single specific pathway. ","confidence":"Medium","size":5,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0010142","count":2},{"id":"GO:0019288","count":2},{"id":"GO:0046835","count":2},{"id":"GO:0006695","count":2},{"id":"GO:0046396","count":2}]},{"hash":"1804189861768204416","title":"Aromatic compound catabolism and detoxification","description":"This cluster centers on metabolism and detoxification of xenobiotic and aromatic compounds. The top GO terms include several catabolic pathways (1,2-dichloroethane, 3-phenylpropionate, glucuronoside), the beta-ketoadipate pathway, and cellular oxidant detoxification, which together point to degradation of aromatic compounds and protection from oxidative stress. There are some outliers (e.g., secondary shoot formation) that reduce the strength of a single unifying theme, but the dominant signal is aromatic compound catabolism and detoxification.","confidence":"Medium","size":5,"edges":7,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019260","count":1},{"id":"GO:0010223","count":1},{"id":"GO:0042952","count":1},{"id":"GO:0019380","count":1},{"id":"GO:0098869","count":1}]},{"hash":"2097100725973888391","title":"Neurovascular Development and Immune Signaling","description":"The cluster features strong angiogenesis and multicellular development signals, plus immune-related terms (innate immune response, IL-2 signaling) and neural development cues (axon fasciculation, pain-related behavior), suggesting a theme of coordinating vascular growth with neural development and immune responses; cytoskeletal/microtubule localization supports neuronal transport aspects. ","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":2},{"id":"GO:0051092","count":2},{"id":"GO:0045766","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0045087","count":2}]},{"hash":"1258858653930916908","title":"Intracellular Protein Trafficking and Quality Control","description":"This cluster is best captured by the recurring themes of intracellular protein movement and processing: import into peroxisomes, receptor recycling, and ER-to-Golgi transport, plus ubiquitin-dependent ERAD-related quality control. While some terms touch on development or apoptosis, the strongest shared signal is protein trafficking and quality control across organelles, with related stress responses.","confidence":"Medium","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0001824","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0016558","count":2},{"id":"GO:0070987","count":2}]},{"hash":"388665578489412387","title":"Bacterial Peptidoglycan Synthesis and Division","description":"The terms coalesce around bacterial envelope biosynthesis\u2014peptidoglycan biosynthesis, Gram-negative cell wall biogenesis, and cell wall organization\u2014along with cell division and cell cycle, pointing to proteins involved in building and remodeling the peptidoglycan layer and coordinating cytokinesis in bacteria. An outlier term about ubiquitin-dependent proteasomal degradation appears but does not define the cluster. Overall, the group aligns with bacterial peptidoglycan synthesis and division.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006486","count":1},{"id":"GO:0043164","count":1},{"id":"GO:0071555","count":1},{"id":"GO:0009252","count":1},{"id":"GO:0051301","count":1}]},{"hash":"77990767253355437","title":"Cofactor Biosynthesis","description":"The GO terms are dominated by biosynthetic processes for vitamins and cofactors (thiamine, molybdopterin cofactor, biotin, protoporphyrinogen IX/heme, PQQ, tRNA queuosine, etc.), suggesting the proteins collectively participate in cofactor assembly or maturation rather than a single specific pathway. A trafficking term appears but likely noise; thus the cohesive theme is cofactors biosynthesis.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009228","count":2},{"id":"GO:0006777","count":2},{"id":"GO:0043497","count":2},{"id":"GO:0032258","count":2},{"id":"GO:0006782","count":1}]},{"hash":"563784411518430372","title":"Oxidative stress and metal ion response","description":"This cluster is enriched for redox-related and metal stress processes: detoxification of oxidants, glutathione biosynthesis, and responses to zinc and aluminum ions, plus ROS generation regulation. While there are some general cellular processes (growth regulation, translation), the dominant pattern ties to managing oxidative stress and metal ion challenges.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0040008","count":5},{"id":"GO:0002182","count":5},{"id":"GO:0010043","count":5},{"id":"GO:0010044","count":5},{"id":"GO:1901687","count":5}]},{"hash":"2232051730040966846","title":"Mannoprotein glycosylation and cell wall biosynthesis","description":"The top GO terms point to glycosylation-dependent production of cell wall/mucilage components (cell wall mannoprotein biosynthetic process, mucilage biosynthetic process, and protein N-linked glycosylation). These together suggest a theme of glycoprotein synthesis shaping extracellular matrices. The other terms occur at low counts and seem incidental rather than core to the cluster. ","confidence":"Medium","size":5,"edges":7,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000032","count":2},{"id":"GO:0010192","count":2},{"id":"GO:0006487","count":2},{"id":"GO:0000189","count":1},{"id":"GO:0097156","count":1}]},{"hash":"2183170968234177151","title":"Acetylation-focused amino acid metabolism","description":"The cluster shows several acetylation-related GO terms (putrescine, spermine, N-terminal, and propionylation) alongside amino acid metabolic processes (arginine biosynthesis, N-acetylglucosamine metabolism, mycothiol biosynthesis). While there are some additional terms related to cell cycle and angiogenesis, the acetylation theme appears most prominent, suggesting a functional grouping around acetylation of amino acids and proteins with supporting metabolism.","confidence":"Medium","size":5,"edges":6,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032920","count":3},{"id":"GO:0006044","count":3},{"id":"GO:0060358","count":3},{"id":"GO:0017196","count":3},{"id":"GO:0006526","count":3}]},{"hash":"1584616969950028740","title":"Unknown","description":"The GO terms span chaperone-mediated protein complex assembly, mitochondrial import, cell division, RNA localization to Cajal bodies, stress responses (ischemia, heat, ATP), reproductive binding, and TNF production. This mix spans multiple cellular compartments and processes with no clear shared function, so a cohesive, specific label isn\u2019t supported.","confidence":"","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051131","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0045041","count":3},{"id":"GO:0090666","count":2},{"id":"GO:0002931","count":2}]},{"hash":"1559497712670511101","title":"Lipid Metabolism and Inflammatory Signaling","description":"The top GO terms indicate strong lipid metabolism involvement (fatty acid oxidation, cholesterol biosynthetic process) alongside immune/inflammatory signaling (regulation of cytokine production in inflammatory response, interleukin-2-mediated signaling). There are also hormone-responsive terms (cellular response to peptide hormone stimulus, FSH), suggesting a broader metabolic-hormonal and inflammatory signaling theme. A few neuronal-related terms appear but are not dominant. This makes a cohesive, specific label reasonable but not perfect, hence Medium confidence.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":2},{"id":"GO:0019395","count":2},{"id":"GO:1900015","count":2},{"id":"GO:0071375","count":2},{"id":"GO:0071372","count":2}]},{"hash":"912165695654071545","title":"Phosphate Metabolism and Proteoglycan Biosynthesis","description":"This cluster centers on phosphate-related metabolism and signaling, including dephosphorylation, cellular responses to phosphate starvation, and inositol phosphate biosynthesis/metabolism, with additional terms pointing to glycosaminoglycan (proteoglycan) biosynthesis (chondroitin and heparan sulfate). The shared theme appears to be phosphate-driven signaling and metabolism, with a secondary link to extracellular matrix component biosynthesis, suggesting proteins involved in both phosphate regulation and proteoglycan production. ","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016311","count":2},{"id":"GO:0016036","count":2},{"id":"GO:0060168","count":2},{"id":"GO:2001311","count":2},{"id":"GO:0050650","count":2}]},{"hash":"1114647914639385582","title":"Neural development and synaptic signaling","description":"The cluster is clearly enriched for neural-related processes: neuron differentiation, excitatory postsynaptic potential, and regulation of postsynaptic calcium, plus Schwann cell development. These point to neural development and synaptic signaling. Some terms like lung development, cell cycle transition, or miRNA processing are broader regulatory roles and may reflect pleiotropic functions, but the dominant theme is neural differentiation and synaptic activity.","confidence":"Medium","size":5,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0060079","count":2},{"id":"GO:0051037","count":2},{"id":"GO:0099566","count":2},{"id":"GO:0030324","count":2},{"id":"GO:0014044","count":2}]},{"hash":"1257262355781128663","title":"Neural development and nerve branching morphogenesis","description":"This cluster is enriched for neural development terms, notably substantia nigra development and regulation of branching morphogenesis of a nerve, suggesting a theme of neural development and nerve morphogenesis. Supporting terms related to gene expression regulation, protein transport, and vesicle trafficking likely reflect essential cellular processes underpinning neural development, while chromatin organization and ribosomal export are broader housekeeping functions that accompany development. Overall, the neural development/morphogenesis signal is the strongest thread.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0021762","count":4},{"id":"GO:0006348","count":4},{"id":"GO:0010628","count":4},{"id":"GO:0071963","count":4},{"id":"GO:0000001","count":4}]},{"hash":"611693147740950361","title":"Mating pheromone signaling","description":"This cluster centers on GO terms tied to mating and pheromone-dependent signal transduction involved in conjugation with cellular fusion, indicating a shared role in mating signaling pathways. The two terms are directly related to mating processes, suggesting the proteins participate in pheromone-mediated communication during mating. ","confidence":"High","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000750","count":1},{"id":"GO:0007618","count":1}]},{"hash":"147297029538428589","title":"Mitochondrial protein import and energy production","description":"This cluster is best labeled around mitochondrial processes: assembly of mitochondrial respiratory chain components, outer membrane translocase assembly, proton-driven ATP synthesis, and proton transmembrane transport. While a few terms are developmental or vesicular in nature, the strongest signals are mitochondrial import/assembly and energy production, suggesting this label captures the core function of the cluster.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035675","count":1},{"id":"GO:0007430","count":1},{"id":"GO:0042777","count":1},{"id":"GO:0015991","count":1},{"id":"GO:0007034","count":1}]},{"hash":"1484492170090181924","title":"Unknown","description":"The GO terms cover a broad mix: nucleosome disassembly and gene expression regulation point to chromatin dynamics; proteasomal ubiquitin-dependent degradation relates to protein turnover; other terms refer to metabolism, brain development, and even viral transcription, with several obsolete entries. There is no clear, cohesive biological theme uniting all proteins, so a single interpretable label isn't supported.","confidence":"","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045793","count":2},{"id":"GO:0005987","count":2},{"id":"GO:0032435","count":2},{"id":"GO:0044109","count":2},{"id":"GO:0021987","count":2}]},{"hash":"365027835095069916","title":"ER-Golgi trafficking and phagocytosis regulation","description":"The top GO terms point to cotranslational targeting to membranes and ER-to-Golgi vesicle transport, together with a role in positively regulating phagocytosis. This suggests a coherent theme: proteins involved in intracellular trafficking along the ER-Golgi pathway that can modulate phagocytic processes. The cluster likely reflects vesicle transport functions linked to phagocytosis.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006613","count":1},{"id":"GO:0050766","count":1},{"id":"GO:0006888","count":1}]},{"hash":"585802561856903632","title":"Unknown","description":"The top GO terms span signaling regulation (GPCR), ER targeting, mitochondrial distribution, ubiquitination, oxidative stress response, and protein folding, with no single cohesive biological function emerging for this small cluster. This makes a precise, representative label unlikely.","confidence":"","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0008277","count":1},{"id":"GO:1902391","count":1},{"id":"GO:0006620","count":1},{"id":"GO:0046548","count":1},{"id":"GO:0048312","count":1}]},{"hash":"799286237217349051","title":"Proteostasis and Vesicle Trafficking","description":"This cluster centers on protein quality control and intracellular trafficking: chaperone-mediated assembly, proteasome assembly, endosomal microautophagy, vesicle transport between Golgi compartments, and related protein handling processes. Although a couple of terms touch stress responses or aging, the core set points to maintaining protein homeostasis and proper intracellular sorting.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016485","count":1},{"id":"GO:0061738","count":1},{"id":"GO:0070682","count":1},{"id":"GO:0001319","count":1},{"id":"GO:0019079","count":1}]},{"hash":"109305168223116425","title":"Unknown","description":"The protein set shows a highly diverse set of GO terms spanning translation, antibiotic and cycloheximide response, multiple lipid biosynthetic pathways (triterpenoids and hopanoids), and neural/immune signaling. This lack of a single coherent biological theme means a reliable, specific cluster label cannot be inferred; thus Unknown with no confidence.","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0046898","count":1},{"id":"GO:0010686","count":1},{"id":"GO:0010263","count":1}]},{"hash":"2085368112833197751","title":"Heart development and transcriptional regulation","description":"The terms point to early cardiac morphogenesis (atrioventricular canal and cardiac jelly development) combined with transcriptional control and protein turnover (RNA Pol II preinitiation, mRNA stability, proteasomal degradation), plus signaling pathways (Wnt, NF-kB) that commonly influence heart development. A T cell receptor signaling term is present but less directly related, likely incidental. Overall, the cluster centers on heart development with gene-regulatory signaling.","confidence":"Medium","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0036302","count":1},{"id":"GO:0051123","count":1},{"id":"GO:1905072","count":1},{"id":"GO:0031146","count":1},{"id":"GO:0010043","count":1}]},{"hash":"1421823760862756018","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0017038","count":2},{"id":"GO:0000393","count":2},{"id":"GO:0060303","count":2},{"id":"GO:0001113","count":2},{"id":"GO:0006605","count":2}]},{"hash":"666715652418507524","title":"Unknown","description":"The top GO terms are highly heterogeneous, spanning lipid metabolism (retinol, bile acids, cholesterol), hormone biosynthesis (testosterone), metabolism of hydrocarbons (naphthalene), and stress/response processes (hydrogen peroxide, jasmonic acid, peptide) across potentially different organisms. There is no single cohesive function linking these terms, so the cluster appears functionally diverse rather than a defined module.","confidence":"","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1900053","count":3},{"id":"GO:0042572","count":3},{"id":"GO:0006699","count":3},{"id":"GO:0018931","count":3},{"id":"GO:0061370","count":3}]},{"hash":"392678275454241252","title":"Unknown","description":"The GO terms are scattered across actin-based movement, nuclear import, and various obsolete or unrelated processes, with no clear, shared function that tightly binds the four proteins. Because a single coherent theme cannot be established, Unknown is the most appropriate label.","confidence":"","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006796","count":1},{"id":"GO:0007396","count":1},{"id":"GO:0006607","count":1},{"id":"GO:0030048","count":1},{"id":"GO:0000061","count":1}]},{"hash":"952324316090392774","title":"Cell cycle and transcription regulation cluster","description":"The top GO terms point to cell proliferation, division, mitotic cycle regulation, and broad transcriptional control by RNA polymerase II, with some kinase activation signals; together these suggest a cohesive role in coordinating cell cycle progression with transcriptional regulation.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0008283","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0007127","count":1},{"id":"GO:0060303","count":1}]},{"hash":"611825908712076073","title":"Photoreceptor membrane biogenesis and exocytosis","description":"The GO terms point toward photoreceptor-specific processes: rhabdomere membrane biogenesis and phototaxis, combined with vesicle docking/tethering in exocytosis and SNARE regulation, suggesting a cohesive module for photoreceptor membrane formation and vesicle trafficking. Other terms like metal ion stress and cardiac development appear incidental noise in this cluster.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006474","count":1},{"id":"GO:1990169","count":1},{"id":"GO:0060912","count":1},{"id":"GO:0048659","count":1},{"id":"GO:1990359","count":1}]},{"hash":"792534997944697500","title":"Unknown","description":"The GO terms cover a broad, disconnected set of functions (biosynthesis, protein processing, cilium movement, autophagy, proteasome assembly, vesicle transport, aging, viral replication), and there are no internal edges to suggest a cohesive pathway. There\u2019s no clear shared function tying the proteins together, so labeling as Unknown is appropriate.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006592","count":1},{"id":"GO:0033050","count":1},{"id":"GO:0006526","count":1},{"id":"GO:0016485","count":1},{"id":"GO:0003341","count":1}]},{"hash":"759643475993132685","title":"Unknown","description":"The top GO terms reflect a broad mix of neural development, muscle development, cytoskeletal/motor processes, cell division, and organelle inheritance, with no single cohesive theme linking the proteins. Therefore, a specific, representative label cannot be assigned.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0021762","count":2},{"id":"GO:0048741","count":2},{"id":"GO:0030240","count":1},{"id":"GO:0090131","count":1},{"id":"GO:0070527","count":1}]},{"hash":"223540416382135156","title":"Transcription Regulation and Cell Cycle Control","description":"This cluster centers on transcription-related processes (DNA-templated transcription, regulation of transcription including miRNA transcription) and cell-cycle\u2013associated activities (sister chromatid cohesion; meiotic regulation). Supporting terms touch on protein homeostasis (peptidyl-lysine deacetylation; polyubiquitinated misfolded protein transport) and stress responses (hydrogen peroxide\u2013triggered programmed cell death). While a couple terms like regulation of skeletal muscle development and jasmonic acid/ethylene\u2013dependent systemic resistance are more tissue- or species-specific, the dominant signal is transcriptional control linked to cell cycle and protein regulation.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0048742","count":3},{"id":"GO:0009861","count":2},{"id":"GO:0007062","count":2},{"id":"GO:0070845","count":2}]},{"hash":"1854179969421593660","title":"Cellular stress response and cytoskeletal remodeling","description":"The top GO terms point to broad stress-response processes (cellular response to xenobiotic stimulus, detection of hypoxia, regulation of interferon signaling) and cytoskeletal changes (actin rod assembly, chemotaxis), with supporting hints from chaperone assembly and metabolic adjustments (pyruvate decarboxylation, respiration). Together, these suggest a theme of cells sensing and adapting to stress with remodeling of the cytoskeleton and metabolism.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":2},{"id":"GO:0010510","count":1},{"id":"GO:0006261","count":1},{"id":"GO:0031247","count":1},{"id":"GO:0006935","count":1}]},{"hash":"2214854871617577885","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0072520","count":3},{"id":"GO:0000209","count":3},{"id":"GO:0000348","count":3},{"id":"GO:0070979","count":3},{"id":"GO:0000132","count":3}]},{"hash":"1877048643773672875","title":"Iron-Sulfur Cluster Assembly","description":"The top GO term for this cluster is iron-sulfur cluster assembly, pointing to proteins involved in Fe-S cluster biogenesis; with three proteins annotated to this process, the label directly reflects the shared function.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016226","count":1}]},{"hash":"1732903333711291206","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0061179","count":3},{"id":"GO:0055010","count":2},{"id":"GO:1903779","count":2},{"id":"GO:0019227","count":2},{"id":"GO:0051775","count":2}]},{"hash":"1020298408565537228","title":"Nuclear import and GTPase-regulated signaling","description":"The top GO terms show a notable emphasis on NLS-bearing protein import into the nucleus and positive regulation of GTPase activity, suggesting a core theme around signaling regulation linked to nuclear transport. Additional terms point to broader signaling roles (GPCR and T cell receptor signaling, cytokine pathways, calcium transport, acrosome reaction), indicating a diversified but interconnected signaling cluster. The label captures the most pronounced shared features while acknowledging the mixed functional diversity. ","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006607","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0008277","count":1},{"id":"GO:0032735","count":1},{"id":"GO:0007340","count":1}]},{"hash":"1386876492025591159","title":"Unknown","description":"The GO terms across the proteins are highly varied, including responses to ethanol, viral and symbiont-related processes, multiple protein catabolic and proteolysis-related terms, and protein oligomerization. There is no single coherent function or pathway common to all members, making it impossible to assign a meaningful, specific label. Therefore the cluster is Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045471","count":2},{"id":"GO:0046718","count":1},{"id":"GO:0032461","count":1},{"id":"GO:0045861","count":1},{"id":"GO:0044257","count":1}]},{"hash":"839978837017431721","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by GO terms for ribosome biogenesis, ribosomal large subunit assembly, cytoplasmic translation, and SRP-dependent cotranslational targeting to membrane, pointing to proteins involved in ribosome assembly and protein synthesis. Some terms about transcription elongation and p53-mediated apoptosis appear, but the core signal centers on ribosome production and translation.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006614","count":1},{"id":"GO:0071353","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0002181","count":1},{"id":"GO:0000027","count":1}]},{"hash":"2204674137428826938","title":"Unknown","description":"The top GO terms are highly diverse, spanning antibiotic response, nucleotide-excision repair, peroxisomal fatty acid import, MHC class I antigen processing, intracellular pH changes, secretion system, membrane potential, cytochrome assembly, RNA endoribonuclease regulation, and xenobiotic transport. There is no single cohesive functional theme linking these terms, suggesting no shared, specific activity among the proteins. Therefore, I cannot assign a meaningful, representative label.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0006289","count":1},{"id":"GO:0015910","count":1},{"id":"GO:0019885","count":1},{"id":"GO:0051454","count":1}]},{"hash":"1596043643078443250","title":"Mitotic DNA Replication Machinery","description":"The cluster is enriched with GO terms tied to DNA replication initiation and elongation during cell division (mitotic DNA replication preinitiation complex assembly, DNA strand elongation in mitotic replication) and factors like the GINS complex, indicating a cohesive set of replication machinery components. While a few terms touch broader nucleic acid metabolism, the dominant theme points to replication complex assembly and activity in mitosis.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":1},{"id":"GO:0000722","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0090342","count":1},{"id":"GO:1902975","count":1}]},{"hash":"1195043460809003603","title":"Plant Growth and Stress Response","description":"The top GO terms point to plant development and environmental response: regulation of chlorophyll biosynthetic process, positive regulation of root meristem growth, cell size and hormone biosynthesis regulation, and responses to UV and osmotic stress, suggesting a cohesive plant growth-regulation cluster. An outlier term on pituitary gland development likely reflects annotation noise rather than a true shared function. ","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010380","count":1},{"id":"GO:0045793","count":1},{"id":"GO:0021983","count":1},{"id":"GO:0035522","count":1},{"id":"GO:1900033","count":1}]},{"hash":"644148653323890861","title":"Unknown","description":"The GO terms cover diverse developmental contexts (bile duct, enteric nervous system, pancreas, trachea cartilage, photoreceptor differentiation) and broad regulatory processes (transcriptional repression, spindle assembly, glial proliferation, tolerance regulation), with no single unifying function, so a coherent cluster label isn't apparent.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035622","count":1},{"id":"GO:0048484","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0046533","count":1},{"id":"GO:0090139","count":1}]},{"hash":"2192990645491894522","title":"Broad-substrate membrane transporters","description":"The GO terms point to transmembrane transport of a wide variety of substrates (nitrate/nitrite, galactose, sialic acid, fucose, vitamins, potassium, xenobiotics) plus a neurotransmitter loading step, suggesting these proteins function as transporters with broad substrate specificity rather than a single substrate or fixed catalytic activity. This motivates labeling the cluster as multisubstrate membrane transporters.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0098700","count":1},{"id":"GO:0006855","count":1},{"id":"GO:0015706","count":1},{"id":"GO:0035461","count":1},{"id":"GO:0042128","count":1}]},{"hash":"2232003261666581572","title":"Seed lipid metabolism and seed development","description":"Proteins in this cluster collectively show enrichment for plant lipid metabolism, especially fatty-acid processing across various chain lengths (medium-, long-, and very-long-chain fatty acids) and transport, alongside seed-specific processes (seed germination regulation and seed coat development) and related phenylpropanoid metabolism. This pattern suggests a module centered on seed lipid metabolism in plants and its connection to seed biology.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0036112","count":3},{"id":"GO:0010030","count":3},{"id":"GO:0009698","count":3},{"id":"GO:0019654","count":3},{"id":"GO:0090410","count":3}]}]