[{"hash":"1835758321921888983","title":"Developmental growth with mitosis and secretory trafficking","description":"This cluster features brain development and multicellular growth alongside mitotic processes (mitotic spindle assembly, mitotic cell cycle) and protein-synthesis/trafficking pathways (ribosome biogenesis, COPII vesicle budding, Golgi-to-ER transport), suggesting a coordinated program of cellular proliferation with an active secretory machinery.","confidence":"High","size":29,"edges":10,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007420","count":8},{"id":"GO:0008283","count":6},{"id":"GO:0051301","count":5},{"id":"GO:0090114","count":5},{"id":"GO:0035264","count":5}]},{"hash":"146141805681297743","title":"Embryonic and organ development","description":"This cluster centers on multiple tissue- and organ-specific developmental processes (pituitary, cartilage, retina, metencephalon, dorsal spinal cord, endocardial cushion EMT, pancreatic differentiation) and general multicellular development. While some terms relate to non-developmental processes (oxidant detoxification, apoptosis), the dominant pattern is broad developmental/differentiation activity across diverse tissues, justifying a general development-focused name. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021983","count":5},{"id":"GO:0051216","count":4},{"id":"GO:0098869","count":4},{"id":"GO:0006915","count":4},{"id":"GO:0003198","count":3}]},{"hash":"770590127026159690","title":"Core cell growth and division machinery","description":"The top GO terms cluster around fundamental cellular processes: ribosome biogenesis, protein processing and quality control (ERAD), vesicle transport between ER and Golgi, cytoskeletal dynamics (microtubule severing), chromatin assembly during cell division, and general cell division. While some terms like brain development and xylan catabolic process are less directly related, the dominant themes point to core housekeeping activities essential for growth, division, and intracellular trafficking. This supports labeling the cluster as a set of core cellular machinery for growth and division.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0046677","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0045493","count":4},{"id":"GO:0061641","count":3},{"id":"GO:0051301","count":3}]},{"hash":"1436181490287763613","title":"Developmental signaling and cell cycle regulation","description":"These proteins show strong signals for DNA replication and centrosome cycle (cell cycle) together with several developmental and signaling pathways (Wnt, ephrin, cranial skeleton morphogenesis, dendritic spine morphogenesis, and T cell receptor signaling). The combination suggests a cluster centered on coordinated signaling during development and cell proliferation, thus a label reflecting both aspects.","confidence":"Medium","size":29,"edges":4,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":14},{"id":"GO:0048701","count":14},{"id":"GO:0090263","count":14},{"id":"GO:0006915","count":14},{"id":"GO:0048013","count":13}]},{"hash":"2212284134809194472","title":"Brain development and interneuron differentiation","description":"Based on the Top Terms, the cluster is enriched for neural development, especially brain regions and interneuron differentiation, including cerebral cortex GABAergic interneurons, hypothalamus and diencephalon morphogenesis, and neuron migration. Although a few terms reference non-neural morphogenesis (ureteric bud, fungiform papilla, endodermal fate), the predominant signals point to neural development and interneuron specialization. Therefore the name Brain development and interneuron differentiation captures the dominant theme.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072107","count":1},{"id":"GO:2000836","count":1},{"id":"GO:0042663","count":1},{"id":"GO:0007420","count":1},{"id":"GO:0061197","count":1}]},{"hash":"2085291064064398726","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":13,"triangles":0,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006986","count":4},{"id":"GO:0070389","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0036494","count":3},{"id":"GO:0090084","count":3}]},{"hash":"2108152195949348508","title":"Unknown","description":"Top GO terms are highly diverse across immunology (germinal center formation, B cell receptor signaling), plant development (brassinosteroid signaling, flower development), physiology (swimming, skeletal muscle development, distal tubule morphogenesis), circadian regulation, and tRNA modification (wybutosine biosynthetic process). This lack of a single cohesive biological theme suggests the proteins do not share a common function, so a specific label is not supported.","confidence":"","size":29,"edges":10,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0002467","count":9},{"id":"GO:0050853","count":9},{"id":"GO:0042787","count":9},{"id":"GO:0009742","count":7},{"id":"GO:0042752","count":7}]},{"hash":"937967772332621531","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0002181","count":2},{"id":"GO:0006400","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0043547","count":2}]},{"hash":"245242813518702785","title":"Nuclear RNA Processing and Protein Quality Control","description":"The top terms cluster around nuclear-centered activities: mRNA splicing via spliceosome and ribosomal large subunit export from the nucleus, plus ubiquitin-dependent ERAD involved in protein quality control; these point to roles in RNA processing and protein homeostasis within the cell, with additional stress and signaling terms that may reflect regulatory cross-talk rather than core function.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0000055","count":2},{"id":"GO:1904751","count":2},{"id":"GO:0006970","count":2}]},{"hash":"264242098599636627","title":"Transcription Regulation and Ubiquitin-Proteasome Proteostasis","description":"The cluster prominently features DNA-templated transcription along with ubiquitin-dependent protein catabolic processes (ERAD and SCF-proteasomal), plus ER-to-Golgi transport and immune-related defense signals. This suggests a cohesive theme where gene expression is coordinated with protein quality control and trafficking, especially in response to cellular stress or immune cues, rather than a single narrow function.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0050830","count":6},{"id":"GO:0006888","count":6},{"id":"GO:0051301","count":5},{"id":"GO:0030433","count":5}]},{"hash":"1377936589347306450","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0016032","count":2},{"id":"GO:0043044","count":2},{"id":"GO:0035390","count":2},{"id":"GO:0071031","count":2}]},{"hash":"1218705507620532814","title":"RNA Metabolism and Meiotic Germline Regulation","description":"Top GO terms indicate RNA metabolism (NMD, miRNA processing, RNA editing, mRNA destabilization, mRNA methylation) alongside meiotic/germline processes (meiotic cell cycle, germarium-derived germline cyst encapsulation). The combination suggests a cluster of proteins coordinating RNA processing with meiosis and germline development.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070478","count":1},{"id":"GO:1990744","count":1},{"id":"GO:0007329","count":1},{"id":"GO:0006382","count":1},{"id":"GO:0000742","count":1}]},{"hash":"1714171430149225435","title":"Unknown","description":"The cluster's top GO terms span unrelated areas\u2014GPI anchor biosynthesis; plant hypersensitive response; bile acid transport; epithelial proliferation; ammonia assimilation; nitrogen metabolism and fixation; nitrogen starvation response; protein oligomerization; and glutamatergic synaptic transmission. With no edges and only scattered, diverse functions, there isn\u2019t a single cohesive biological theme linking these proteins. ","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":2},{"id":"GO:0009626","count":1},{"id":"GO:0015721","count":1},{"id":"GO:0050679","count":1},{"id":"GO:0019676","count":1}]},{"hash":"2214658578330149720","title":"RNA Methylation and Ribosome Biogenesis Enzymes","description":"The top GO terms cluster around RNA modification and ribosome biogenesis: tRNA methylation, tRNA wobble uridine modification, rRNA modification, and ribosomal small subunit export from the nucleus. The presence of peptidyl-arginine methylation also supports a broader methyltransferase theme. Some antibiotic/xenobiotic response terms appear, but the dominant signal points to RNA methylation and ribosome assembly/processing functions.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030488","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0000056","count":2},{"id":"GO:0000154","count":2},{"id":"GO:0019919","count":2}]},{"hash":"2084886067266947328","title":"Tyrosine phosphatase\u2013mediated immune signaling regulation","description":"This cluster centers on peptidyl-tyrosine dephosphorylation and negative regulation of signaling pathways (ERK/MAPK, T cell receptor signaling, IL-2 signaling) and includes NK cell\u2013mediated cytotoxicity and suppression of cell proliferation. While a few terms relate to membrane potential or cardiac development, the dominant theme is phosphatase-driven attenuation of immune signaling, suggesting a coherent module of protein tyrosine phosphatases modulating immune responses.","confidence":"Medium","size":28,"edges":374,"triangles":3178,"max_degree":27,"top_function":null,"top_go_terms":[{"id":"GO:0035335","count":17},{"id":"GO:0000200","count":15},{"id":"GO:0070373","count":15},{"id":"GO:0050860","count":15},{"id":"GO:0042267","count":11}]},{"hash":"1255960966559958285","title":"Nuclear DNA replication and repair machinery","description":"The terms center on genome maintenance, including DNA replication, UV-damage repair, translesion synthesis, and cell division, suggesting these proteins function together in nuclear genome maintenance. The presence of mRNA export and ER-Golgi transport terms likely reflects broader cellular coupling or multi-functional proteins rather than a single cohesive pathway.","confidence":"Medium","size":28,"edges":7,"triangles":0,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0006406","count":4},{"id":"GO:0070914","count":4},{"id":"GO:0051260","count":4},{"id":"GO:0006888","count":4}]},{"hash":"918106882371749949","title":"Nuclear import and nuclear pore assembly","description":"The cluster\u2019s top GO terms cluster around import of proteins into the nucleus (NLS-bearing import, ribosomal protein import), assembly of the nuclear pore complex, and regulation of transport-related processes (e.g., GTPase activity). These signals point to a cohesive theme of nucleocytoplasmic transport and associated nuclear pore functions, with secondary ties to nuclear regulation such as desumoylation and cell cycle-related nuclear events. Overall, the data suggest a nuclear transport/ribosome biogenesis-centric cluster.","confidence":"High","size":28,"edges":104,"triangles":181,"max_degree":20,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0043547","count":14},{"id":"GO:0006607","count":14},{"id":"GO:0015991","count":12},{"id":"GO:0016477","count":11},{"id":"GO:0042176","count":11}]},{"hash":"2157023279715561791","title":"Metabolic and Developmental Processes","description":"The cluster centers on core metabolism: biotin biosynthesis, lysine/leucine/alanine catabolic processes, glycolysis, porphyrinogen IX biosynthesis (heme precursor), and redox homeostasis, suggesting a metabolic-focused group. The presence of heart development and post-embryonic development terms adds a developmental context but they are not the dominant signal, so the cluster appears to be primarily metabolic with some developmental associations. ","confidence":"Medium","size":28,"edges":6,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0019878","count":3},{"id":"GO:0009102","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0009791","count":3},{"id":"GO:0006552","count":3}]},{"hash":"2102965255658719474","title":"Developmental and Hormonal Regulation","description":"Many terms point to developmental and reproductive biology (pituitary gland development, cartilage development, sperm capacitation, and gamete-related methylation). Hormone biosynthetic process and chromatin binding regulation further support a regulatory, endocrine/reproductive theme, with apoptosis providing a common cellular control mechanism. Despite some obsolete terms, the core signal links developmental processes with hormonal and reproductive regulation. Confidence: Medium","confidence":"","size":28,"edges":9,"triangles":0,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0021983","count":8},{"id":"GO:0006915","count":8},{"id":"GO:0045654","count":6},{"id":"GO:0043046","count":6},{"id":"GO:0055114","count":6}]},{"hash":"1853523446054401853","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by GO terms tied to ribosome assembly and function: maturation of SSU and LSU rRNA, ribosomal large subunit biogenesis, and translation. While there are a few auxiliary terms (regulatory RNA silencing, DNA-related processes) they appear less central, making ribosome biogenesis and translation the most coherent overarching theme for the cluster.","confidence":"High","size":28,"edges":237,"triangles":1070,"max_degree":27,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000462","count":11},{"id":"GO:0042273","count":11},{"id":"GO:0006412","count":10},{"id":"GO:0031047","count":9},{"id":"GO:0006306","count":9}]},{"hash":"1248062624654540034","title":"Transcription and Cell Cycle Regulation","description":"This cluster is dominated by GO terms for DNA-templated transcription and mitotic cell cycle, plus mRNA transport and regulation of G0 to G1, indicating a core theme around nuclear gene expression controlling cell division. Secondary terms like actin nucleation (Arp2/3), hypoxia response, and skin development likely reflect broader cellular regulation and tissue contexts rather than defining the cluster. Overall, the set points toward coordinated transcriptional control and cell-cycle processes.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0000920","count":7},{"id":"GO:2000601","count":7},{"id":"GO:0071456","count":7},{"id":"GO:0043588","count":7}]},{"hash":"423994276444955492","title":"Diverse Metabolite Biosynthesis and Drug Response","description":"The cluster includes multiple biosynthetic processes (melanin, retinoic acid, estrogen, very long-chain fatty acids, phylloquinone, tetrahydrobiopterin, etc.) and also responses to antibiotics and methotrexate, suggesting a broad biosynthesis/metabolism core with drug-response signals. The label aims to capture this breadth without over-committing to a single pathway.","confidence":"Medium","size":28,"edges":248,"triangles":1087,"max_degree":27,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0042438","count":23},{"id":"GO:0002138","count":23},{"id":"GO:0046677","count":23},{"id":"GO:0031427","count":23},{"id":"GO:0006703","count":23}]},{"hash":"1204515058228183832","title":"Transmembrane Transport Proteins","description":"This cluster is dominated by GO terms for transmembrane transport (nitrite, sodium, arabinose, potassium, vitamin, xenobiotic) and a vesicular neurotransmitter loading term, pointing to membrane transporter and vesicle transport roles. A peripheral metabolic term (fucose metabolic process) does not strongly alter the overall theme.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":25},{"id":"GO:0035725","count":25},{"id":"GO:0015751","count":25},{"id":"GO:0006004","count":25},{"id":"GO:0006855","count":25}]},{"hash":"1475175844907363118","title":"Ribosome biogenesis and DNA replication","description":"The top terms cluster around ribosome assembly (LSU maturation, large subunit biogenesis) and core genome maintenance activities (DNA replication, mitotic cell cycle, DNA damage repair). This suggests a functional group where ribosome biogenesis is linked with cell-cycle progression and genome integrity processes. ","confidence":"High","size":28,"edges":7,"triangles":1,"max_degree":5,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":5},{"id":"GO:0000463","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0070987","count":3}]},{"hash":"1462462260592382874","title":"Ribosome Biogenesis and Translation","description":"The majority of the top GO terms point to ribosome-related processes and protein synthesis (translation, cytoplasmic translation, ribosome biogenesis, ribosomal large subunit assembly). This suggests the cluster comprises proteins involved in ribosome assembly and the translation machinery. Some other terms like cell cycle/division and folic acid biosynthesis may reflect broader growth and nucleotide metabolism connections, but the core signal is ribosome biogenesis and translation.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0002181","count":2},{"id":"GO:0046656","count":2},{"id":"GO:0000027","count":2}]},{"hash":"85744467734660883","title":"Nutrient-sensing signaling and exosome secretion","description":"This cluster prominently features exosomal secretion and negative regulation of TORC1 signaling, suggesting a theme around nutrient-responsive communication via vesicles. Phosphorylation and a few amino-acid biosynthesis terms add supporting regulatory context, but the strongest, most consistent signals are vesicle secretion and TORC1-related signaling. Some entries (like obsolete biosynthetic terms) may reflect annotation noise rather than core biology of the cluster.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990182","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0016310","count":1},{"id":"GO:0019877","count":1},{"id":"GO:0006561","count":1}]},{"hash":"1716102525964359528","title":"Glycogen and starch metabolism","description":"The cluster\u2019s top GO terms are centered on glycogen and starch biosynthesis and metabolism (glycogen metabolic process, starch/amylopectin biosynthesis, and regulation of glycogen biosynthetic processes). Additional terms related to intracellular transport and Golgi-to-vacuole traffic may reflect the cellular machinery involved in processing and trafficking carbohydrate- and protein-containing vesicles, but the dominant signal is carbohydrate metabolism.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051017","count":2},{"id":"GO:0006886","count":2},{"id":"GO:2000467","count":1},{"id":"GO:0005981","count":1},{"id":"GO:0019252","count":1}]},{"hash":"1635360557786627798","title":"Ubiquitin-Proteasome Mediated Proteolysis and Cytoskeleton","description":"Top terms show strong enrichment for ubiquitin-dependent protein catabolic processes (including SCF-dependent and K11-linked ubiquitination) and proteasomal degradation, with additional signals of stress fiber assembly and Rho signaling modulation. This suggests a core role in regulated protein turnover linked to cytoskeletal remodeling, rather than a specific immune or meiotic function.","confidence":"High","size":28,"edges":243,"triangles":755,"max_degree":26,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1902564","count":14},{"id":"GO:0042787","count":10},{"id":"GO:0031146","count":7},{"id":"GO:1902104","count":5},{"id":"GO:0051759","count":5}]},{"hash":"366902924297617585","title":"Mitochondrial Translation and Ribosome Biogenesis","description":"The top GO terms center on translation, rRNA maturation, and mitochondrial protein import, highlighting a cluster of proteins involved in mitochondrial ribosome assembly and protein synthesis. The inclusion of metabolism-related terms (one-carbon metabolism, serine/valine biosynthesis) aligns with mitochondrial metabolic processes that couple translation to metabolism. Overall, the pattern points to mitochondrial translation machinery with linked metabolic roles.","confidence":"Medium","size":27,"edges":351,"triangles":2925,"max_degree":26,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0055114","count":3},{"id":"GO:0000462","count":2},{"id":"GO:0006564","count":2},{"id":"GO:0009099","count":2}]},{"hash":"1865231407998286393","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":92,"triangles":186,"max_degree":17,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006541","count":4},{"id":"GO:0006508","count":4},{"id":"GO:0070365","count":3},{"id":"GO:0044210","count":3},{"id":"GO:0006207","count":3}]},{"hash":"658220338371162584","title":"RNA modification and vitamin biosynthesis","description":"The cluster centers on RNA-related processes such as rRNA and tRNA methylation and ribosomal subunit export, plus broad protein methylation activities, suggesting a core of RNA-processing enzymes. The presence of cobalamin and biotin biosynthetic terms, along with an antibiotic biosynthetic process, indicates involvement in vitamin/cofactor biosynthesis and secondary metabolism in a related microbial context. This combination points to a cohesive theme around RNA modification coupled with vitamin biosynthesis pathways, though some terms reflect broader metabolic activity.","confidence":"Medium","size":27,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":8},{"id":"GO:0035690","count":7},{"id":"GO:0017000","count":7},{"id":"GO:0009102","count":7},{"id":"GO:0016049","count":7}]},{"hash":"394999618027430784","title":"Steroid Hormone Biosynthesis & Xenobiotic Metabolism","description":"This cluster is dominated by GO terms for biosynthesis of steroid hormones and related regulatory processes (calcitriol, aldosterone, ecdysone) and hormone-regulated physiological events (e.g., uterus development, blood volume regulation). The presence of detoxification-related terms (insecticide metabolism, coumarin catabolism, fatty acid omega-oxidation, copper response) suggests a broader link to xenobiotic metabolism often coordinated with steroid hormone pathways. Together, these terms indicate a cohesive theme around steroid hormone production and associated metabolic detoxification, justifying the label.","confidence":"High","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0060065","count":26},{"id":"GO:0010430","count":22},{"id":"GO:0036378","count":22},{"id":"GO:0002017","count":22},{"id":"GO:0070365","count":22}]},{"hash":"113914681753167961","title":"Mitotic spindle assembly and microtubule dynamics","description":"The cluster is dominated by GO terms related to microtubule nucleation, polymerization, astral microtubule organization, spindle elongation, and exit from mitosis, as well as cystoblast division. This pattern points to coordinated microtubule dynamics driving mitotic progression and cell division, with a secondary nod to processes like mRNA stabilization and cell migration that can connect to cytoskeletal regulation. Overall, the core theme is mitotic spindle organization and microtubule dynamics.","confidence":"High","size":27,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0048255","count":2},{"id":"GO:0034453","count":2},{"id":"GO:1903690","count":2},{"id":"GO:0010458","count":2},{"id":"GO:0035099","count":2}]},{"hash":"272121827633168595","title":"Steroid and Xenobiotic Metabolism","description":"This cluster includes clear signals of steroid and vitamin D pathways (calcitriol biosynthesis from calciol; aldosterone biosynthesis; regulation of blood volume by aldosterone; response to vitamin D), as well as xenobiotic and lipid metabolism (insecticide metabolism; coumarin catabolism; fatty acid omega-oxidation; copper ion response). The combination points to a cohesive theme around metabolism of endogenous steroids/vitamins and detoxification/processing of xenobiotics, with some liver-associated differentiation context. Confidence: High","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033280","count":7},{"id":"GO:0010430","count":6},{"id":"GO:0036378","count":6},{"id":"GO:0002017","count":6},{"id":"GO:0070365","count":6}]},{"hash":"373574682306833425","title":"Mitotic Regulation and Translation Initiation","description":"This cluster centers on cell division and mitotic control (APC/C-dependent processes, anaphase-promoting complex), coupled with components of translation initiation (reinitiation and preinitiation complex formation). Ubiquitin ligase activity and vesicle trafficking terms further suggest coordinated protein turnover and trafficking during mitosis. Together, these terms point to a theme of coordinating cell cycle progression with protein synthesis and quality control.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":7},{"id":"GO:0002188","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0070262","count":5},{"id":"GO:0006890","count":5}]},{"hash":"1921590589537073428","title":"Unknown","description":"The top terms span transcription regulation, cell cycle, development, sensory perception, ER-stress\u2013driven apoptosis, metal-ion response, and immune defense, with no dominant pathway linking them. This lack of a cohesive functional theme makes it inappropriate to assign a more specific label.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006349","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0001403","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0001893","count":2}]},{"hash":"505707990467121555","title":"RNA Methylation & Ribosome Biogenesis","description":"The top GO terms are dominated by RNA modification and ribosome-related processes, including RNA (guanine-N7)-methylation, rRNA and tRNA methylation, rRNA modification, tRNA wobble uridine modification, and export of the ribosomal small subunit from the nucleus, pointing to a cluster of proteins involved in RNA modification priming ribosome biogenesis. Some broad terms like xenobiotic response or antibiotic biosynthesis may be incidental annotations, but the central theme centers on RNA methylation linked to ribosome assembly and maturation.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0036265","count":9},{"id":"GO:0031167","count":7},{"id":"GO:0000056","count":7},{"id":"GO:0000154","count":7},{"id":"GO:0019919","count":7}]},{"hash":"878231442468876476","title":"Nuclear Gene Expression and Ribosome Export","description":"The cluster is dominated by nuclear processes: DNA-templated transcription, mRNA export, and ribosomal subunit export (both small and large), plus regulation of GTPase activity, likely reflecting Ran-dependent nucleocytoplasmic transport. These together point to a coordinated nuclear gene expression and ribosome biogenesis/export program, with cell growth/division terms aligning to a proliferative state. Some terms like brain development appear tangential, but do not override the central nuclear/export theme.","confidence":"High","size":27,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0042176","count":3},{"id":"GO:0000056","count":3},{"id":"GO:0006406","count":3}]},{"hash":"2221649900569484107","title":"Membrane Lipid Transport and Biosynthesis","description":"This cluster is driven by GO terms for phosphate ion transmembrane transport, phospholipid biosynthesis, sphingoid long-chain base transport, and lipid signaling, suggesting a cohesive theme around membrane lipid metabolism and trafficking, with related stress responses and a connection to cell wall biosynthesis in lipid-associated processes. Some outlier terms (egg activation, endocannabinoid signaling) may reflect broader or non-specific annotations, but the core signals point to lipid transport and membrane biogenesis.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":2},{"id":"GO:0008654","count":2},{"id":"GO:0006950","count":2},{"id":"GO:1905329","count":2},{"id":"GO:0006078","count":1}]},{"hash":"57918509189619466","title":"Unknown","description":"The top GO terms are a wide mix of processes (negative regulation of pinocytosis, exocytosis, phagocytosis, leukocyte differentiation), nucleotide biosynthesis (UTP, dGTP), and general regulatory activities (protein autophosphorylation, protein complex oligomerization). With no edges and only singleton terms, there isn\u2019t a clear, cohesive function linking these proteins, so a specific label isn\u2019t justifiable. ","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048550","count":1},{"id":"GO:0006228","count":1},{"id":"GO:0030819","count":1},{"id":"GO:0070301","count":1},{"id":"GO:0002762","count":1}]},{"hash":"2199122052089318137","title":"Neural development and synaptic signaling","description":"The top GO terms are dominated by neural-related functions: excitatory postsynaptic potential, long-term synaptic potentiation, visual perception, and Schwann cell development, pointing to neural development and synaptic signaling as the main theme. While there are adjacent terms about the mitotic cell cycle and heart development that suggest broader developmental roles, the neural terms are the most representative of the cluster\u2019s function. Confidence: Medium","confidence":"","size":26,"edges":14,"triangles":1,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":16},{"id":"GO:0010800","count":15},{"id":"GO:0060079","count":15},{"id":"GO:0007601","count":15},{"id":"GO:0000086","count":15}]},{"hash":"2282283304478266595","title":"Multicellular development and tissue differentiation","description":"The GO terms point to developmental processes across tissues (skin, retina, gastrulation) and overall multicellular development, along with transcriptional regulation and basic cell cycle activity. This pattern suggests proteins involved in developmental programs and tissue specification, rather than a single signaling axis. Therefore, the cluster reflects multicellular development and tissue differentiation.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0016575","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0070059","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1375862517624250440","title":"Amino acid biosynthesis and catabolism","description":"Proteins in this cluster are enriched for pathways that produce and break down amino acids, with lysine biosynthesis and saccharopine/diaminopimelate routes appearing most frequently. Additional terms point to related metabolic processes (aspartate, kynurenine, sphinganine, protoporphyrinogen) and a transcriptional direction, consistent with a broader amino acid metabolism program.","confidence":"Medium","size":26,"edges":287,"triangles":1875,"max_degree":25,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019878","count":12},{"id":"GO:0033512","count":10},{"id":"GO:0006351","count":9},{"id":"GO:0019551","count":9},{"id":"GO:0009862","count":8}]},{"hash":"2015569311382770878","title":"Redox Balance and Cofactor Biosynthesis","description":"The top GO terms show emphasis on redox homeostasis (oxidation-reduction processes, redox balance) and biosynthesis of cofactors such as thiamine diphosphate and heme (porphyrinogen IX). This pattern points to proteins involved in managing cellular redox state and core metabolic cofactor production. Some terms (sperm capacitation, corticosterone response, lipopolysaccharide response) are unrelated to metabolism and may reflect broad annotations; overall the cluster aligns best with redox maintenance and cofactor biosynthesis.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":10},{"id":"GO:0045454","count":8},{"id":"GO:0009229","count":7},{"id":"GO:0009228","count":7},{"id":"GO:0051572","count":6}]},{"hash":"869140235832633468","title":"Immune Regulation and Chromatin Remodeling","description":"The cluster shows clear signals of immune regulation (negative regulation of IgE isotype switching, IL-4 production, and T cell proliferation) alongside chromatin-related processes (nucleosome assembly, chromatin remodeling), suggesting epigenetic control of immune development. There are also developmental terms related to mesoderm-derived tissues (heart development, axial mesoderm morphogenesis) and hematopoietic differentiation, which align with immune system formation. The insulin signaling term is less central but may reflect broader signaling connections observed in these contexts.","confidence":"Medium","size":26,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0048294","count":2},{"id":"GO:0008286","count":2},{"id":"GO:0032713","count":2},{"id":"GO:0042130","count":2},{"id":"GO:0006334","count":2}]},{"hash":"1732610403018436491","title":"Multi-organ Development and Differentiation","description":"These top GO terms cover diverse organogenesis and tissue differentiation across gonads, uterus, kidney, pancreas, inner ear, brain (metencephalon), and pharyngeal system, with an additional broad regulatory term (negative regulation of transcription by RNA Pol II). The lack of edges and triangles suggests no tight functional module, so the cluster likely reflects a broad developmental theme rather than a single pathway. The label 'Multi-organ Development and Differentiation' captures this general theme while avoiding overcommitment to a specific tissue.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":8},{"id":"GO:0072107","count":5},{"id":"GO:0008584","count":5},{"id":"GO:0003309","count":5},{"id":"GO:0007338","count":5}]},{"hash":"179900818953897268","title":"Cell envelope biosynthesis and biofilm formation","description":"This cluster is dominated by GO terms tied to the synthesis of cell envelope components\u2014lipid A and lipopolysaccharides, and the undecaprenyl phosphate\u2013linked biosynthetic pathway for cell wall assembly\u2014along with biofilm formation and antibiotic response. While a few terms (like allantoin catabolism and xylan degradation) are divergent, the strongest signals point to envelope biogenesis and surface-associated lifestyle features across organisms, including spore wall-related processes. Confidence: Medium","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009245","count":6},{"id":"GO:0046677","count":5},{"id":"GO:0019428","count":4},{"id":"GO:0042244","count":4},{"id":"GO:0036108","count":4}]},{"hash":"1437253221338758124","title":"Protein Processing and Antigen Presentation","description":"The terms cluster around proteolytic maturation and processing (protein autoprocessing, angiotensin maturation, digestion, negative regulation of APP biosynthesis/amyloid-beta metabolism) and immune handling (antigen processing and presentation via MHC II, antibacterial peptide production). Regulation of GTPase activity likely connects to vesicle trafficking and processing pathways that underlie both proteolysis and antigen presentation, with additional links to hormone-like regulation (blood volume, drinking behavior). Overall, the cluster centers on proteolytic processing intertwined with immune and endocrine signaling.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0002016","count":4},{"id":"GO:0042985","count":4},{"id":"GO:0016540","count":4},{"id":"GO:0050435","count":4}]},{"hash":"1437104029280371429","title":"Nuclear DNA replication and cell-cycle regulation","description":"Primarily reflects nuclear DNA replication, mitotic cell cycle, transcription, and DNA repair, suggesting a DNA maintenance and cell-cycle regulatory module. A few terms (exocytosis, nervous system development, cardiac differentiation, adhesion, imprinting, biofilm) appear as peripheral annotations and do not define the core function.","confidence":"High","size":26,"edges":39,"triangles":13,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":24},{"id":"GO:0000278","count":23},{"id":"GO:0006351","count":22},{"id":"GO:0006281","count":21},{"id":"GO:0045956","count":20}]},{"hash":"1876191607106461862","title":"Ubiquitin-dependent protein turnover and immune signaling","description":"This cluster is dominated by ubiquitination-related terms (ubiquitin-dependent protein catabolic process, protein autoubiquitination, K6-linked ubiquitination) and immune/defense terms (defense response to virus, TNF signaling, V(D)J recombination), suggesting proteins involved in ubiquitin-mediated proteostasis and antiviral/immune signaling pathways.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:0051865","count":6},{"id":"GO:1903265","count":6},{"id":"GO:0033209","count":5},{"id":"GO:1901253","count":5}]},{"hash":"1973552801837910461","title":"Hormone biosynthesis and xenobiotic detoxification","description":"The top GO terms cluster around the production of lipid- and hormone-derived molecules (prostaglandin, calcitriol, ecdysone) alongside multiple xenobiotic/metabolite detoxification processes (xenobiotic catabolic, insecticide metabolic, coumarin catabolic), with supporting fatty acid oxidation and metal response terms. This suggests a functional theme combining hormone biosynthesis with detoxification/metabolism of foreign compounds. ","confidence":"Medium","size":26,"edges":75,"triangles":136,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":19},{"id":"GO:0042738","count":15},{"id":"GO:0010430","count":13},{"id":"GO:0036378","count":13},{"id":"GO:0002017","count":13}]},{"hash":"488401449594094029","title":"DNA replication and cell cycle regulation","description":"The cluster is dominated by GO terms tied to DNA replication, DNA-templated transcription, regulation of nuclear DNA replication during the cell cycle, and mitotic/centrosome-related processes, with hippo signaling also linked to cellular proliferation. While there are a few terms related to ion transport or dopamine response, the core theme is nuclear DNA replication and cell cycle control.","confidence":"High","size":26,"edges":38,"triangles":20,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":15},{"id":"GO:0006351","count":12},{"id":"GO:0010571","count":12},{"id":"GO:0007098","count":12},{"id":"GO:0006813","count":12}]},{"hash":"340719068406396893","title":"Ion transport and synaptic signaling proteins","description":"This cluster is dominated by GO terms for ion transport (sodium/potassium transmembrane transport and sialic acid transport) and for synaptic activity (glutamatergic transmission and synapse assembly), suggesting roles in membrane transport and neuronal communication. Other terms like innate immune response and Hippo signaling appear secondary to these core themes.","confidence":"Medium","size":26,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":3},{"id":"GO:0071805","count":3},{"id":"GO:0015739","count":3},{"id":"GO:0035725","count":3},{"id":"GO:0051965","count":2}]},{"hash":"1206998730624101228","title":"Secretory pathway and Wnt signaling","description":"The terms strongly point to ER-to-Golgi trafficking, ER exit regulation, and Golgi organization, with a notable emphasis on Wnt protein secretion. The axis specification terms align with Wnt signaling roles in development, suggesting these proteins participate in secretion-driven signaling pathways rather than other functions. Overall, the cluster appears to center on the secretory pathway and Wnt-mediated signaling.","confidence":"High","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070863","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0006626","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0048042","count":2}]},{"hash":"282142222223641181","title":"Plant cell wall biosynthesis and remodeling","description":"The top GO terms cluster around plant-type cell wall modification, biosynthesis, and xyloglucan metabolism, with an additional term for detection of fungal-origin molecules and related vesicle/compartment functions (vacuolar transport and fusion) that support wall deposition and cell shape regulation. This suggests proteins focused on cell wall construction/remodeling, with some involvement in recognizing fungal components.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009831","count":2},{"id":"GO:0031505","count":2},{"id":"GO:0006037","count":2},{"id":"GO:0010411","count":2},{"id":"GO:0042546","count":2}]},{"hash":"20778493744986643","title":"GTPase-driven cardiovascular development and angiogenesis","description":"The GO terms cluster around heart development, endothelial tube formation, and sprouting angiogenesis, indicating a vascular development program. The inclusion of small GTPase signaling and NFAT-related regulation supports a GTPase-driven signaling module in cardiovascular/angiogenic contexts, with trafficking terms reflecting underlying cellular logistics. Overall, this cluster seems to represent GTPase-regulated vascular development.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":3},{"id":"GO:0090051","count":3},{"id":"GO:0007264","count":3},{"id":"GO:0051531","count":3},{"id":"GO:0051683","count":3}]},{"hash":"227622782672165014","title":"Unknown","description":"The GO terms are highly diverse (xenobiotic response, aging, dephosphorylation, ECM biosynthesis, trophectoderm differentiation, erythrocyte homeostasis, calcium signaling, guanine salvage, energy homeostasis, germinal center regulation) with no clear shared function, and the cluster has no edges, so there\u2019s no cohesive theme to name. ","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":3},{"id":"GO:0007568","count":3},{"id":"GO:0016311","count":2},{"id":"GO:0050650","count":2},{"id":"GO:0001829","count":2}]},{"hash":"186354012053678058","title":"Neurocardiac development and exocytosis","description":"This cluster is characterized by terms such as central nervous system projection neuron axonogenesis, nervous system development, heart development, and positive regulation of cardiac muscle cell differentiation, plus calcium ion-dependent exocytosis and cell\u2013matrix adhesion regulation. Together they point to proteins involved in coordinating neural and cardiac development and associated signaling.","confidence":"High","size":25,"edges":66,"triangles":63,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045956","count":17},{"id":"GO:0007266","count":17},{"id":"GO:0007124","count":17},{"id":"GO:0001501","count":17},{"id":"GO:0007399","count":17}]},{"hash":"180506354383128909","title":"Vacuolar amino acid transporters","description":"The Top Terms show transmembrane transport of several amino acids into or out of the vacuole (serine, lysine, glutamate, arginine, asparagine, proline, etc.), plus a general lithium ion transport term. The lone non-transport term (root cap development) likely reflects tissue context rather than core function. This pattern supports a cohesive group of vacuolar amino acid transport proteins. Confidence: High","confidence":"","size":25,"edges":9,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0090516","count":2},{"id":"GO:0089707","count":2},{"id":"GO:0090452","count":2},{"id":"GO:0090515","count":2},{"id":"GO:0090517","count":2}]},{"hash":"562059904958394614","title":"Neural development and drug response","description":"The top GO terms emphasize nervous system development and function (Schwann cell development, substantia nigra development, excitatory postsynaptic potential) along with responses to xenobiotics and cocaine, indicating a neural/ synaptic focus with drug responsiveness. Some terms also touch on signaling pathways (calcineurin-NFAT, insulin signaling) and other tissues, but the prominent theme centers on neural development and neurotransmission with xenobiotic sensitivity.","confidence":"Medium","size":25,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":3},{"id":"GO:0042220","count":3},{"id":"GO:0060079","count":3},{"id":"GO:0014044","count":3},{"id":"GO:0021762","count":3}]},{"hash":"1281120997412986833","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0000462","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0048701","count":2},{"id":"GO:0000472","count":2}]},{"hash":"1615200608848857091","title":"Unknown","description":"The top GO terms are highly disparate, spanning angiogenesis (animal development), bacterial metabolite pathways (acetoin catabolic and ectoine biosynthesis), various N-terminal and histone acetylation terms, and chromatin-related processes (subtelomeric heterochromatin formation, centromeric cohesion). This mix, including several obsolete terms, lacks a coherent single function for the cluster, so a precise label isn\u2019t discernible.","confidence":"","size":25,"edges":27,"triangles":24,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001525","count":9},{"id":"GO:0045150","count":7},{"id":"GO:0019491","count":7},{"id":"GO:0017198","count":7},{"id":"GO:0061606","count":6}]},{"hash":"586215406100057955","title":"Steroid and Oxylipin Hormone Biosynthesis with Detoxification","description":"The terms show a clear focus on lipid- or steroid-derived hormone biosynthesis (oxylipins, ecdysone, calcitriol from calciol, aldosterone regulation) combined with xenobiotic/detoxification processes (insecticide metabolism, coumarin catabolism, copper ion response), suggesting a cluster centered on lipid hormone production intertwined with detox pathways.","confidence":"Medium","size":25,"edges":37,"triangles":3,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0031408","count":6},{"id":"GO:0010193","count":6},{"id":"GO:0010430","count":4},{"id":"GO:0036378","count":4},{"id":"GO:0002017","count":4}]},{"hash":"952600248831077073","title":"DNA replication and transcription regulation","description":"Dominant GO terms point to nuclear processes: regulation of DNA-templated transcription, DNA replication, and pre-replicative complex assembly, along with heterochromatin formation and chromosome-level chromatin events; a few translation-related terms and a heme biosynthetic term appear as outliers, but the core theme is nuclear genome expression and replication.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0006267","count":1},{"id":"GO:0007307","count":1},{"id":"GO:0030466","count":1},{"id":"GO:0006260","count":1}]},{"hash":"1199623007114000440","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0031290","count":2},{"id":"GO:0061087","count":2},{"id":"GO:0000492","count":2},{"id":"GO:0051225","count":2}]},{"hash":"1387206867081054086","title":"APC/C-Driven Cell Cycle and Proteostasis","description":"This cluster is dominated by terms tied to mitotic cell cycle control and ubiquitin-mediated proteolysis, especially APC/C-dependent degradation and K11-linked ubiquitination, indicating regulation of mitosis via targeted protein turnover. Other terms point to proteostasis (unfolded protein response) and translation, with a few immune/stress response signals that may reflect broader cellular stress. Overall, the core theme is APC/C-mediated regulation of the cell cycle through ubiquitin-based degradation, with related proteostasis processes.","confidence":"High","size":25,"edges":12,"triangles":0,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0042787","count":5},{"id":"GO:0070979","count":4},{"id":"GO:0051607","count":3},{"id":"GO:0000278","count":3}]},{"hash":"1462614170176422374","title":"Developmental transcriptional regulators","description":"This cluster is mainly enriched for DNA-templated transcription and multicellular organism development, with neural tube closure as a specific developmental process, suggesting proteins that regulate gene expression during embryogenesis. Additional terms related to cell-cycle transitions and VEGF signaling imply roles in coordinating proliferation and developmental signaling during development. Confidence: Medium","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0001843","count":4},{"id":"GO:0034260","count":4},{"id":"GO:0006349","count":3}]},{"hash":"1216615014343295562","title":"Neuronal microtubule dynamics and dendrite morphogenesis","description":"The GO terms cluster around microtubule organization and dynamics (microtubule sliding, polymerization, bundle formation), together with dendrite morphogenesis and protein localization to synapses, plus intracellular mitochondrial distribution. This pattern points to a cohesive function in neuronal cytoskeleton remodeling and dendrite development, aided by mitochondria transport along microtubules. Other terms are ancillary but do not override the central theme.","confidence":"High","size":25,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1900034","count":1},{"id":"GO:0048813","count":1},{"id":"GO:0032930","count":1},{"id":"GO:0048312","count":1},{"id":"GO:1902856","count":1}]},{"hash":"831976122520697251","title":"GTPase Signaling and Cytoskeletal Dynamics","description":"Top GO terms indicate regulation and signaling of small GTPases and Rac pathways, highlighting a core theme of GTPase-driven signaling that controls cytoskeletal dynamics and cell movement, including neuronal migration-related processes. While immune and differentiation terms are present, the predominant signal revolves around GTPase-mediated signaling influencing cytoskeleton and motility.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0045953","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0021816","count":2},{"id":"GO:0048009","count":2}]},{"hash":"2133556994250773419","title":"Cell trafficking and signaling regulation","description":"The GO terms point to both membrane trafficking (Golgi to plasma membrane transport; endosome to melanosome transport) and regulation of signaling processes (protein kinase activity; autoubiquitination), plus developmental and morphogenesis cues (axon/dendrite development; epithelial\u2013mesenchymal signaling). This suggests a coherent theme where proteins coordinate trafficking with signaling to shape cell architecture and interactions. ","confidence":"Medium","size":25,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043001","count":4},{"id":"GO:0045773","count":4},{"id":"GO:0031578","count":4},{"id":"GO:0051291","count":4},{"id":"GO:0045859","count":4}]},{"hash":"213824149982104879","title":"RNA Processing and Transcription Initiation","description":"This cluster is enriched for terms tied to nuclear RNA biology and transcription: mRNA capping, spliceosomal snRNP assembly, and RNA polymerase II preinitiation complex assembly, along with transcription initiation at Pol II promoters. These points, together with a theme of RNA processing and gene-expression regulation, suggest a cohesive module centered on transcription initiation and RNA maturation. Some minor signals (estrogen receptor signaling, histone acetylation regulation, cell-cycle related terms) hint at broader nuclear regulatory roles but do not overwhelm the main theme.","confidence":"Medium","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006446","count":2},{"id":"GO:0006370","count":2},{"id":"GO:0000387","count":2},{"id":"GO:0051123","count":1},{"id":"GO:0030520","count":1}]},{"hash":"464261450067679745","title":"ER-Golgi trafficking and Golgi organization","description":"This cluster is dominated by GO terms linked to ER-Golgi membrane trafficking, such as ER membrane fusion, retrograde Golgi-to-ER transport, and regulation of Golgi organization, indicating a cohesive module for vesicle transport and Golgi dynamics. Other transport-related terms support a membrane trafficking theme, though with some secondary signals. Confidence: High.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016320","count":2},{"id":"GO:0051301","count":2},{"id":"GO:1903358","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0019918","count":1}]},{"hash":"1631409364617923832","title":"Gene Expression and Proteostasis","description":"The top GO terms cover transcription, RNA processing (splicing, translation preinitiation complex, translation reinitiation), translation control (GCN2 signaling), and protein turnover via ubiquitination/ERAD. This mix points to a cluster involved in coordinating gene expression with proteome quality control and stress-responsive degradation, with chromatin modification (histone methylation) further supporting transcriptional regulation. Confidence: Medium","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0002188","count":5},{"id":"GO:0060733","count":5},{"id":"GO:0000398","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0006351","count":4}]},{"hash":"525044368539977251","title":"Ubiquitin-Proteasome Proteostasis and Cytoskeletal Dynamics","description":"The cluster is dominated by ubiquitin-proteasome related processes: ubiquitin-dependent protein catabolic process, SCF-dependent proteasomal ubiquitin-dependent protein catabolic process, and protein polyubiquitination, suggesting a core function in protein turnover. Additional terms point to cytoskeletal dynamics, including microtubule polymerization and spindle assembly, implying a link between proteostasis and cell division machinery. Some stress-related terms (response to cadmium, oxidative stress-induced apoptotic signaling) suggest stress-responsive regulation that ties into proteostasis and cytoskeletal maintenance. Overall, a coherent theme is proteostasis via ubiquitin-proteasome pathways linked to microtubule/cell division processes.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042787","count":9},{"id":"GO:0031146","count":8},{"id":"GO:0000209","count":8},{"id":"GO:0071276","count":7},{"id":"GO:0008285","count":7}]},{"hash":"395822855537975374","title":"Mitotic spindle and Rho GTPase\u2013driven cytoskeleton dynamics","description":"This cluster centers on mitotic machinery (spindle assembly and orientation) and cytoskeletal regulatory signaling (Rac/Rho GTPases) that drive actin remodeling, stress fibers, and filopodia, plus cell spreading, suggesting coordinated cytoskeleton dynamics during mitosis and adhesion. COPII vesicle budding may reflect linked trafficking in these processes.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090307","count":5},{"id":"GO:0043547","count":4},{"id":"GO:0000132","count":4},{"id":"GO:0016601","count":3},{"id":"GO:0051496","count":3}]},{"hash":"627730127950291958","title":"Ubiquitin-Proteasome\u2013Mediated Cell Cycle Regulation","description":"The dominant GO terms point to ubiquitin-dependent proteolysis, including SCF-dependent proteasomal degradation and polyubiquitination, as well as regulation of G1/S transition, DNA replication initiation, and G1 DNA damage checkpoint signaling, all coherently tying proteostasis to cell-cycle control. Secondary terms about circadian rhythm and responses to arsenic or cadmium reflect regulatory and stress-response connections to ubiquitin-mediated pathways. Together, these themes define a cohesive cluster centered on proteostasis governing cell-cycle progression, with contextual stress signaling.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000083","count":6},{"id":"GO:0042787","count":6},{"id":"GO:0031146","count":6},{"id":"GO:0000209","count":6},{"id":"GO:0042752","count":5}]},{"hash":"1874452254620953597","title":"GTPase-regulated cytoskeletal signaling in nervous system","description":"The top GO terms cluster around regulation of small GTPases (Rac/Rho) and downstream cytoskeletal dynamics, alongside neural development processes such as synaptic vesicle trafficking, myelination, and microglial migration. While a few terms pertain to other tissues (e.g., spermatid differentiation), the dominant signal points to GTPase-mediated signaling and neuronal/cytoskeletal functions, indicating a coherent theme of cytoskeletal regulation in the nervous system.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0035021","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0007289","count":2},{"id":"GO:0043044","count":2}]},{"hash":"1518706104670054423","title":"Unknown","description":"The terms cover hair follicle and skeletal muscle development, circadian rhythm regulation, various signaling processes, egg activation, plant-specific signaling, and even RNA modification, with no clear shared function linking the proteins. The lack of edges and the presence of mixed, likely non-coherent GO terms suggest there is no interpretable common theme for a concise label.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048820","count":4},{"id":"GO:0043087","count":4},{"id":"GO:0007343","count":3},{"id":"GO:0007252","count":3},{"id":"GO:0007519","count":2}]},{"hash":"1735208621018999316","title":"Diverse biosynthetic pathways","description":"The proteins are enriched for GO terms describing biosynthesis across multiple metabolite classes (amino acids like serine and threonine, fatty acids, lipopolysaccharide, porphyrinogen/heme precursors, biotin, siderophores, lipoteichoic acid, bile acids, etc.), indicating a shared theme of metabolite production rather than a single specific pathway. This justifies labeling the cluster as Diverse biosynthetic pathways.","confidence":"High","size":24,"edges":252,"triangles":1581,"max_degree":23,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006564","count":7},{"id":"GO:0006633","count":7},{"id":"GO:0009103","count":6},{"id":"GO:0019518","count":6},{"id":"GO:0006782","count":6}]},{"hash":"658125752472477152","title":"Bacterial central metabolism and envelope biosynthesis","description":"The cluster centers on central carbon metabolism and envelope construction: TCA cycle, gluconeogenesis, glycogen and leucine metabolism, and lipopolysaccharide biosynthesis plus cell wall organization, suggesting a cohesive group of proteins involved in energy metabolism and bacterial envelope biogenesis; an outlier GO term (liver development) may reflect annotation noise.","confidence":"Medium","size":24,"edges":43,"triangles":25,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":6},{"id":"GO:0055114","count":5},{"id":"GO:0009103","count":5},{"id":"GO:0001889","count":4},{"id":"GO:0042594","count":4}]},{"hash":"1793714894248074784","title":"RNA Splicing Regulation and ncRNA Silencing","description":"The top GO terms indicate a cluster centered on post-transcriptional RNA control, with strong signals for ncRNA-mediated and miRNA-mediated gene silencing and for multiple spliceosome-related steps (mRNA splicing, splice-site recognition, translation reinitiation). This pattern points to a cohesive module coordinating RNA processing with gene silencing pathways, including stress-related mRNA stability and polyadenylation processes. Overall, the proteins appear to function together in RNA processing and non-coding RNA\u2013mediated regulation of gene expression.","confidence":"High","size":24,"edges":225,"triangles":1163,"max_degree":23,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":16},{"id":"GO:0048026","count":16},{"id":"GO:0010610","count":15},{"id":"GO:0006378","count":14},{"id":"GO:0045292","count":14}]},{"hash":"514649830610702221","title":"RNA Splicing and Translation Regulation","description":"The cluster centers on post-transcriptional RNA processing and translation control, highlighted by spliceosome-mediated mRNA splicing, splice-site recognition, translation reinitiation, and formation of translation preinitiation complex. The inclusion of regulatory ncRNA-mediated silencing and regulatory aspects of RNA Pol II CTD phosphorylation further supports a theme of coordinated RNA processing and translational regulation.","confidence":"High","size":24,"edges":15,"triangles":3,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":13},{"id":"GO:0048026","count":13},{"id":"GO:0002188","count":11},{"id":"GO:0001731","count":11},{"id":"GO:0006378","count":10}]},{"hash":"2233172054353023552","title":"Receptor signaling and cytoskeletal remodeling","description":"The cluster shows convergence on receptor-mediated signaling (EGFR, ephrin) triggering small GTPase\u2013driven actin remodeling, leading to adhesion, ruffle formation, and polarity; other terms (Wnt signaling, synapse plasticity, phagocytosis) reflect related cytoskeletal regulation.","confidence":"High","size":24,"edges":81,"triangles":106,"max_degree":23,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1900026","count":18},{"id":"GO:0097178","count":18},{"id":"GO:0051835","count":18},{"id":"GO:0007173","count":18},{"id":"GO:0071963","count":18}]},{"hash":"1053593204550318423","title":"Developmental signaling and differentiation regulators","description":"Top GO terms cluster around developmental processes and signaling\u2014neural development (long-term synaptic potentiation, CNS projection neuron axonogenesis), mesoderm formation, and cardiac differentiation, plus regulation of cell-matrix adhesion and phosphorylation\u2014suggesting these proteins act as regulators of development and tissue-specific differentiation. Some terms (biofilm formation, imprinting regulation, meiosis kinetochore attachment) may reflect annotation noise, but the core theme is regulatory roles in development and signaling.","confidence":"Medium","size":24,"edges":60,"triangles":13,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060291","count":14},{"id":"GO:0001707","count":14},{"id":"GO:2000727","count":13},{"id":"GO:0001952","count":13},{"id":"GO:0006349","count":13}]},{"hash":"729530127916370265","title":"Chromatin-Linked Transcription Regulation","description":"This cluster is dominated by transcription-related terms (positive regulation of transcription by RNA polymerase II; DNA-templated transcription) and chromatin organization (nucleosome assembly), with supporting roles from protein ubiquitination and RNA modification processes (pseudouridine synthesis), pointing to a module that coordinates transcription, chromatin state, and RNA processing.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045944","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0033138","count":2},{"id":"GO:0006334","count":2},{"id":"GO:0016567","count":2}]},{"hash":"27723177319296641","title":"DNA Replication and Repair","description":"This cluster is dominated by GO terms for DNA replication and repair, including base- and nucleotide-excision repair, replication initiation and lagging-strand elongation, RNA primer removal, and proofreading, indicating a cohesive genome maintenance function (viral replication term is incidental).","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0039693","count":1},{"id":"GO:0042276","count":1},{"id":"GO:0016539","count":1},{"id":"GO:1902975","count":1},{"id":"GO:0006287","count":1}]},{"hash":"2189078048491196233","title":"Embryonic Organ Morphogenesis","description":"This cluster centers on GO terms related to morphogenesis and development across multiple embryonic organs (heart, pituitary, pancreas, digestive tract, ureteric bud branching, retinal axon guidance). The diversity suggests a broad developmental theme rather than a single tissue-specific function, with proteolysis and transcription regulation appearing as general supporting processes. Thus, \u201cEmbryonic Organ Morphogenesis\u201d captures the common thread of embryonic tissue formation. ","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003007","count":3},{"id":"GO:0006508","count":2},{"id":"GO:0043046","count":2},{"id":"GO:0021983","count":2},{"id":"GO:0000122","count":2}]},{"hash":"1198417053760370159","title":"Mitochondrial Respiratory Chain and Lipid Metabolism","description":"The cluster centers on mitochondrial energy production and lipid metabolism, with terms for respirasome and complex IV assembly, fatty-acyl-CoA biosynthesis, beta-oxidation, and carnitine metabolism, plus sterol biosynthesis regulation. This combination strongly suggests proteins involved in mitochondrial respiration paired with lipid biosynthesis/processing across metabolic pathways.","confidence":"High","size":24,"edges":48,"triangles":15,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0032443","count":3},{"id":"GO:0097250","count":2},{"id":"GO:0033617","count":2},{"id":"GO:0006111","count":2}]},{"hash":"887154199434522508","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000472","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0000447","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0030723","count":2}]},{"hash":"1708311690099560069","title":"Fatty acid oxidation and lipid metabolism","description":"Most terms point to lipid processing and energy metabolism: fatty acid transport, positive regulation of beta-oxidation, beta-oxidation via acyl-CoA oxidase, and overall lipid homeostasis. Additional terms touch on ubiquinone and tocopherol biosynthesis, which align with mitochondrial and lipid cofactors, reinforcing the lipid/energy theme. The presence of a Purkinje cell layer morphogenesis term is less related to metabolism and may reflect broader tissue-specific annotations, making the core signal group around lipid metabolism. ","confidence":"Medium","size":24,"edges":70,"triangles":30,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0010795","count":2},{"id":"GO:1901006","count":2},{"id":"GO:0055088","count":2},{"id":"GO:0021692","count":2}]},{"hash":"2187757057642894706","title":"Maternal mRNA localization and translation initiation","description":"The top terms include pole plasm oskar mRNA localization and bicoid mRNA localization, which are classic markers of maternal determinants in Drosophila oocytes, along with formation of translation preinitiation complex, pointing to coordinated localization and initiation of translation in early development. While other terms touch on broader regulatory processes, the strongest, most coherent signal centers on germline/maternal mRNA localization and its control of translation. The cluster label reflects this core theme rather than broader unrelated functions.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007283","count":2},{"id":"GO:0060625","count":1},{"id":"GO:0045451","count":1},{"id":"GO:0043161","count":1},{"id":"GO:0007250","count":1}]},{"hash":"1039819664101085996","title":"Cell Cycle and Growth Signaling","description":"The proteins cluster around core cell cycle and proliferation processes (cell division, cell population proliferation, mitotic cell cycle) and growth regulation (TORC1 signaling, multicellular organism growth). Additional terms point to related processes like translation and RNA decay, autophagy, and DNA damage response, which are often coordinated with cell cycle control. Overall, the dominant theme is cell cycle progression coupled with growth signaling, justifying the label.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0008283","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0035264","count":3},{"id":"GO:0038202","count":3}]},{"hash":"2164385773860438055","title":"Embryonic placental development and patterning","description":"This cluster\u2019s top GO terms center on placental and embryonic development (trophoblast differentiation, EMT in placental structures, placenta-related regulation of differentiation, endocrine system development, pancreatic cell development, left-right pattern formation, cartilage morphogenesis), indicating a shared theme of early developmental processes and tissue patterning. A few terms appear less coherent with this theme (cellulose catabolic process, antibiotic biosynthetic process, cellular oxidant detoxification), but they do not dominate the set. ","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060707","count":3},{"id":"GO:0060972","count":3},{"id":"GO:0003198","count":3},{"id":"GO:0035270","count":3},{"id":"GO:0003323","count":3}]},{"hash":"2026284246197193963","title":"Endosomal sorting and exosome secretion","description":"The cluster is dominated by GO terms related to endosomal pathways and vesicle trafficking: ubiquitin-dependent and -independent protein catabolic processes via the multivesicular body (MVB) sorting pathway, protein transport to vacuole via this pathway, and positive regulation of exosomal secretion, plus transport between early and late endosomes. Cilium assembly also hints at vesicle trafficking associated with membranes. A few terms (e.g., antimicrobial peptide production, cell migration regulation) are peripheral noise, but the core theme points to endosomal/MVB sorting and exosome biogenesis/secretion.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060271","count":2},{"id":"GO:0007299","count":1},{"id":"GO:0090611","count":1},{"id":"GO:0043162","count":1},{"id":"GO:0043328","count":1}]},{"hash":"1726761361361822782","title":"Regulation of Cell Cycle and Adhesion","description":"The top GO terms span DNA replication and cell-cycle regulation, multiple signaling and phosphorylation events, and regulation of cell adhesion and integrin-mediated adhesion, with additional development-related terms. This mix suggests a broad regulatory cluster rather than a single pathway, centered on controlling cell division and how cells interact with their matrix and neighbors. Some terms (like biofilm formation) may be less coherent with eukaryotic regulation, likely reflecting annotation breadth; overall the cluster appears to group proteins involved in regulatory processes affecting cycle, signaling, and adhesion.","confidence":"Medium","size":23,"edges":125,"triangles":447,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":18},{"id":"GO:2000727","count":15},{"id":"GO:0001952","count":15},{"id":"GO:0006349","count":15},{"id":"GO:0021952","count":15}]},{"hash":"1428676421895646342","title":"Amino Acid Catabolism","description":"Most of the top GO terms describe catabolic processes of amino acids (glyoxylate, kynurenine, alanine, taurine, branched-chain and aromatic amino acids) and related Ehrlich pathway degradation, suggesting a shared function in amino acid breakdown. The Notch signaling term appears incidental, but the dominant theme is amino acid degradation across multiple substrates, indicating a cluster of proteins involved in amino acid catabolism.","confidence":"High","size":23,"edges":236,"triangles":1451,"max_degree":22,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009436","count":8},{"id":"GO:0097053","count":7},{"id":"GO:0042853","count":7},{"id":"GO:0007219","count":7},{"id":"GO:0019878","count":6}]},{"hash":"2199921030396327372","title":"N-terminal acetylation and chromatin regulation","description":"The GO terms are strongly centered on N-terminal acetylation activities (propionylation, peptidyl-methionine/serine acetylation) and histone acetylation, plus chromatin-related processes like subtelomeric heterochromatin formation and centromeric cohesion. This suggests a function group of acetyltransferases involved in protein N-terminal modification and chromatin regulation.","confidence":"High","size":23,"edges":102,"triangles":163,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0061606","count":15},{"id":"GO:0017196","count":15},{"id":"GO:0043967","count":15},{"id":"GO:0060358","count":15},{"id":"GO:0017198","count":15}]},{"hash":"920948638525925440","title":"Mitochondrial translation and ribosome dynamics","description":"This cluster centers on translation and ribosome-related processes (cytosolic translation, ribosome biogenesis, mitochondrial translation) together with mitochondrial morphology/dynamics (fission, membrane organization). The dominant theme appears to be protein synthesis linked to mitochondria and the structural organization of mitochondrial resources, with a secondary signal of translation-related regulation. ","confidence":"High","size":23,"edges":49,"triangles":18,"max_degree":14,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":10},{"id":"GO:0046677","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0000266","count":4},{"id":"GO:0007006","count":4}]},{"hash":"695464920078469565","title":"Ribosome Biogenesis & Translation Initiation","description":"This cluster is dominated by GO terms for ribosome biogenesis, rRNA maturation (5.8S, LSU/SSU), and formation of translation preinitiation complex, with supporting evidence of RNA methylation and subunit biogenesis. Although some terms touch on transcription and chromatin, the strongest signal is ribosome assembly and initiation of translation, suggesting proteins involved in ribosome production and early translation steps.","confidence":"High","size":23,"edges":234,"triangles":1429,"max_degree":22,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":7},{"id":"GO:0042254","count":6},{"id":"GO:0043547","count":6},{"id":"GO:0000463","count":6},{"id":"GO:0042273","count":5}]},{"hash":"858787306105920232","title":"Autophagy and ubiquitin-mediated protein homeostasis","description":"The terms point to protein quality control via autophagy and ubiquitin-dependent degradation (including ERAD), with links to TORC1-regulated growth, cell-cycle control, and translation reinitiation, implying a coherent cluster of proteostasis and growth-regulation functions.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0006914","count":5},{"id":"GO:0000209","count":5},{"id":"GO:0000122","count":5},{"id":"GO:0030433","count":4},{"id":"GO:0071157","count":4}]},{"hash":"1919955922533410284","title":"Ubiquitin-Dependent ERAD and Immune Signaling","description":"The cluster\u2019s terms center on ubiquitin-dependent protein degradation (ERAD and ubiquitin-mediated catabolism), ER stress responses, lysosomal localization, and immune system activity (innate and adaptive). This combination points to a functional theme of protein quality control tied to immune signaling pathways, with related regulatory signals like JNK and TGF-beta. Some terms (spleen development, skeletal muscle differentiation) are peripheral but don\u2019t override the dominant degradation/immune theme.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0045087","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0048536","count":2},{"id":"GO:0046328","count":2}]},{"hash":"789777288610243362","title":"Signal Transduction Regulators","description":"This cluster centers on regulation of signaling pathways, including GTPase activity, kinase activity, opsin/visual signaling, and cellular responses such as insulin signaling, suggesting a common theme of modulating signal transduction across tissues (heart and eye). A single basal function is suggested, though one term relates to RNA splicing, indicating some functional diversity within the set.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060048","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0022400","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0043547","count":2}]},{"hash":"1052670998425478067","title":"Mitochondrial Energy Production and RNA Processing","description":"The top GO terms point to mitochondrial oxidative phosphorylation (proton motive force-driven ATP synthesis and NADH to ubiquinone electron transport) and mitochondrial translation, as well as RNA processing/editing within mitochondria. This combination strongly suggests a cluster of proteins involved in mitochondrial energy metabolism and RNA maturation, with a secondary mention of RNA processing in chloroplasts likely reflecting shared RNA-processing themes or cross-annotation. The presence of protein complex oligomerization also aligns with assembly of respiratory complexes and mitochondrial ribosomes. ","confidence":"High","size":23,"edges":253,"triangles":1771,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0015986","count":3},{"id":"GO:0032543","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0021762","count":2},{"id":"GO:0035786","count":2}]},{"hash":"48054748075125481","title":"Plant development and cell wall remodeling","description":"The clustered terms point to plant-specific developmental and cell wall processes (pectin catabolic process, phyllotactic patterning, and cell wall organization), with supporting signals and vesicle trafficking (Wnt-related signaling, exocytosis). This suggests a theme of growth regulation tied to cell wall dynamics in plants, despite some general trafficking terms present. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016055","count":3},{"id":"GO:0006397","count":3},{"id":"GO:0006904","count":3},{"id":"GO:0048549","count":3},{"id":"GO:0045490","count":3}]},{"hash":"1709133369604129621","title":"Chromatin assembly and mitotic cell division","description":"Proteins in this cluster are enriched for nucleosome and CENP-A chromatin assembly, mitotic cell cycle, and microtubule dynamics (microtubule severing), pointing to a cohesive theme of chromatin organization paired with chromosome segregation during mitosis. Some terms (e.g., gastrulation) are developmental or obsolete, but the core signals center on chromatin packaging and mitotic machinery.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0006334","count":2},{"id":"GO:0007369","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0043547","count":2}]},{"hash":"882879634510712979","title":"SCF-Dependent Ubiquitination and Circadian Regulation","description":"The proteins in this cluster are strongly enriched for ubiquitin-dependent proteolysis, including SCF-dependent proteasomal degradation and polyubiquitination, with a notable subset linked to circadian rhythm regulation. This suggests a core theme centered on regulated protein turnover, potentially modulated by circadian processes, with auxiliary links to stress responses. ","confidence":"High","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":11},{"id":"GO:0031146","count":7},{"id":"GO:0042752","count":7},{"id":"GO:0000209","count":6},{"id":"GO:0000083","count":6}]},{"hash":"1858966274589880148","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001889","count":3},{"id":"GO:0042594","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0019240","count":2},{"id":"GO:0045984","count":2}]},{"hash":"1216589224558225197","title":"Unknown","description":"The top GO terms span a mix of plant-specific processes (aerenchyma formation, salicylic acid signaling, cellulose catabolism) and animal neural signaling (endocannabinoid signaling, neurotransmitter-related processes) plus various metabolic steps, with no clear, unified function tying all proteins together. Therefore there isn\u2019t a cohesive theme to label this cluster beyond Unknown.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":8},{"id":"GO:0019433","count":7},{"id":"GO:0042136","count":7},{"id":"GO:0046340","count":7},{"id":"GO:0019369","count":6}]},{"hash":"450228600469465413","title":"Mitochondrial gene expression and translation","description":"Top terms indicate a focus on translation and ribosome assembly, alongside mitochondrial processes (mitochondrial genome maintenance, mitochondrial DNA replication) and oxidative stress response. While there are some developmental terms (ossification, skeletal development) present, the strongest and most consistent signal is core protein synthesis and mitochondrial gene expression, suggesting this as the defining theme for the cluster.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0000027","count":1},{"id":"GO:0097327","count":1},{"id":"GO:0000002","count":1},{"id":"GO:0006351","count":1}]},{"hash":"1326386496702075475","title":"RNA processing and translation control","description":"The top GO terms point to RNA splicing (GO:0006376), mRNA export (GO:0006406), and formation of translation initiation complexes (GO:0001731, GO:0097010), as well as translation reinitiation (GO:0002188) and miRNA-mediated inhibition of translation (GO:0035278). This indicates a cluster focused on RNA maturation/processing and the regulation of translation, including initiation and reinitiation, suggesting a cohesive RNA metabolism/translation control theme.","confidence":"High","size":22,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0075525","count":2},{"id":"GO:0006376","count":2},{"id":"GO:0002188","count":2},{"id":"GO:1905663","count":2},{"id":"GO:0035278","count":2}]},{"hash":"1850459302947142221","title":"Core Metabolism and Growth Processes","description":"The cluster shows a mix of fundamental cellular activities: translation and cell division indicate core growth machinery, while fatty-acid catabolic and biosynthetic processes, nitrate assimilation, and phenylacetate catabolism point to central metabolism. Additional terms like respiratory burst and response to antibiotic reflect broad stress-related responses, suggesting no single specialized pathway but a general ensemble of basic cellular functions.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0010124","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0045730","count":2},{"id":"GO:0006412","count":2}]},{"hash":"2040167601568851884","title":"Ubiquitin-Proteasome\u2013NF-\u03baB Immune Signaling","description":"The cluster combines deubiquitination, non-canonical NF-\u03baB and TNF signaling, MHC I antigen processing, and proteasome assembly, pointing to immune signaling tightly linked to protein degradation. While some terms (Wnt, cell cycle regulation) may reflect cross-talk via ubiquitination and stress responses, the core terms converge on ubiquitin-proteasome\u2013driven immune pathways. This supports a cohesive immune/degradation function cluster with high confidence.","confidence":"High","size":22,"edges":205,"triangles":1124,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":10},{"id":"GO:0038061","count":8},{"id":"GO:0033209","count":7},{"id":"GO:0016032","count":7},{"id":"GO:0010972","count":7}]},{"hash":"353540064773823563","title":"Cholinergic Synaptic Regulation and Learning","description":"The cluster is dominated by GO terms related to acetylcholine metabolism in the synapse, cholinergic synaptic transmission regulation, and learning, indicating a core theme around cholinergic signaling and neural plasticity. Other terms like glucocorticoid response and xenobiotic/alkaloid responses may reflect stress-related modulation of neural function or annotation noise, while metabolic terms (lipid and cellulose processes) appear less central to the main neural theme. Overall, the strongest signal points to cholinergic synaptic regulation and learning.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0030245","count":7},{"id":"GO:0032223","count":6},{"id":"GO:0008285","count":6},{"id":"GO:0007612","count":6},{"id":"GO:0051384","count":6}]},{"hash":"400331348206590477","title":"Mitochondrial Translation and Inner Membrane Insertion","description":"The GO terms strongly highlight translation and translational initiation, plus protein insertion into the mitochondrial inner membrane, complemented by cofactors and modification processes (lipoylation, tRNA methylation/quuosine biosynthesis) linked to aerobic respiration and respiratory complex assembly. This combination suggests a cohesive cluster centered on mitochondrial protein synthesis and assembly of the electron transport machinery, including maturation steps essential for function.","confidence":"High","size":22,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0045039","count":3},{"id":"GO:0009234","count":2},{"id":"GO:0030488","count":2}]},{"hash":"2138434844243069735","title":"Mitochondrial metabolism and respiratory function","description":"The terms point mainly to mitochondrial energy-related processes: assembly of the respiratory chain complex IV, several catabolic pathways (glycerol and D-serine catabolism), thiamine diphosphate biosynthesis, and redox-related activity, suggesting a core theme of mitochondrial metabolism and respiration. A few terms touch on signaling (Rho regulation) and immune response (LPS), which are plausible but less central to the main pattern. Overall, the cluster appears to reflect mitochondrial energy production and metabolism with some peripheral signaling associations.","confidence":"Medium","size":22,"edges":22,"triangles":0,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0035023","count":2},{"id":"GO:0019563","count":2},{"id":"GO:0006579","count":2}]},{"hash":"169882894840920111","title":"Cellular stress response and calcium signaling","description":"The cluster includes GO terms centered on cellular stress responses (autophagy, stress granule localization, NF-kappaB signaling, caffeine response) and calcium handling (release of Ca2+ from the sarcoplasmic reticulum, Ca2+-transport regulation). While a couple terms pertain to plant/heart biology, the predominant pattern ties to stress-related pathways and calcium signaling, suggesting a cohesive functional theme.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901253","count":1},{"id":"GO:0043569","count":1},{"id":"GO:0014808","count":1},{"id":"GO:0098904","count":1},{"id":"GO:0060776","count":1}]},{"hash":"572464729811503204","title":"Plant Chromatin Organization and Gene Regulation","description":"The cluster\u2019s top GO terms cluster around chromatin-related processes (DNA replication-dependent chromatin assembly, chromatin organization, silent heterochromatin formation, nucleosome dynamics) and transcription/splicing activities, with plant-development terms (meristem growth, trichome differentiation) suggesting chromatin-mediated regulation during development. This cohesive theme points to chromatin organization governing gene expression in plants.","confidence":"High","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006335","count":3},{"id":"GO:0061408","count":2},{"id":"GO:1901407","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0042766","count":2}]},{"hash":"1321863999518439270","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":229,"triangles":1501,"max_degree":21,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":5},{"id":"GO:0006412","count":5},{"id":"GO:0006406","count":4},{"id":"GO:0000055","count":4},{"id":"GO:0043547","count":4}]},{"hash":"425852744473254214","title":"Growth factor receptor signaling and GTPase regulation","description":"The top GO terms converge on signaling via growth factor receptors (EGFR, PDGF receptor) and regulation of GTPase activity, including both positive and negative regulation, which often interfaces with MAP kinase signaling. Developmental processes such as forebrain morphogenesis and dendrite extension further support a neuronal growth/signaling theme. A few outliers exist (e.g., NK cell cytotoxicity regulation, bud site selection), but the dominant signal points to growth factor\u2013driven signaling and GTPase regulation in development. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0043407","count":2},{"id":"GO:0048853","count":2},{"id":"GO:0045953","count":2},{"id":"GO:0034260","count":2}]},{"hash":"2074312806523080032","title":"DNA Damage and Oxidative Stress Response","description":"The GO terms show DNA-templated transcription and cell-cycle regulation (G1/S transition) alongside multiple stress responses (gamma radiation, diamide, copper ion, singlet oxygen, heat stress), suggesting a cluster of proteins involved in transcriptional regulation in response to diverse cellular stresses, including DNA damage. The single edge and lack of strong interactions imply a broad, loosely connected set rather than a tight, single pathway.","confidence":"Medium","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000082","count":2},{"id":"GO:0043666","count":2},{"id":"GO:0071480","count":2},{"id":"GO:0072738","count":2}]},{"hash":"1390177897489005915","title":"Unknown","description":"The set of GO terms is highly heterogeneous with no clear shared function: terms range from protein oligomerization and ubiquitin recycling to metabolic and host\u2013pathogen interaction processes, each represented by a single protein and with no network edges. There isn\u2019t a cohesive theme to name a specific, representative cluster label.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051289","count":1},{"id":"GO:0018189","count":1},{"id":"GO:0016032","count":1},{"id":"GO:0046718","count":1},{"id":"GO:1902600","count":1}]},{"hash":"129511581688804933","title":"Mitochondrial translation and cristae biogenesis","description":"The cluster shows strong signals for translation-related processes and mitochondrial translation regulation, plus cristae formation, aligning with mitochondrial gene expression and inner membrane biogenesis. The quinone biosynthesis terms (ubiquinone/menaquinone/phylloquinone) further support a link to mitochondrial electron transport components. A few cytosolic ribosome assembly terms may reflect shared factors or cross-annotation, but the dominant theme is mitochondrial translation and membrane biogenesis.","confidence":"Medium","size":22,"edges":224,"triangles":1406,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0009234","count":2},{"id":"GO:0006744","count":2},{"id":"GO:0042372","count":2},{"id":"GO:0070131","count":2}]},{"hash":"1566294535248083814","title":"Brain development and synaptic remodeling","description":"These proteins are enriched for brain development and synaptic plasticity terms (GO:0007420 and GO:0031915), complemented by actin cytoskeleton remodeling (GO:0034316) and vesicle trafficking between ER and Golgi (GO:0006890, GO:0006888). This combination suggests roles in neuronal growth and structural synaptic changes, with supporting growth-factor signaling and transcriptional regulation contexts.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071364","count":2},{"id":"GO:0031915","count":2},{"id":"GO:0034316","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006890","count":2}]},{"hash":"563820878627034535","title":"Gene Expression and RNA Processing","description":"This cluster is dominated by GO terms for transcription (DNA-templated), spliceosome-mediated mRNA processing, and translation reinitiation, suggesting involvement in core gene expression machinery. Additional terms point to protein oligomerization and regulation of ubiquitin ligase activity, with links to DNA damage response and development, supporting a cohesive theme around RNA processing and gene expression control.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051260","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0000398","count":4},{"id":"GO:0072432","count":3},{"id":"GO:0030042","count":3}]},{"hash":"1143826575763626938","title":"Intracellular trafficking and neural development","description":"The top GO terms cluster around vesicle transport routes (ER-Golgi and endosome-Golgi), ciliary localization, and tubulin/cytoskeleton assembly, with neural development signals such as dendritic spine formation, brain development, and learning. While polarity and organ development terms appear, the strongest coherence is vesicular trafficking and cytoskeletal processes supporting neural structure and function, justifying a label focused on these themes.","confidence":"Medium","size":22,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0034498","count":2},{"id":"GO:0097499","count":2},{"id":"GO:0060999","count":2}]},{"hash":"884881910867974683","title":"Organellar gene expression and genome maintenance","description":"The cluster shows strong signals for organelle-specific processes: mitochondrial translation, chloroplast RNA processing, and organelle RNA editing, suggesting a shared role in organellar gene expression. The presence of DNA replication and DNA repair terms may reflect broader genome maintenance linked to organellar genomes, giving a coherent theme around organelle function and genome integrity.","confidence":"High","size":22,"edges":164,"triangles":568,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0032543","count":2},{"id":"GO:0030420","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0045892","count":2}]},{"hash":"166222994253064418","title":"Neural development and neuromuscular signaling","description":"The terms cluster around neural development and neuromuscular function, including spinal cord motor neuron differentiation, neuromuscular processes controlling balance, and ephrin receptor signaling. Growth-related signaling (insulin-like growth factor receptor signaling and TOR regulation) links to development and tissue growth, while a few entries touch on RNA dynamics and cell-number homeostasis. Overall, a coherent theme centers on neural differentiation with accompanying growth and signaling pathways.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048009","count":1},{"id":"GO:0016441","count":1},{"id":"GO:0050881","count":1},{"id":"GO:0021522","count":1},{"id":"GO:0050885","count":1}]},{"hash":"1570581257190849378","title":"Ribosome biogenesis and transcription","description":"The cluster is enriched for DNA-templated transcription and maturation of rRNA (5.8S/LSU), which together point to ribosome production and RNA processing. Positive regulation of TORC1 signaling further ties these processes to cellular growth and biosynthesis, aligning with ribosome biogenesis control. Some terms indicate broader cell-cycle and cytoskeletal dynamics, reflecting a general growth-regulation theme, though a few entries are obsolete or less directly related. Overall, the dominant signal centers on nucleic acid processing linked to growth signaling.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0000463","count":6},{"id":"GO:0000920","count":6},{"id":"GO:0000466","count":6},{"id":"GO:1904263","count":6}]},{"hash":"69388556093602486","title":"Brain Development and Synaptic Organization","description":"The cluster features several brain-related processes: midbrain morphogenesis, regulation of myelination, synaptic vesicle budding, and actin cytoskeleton organization, all pointing to neural development and neuronal connectivity. Additional terms on microglial migration and Ras signaling fit within the broader brain development and signaling context, though some terms are more general or less specific to neurons, which moderates confidence slightly.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:1904140","count":3},{"id":"GO:0051146","count":3},{"id":"GO:0031641","count":3},{"id":"GO:0016185","count":3},{"id":"GO:0030036","count":3}]},{"hash":"322102992475559599","title":"Stress-Responsive Signaling and Cell Cycle Control","description":"The cluster is dominated by terms related to intracellular signal transduction and the Wnt signaling pathway, with connections to cell cycle regulation and stress-responsive transcription. Although there are a few ancillary terms (polarity, immune modulation), the core theme appears to be signaling pathways that influence cell-cycle progression and transcription in response to stress. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061408","count":3},{"id":"GO:0045083","count":2},{"id":"GO:0090162","count":2},{"id":"GO:0016055","count":2},{"id":"GO:0007205","count":2}]},{"hash":"1174002271006164681","title":"Unknown","description":"The terms span diverse processes (apoptotic signaling, transport, glycosylation, lipid biosynthesis, and plant defense) with little overlap or connectivity, so there is no clear shared function to name; label Unknown.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901029","count":1},{"id":"GO:0034635","count":1},{"id":"GO:0006810","count":1},{"id":"GO:0002229","count":1},{"id":"GO:0006487","count":1}]},{"hash":"102872298039055959","title":"Plant secondary metabolite biosynthesis","description":"The terms show a mix of biosynthetic and metabolic processes across several compounds, including plant-specific secondary metabolites (stilbene, strigolactone, alkaloids), biotin biosynthesis, lipid turnover, nitrogen utilization, and detoxification. There isn\u2019t a single unified pathway but a broad metabolic/genetic module, likely representing plant metabolism and secondary metabolite production.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":5},{"id":"GO:0009102","count":5},{"id":"GO:0046272","count":4},{"id":"GO:1901601","count":4},{"id":"GO:0097755","count":4}]},{"hash":"1825966093976120113","title":"Membrane Transporter Proteins","description":"The top GO terms are dominated by transmembrane transport activities across diverse substrates (nitrite, sodium, arabinose, potassium, vitamins, xenobiotics) and related processes like nitrate assimilation. This pattern indicates a cohesive group of membrane transport proteins with varied substrate specificities, rather than a single enzymatic function. The mention of neurotransmitter loading into synaptic vesicles also aligns with vesicular transport, reinforcing the overall transporter/transport activity theme.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":5},{"id":"GO:0035725","count":5},{"id":"GO:0015751","count":5},{"id":"GO:0006004","count":5},{"id":"GO:0006855","count":5}]},{"hash":"2160122513354615111","title":"Neuronal GPCR Signaling and Synaptic Plasticity","description":"This cluster centers on neuronal signaling and synaptic regulation, highlighted by terms like GPCR signaling pathway, positive regulation of GTPase activity, regulation of calcineurin-NFAT signaling, and regulation of short-term neuronal synaptic plasticity, along with excitatory postsynaptic potential. While a few terms touch on cytoskeletal or cell-cycle aspects, the dominant signal is GPCR-mediated neuronal signaling and plasticity at synapses.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0051531","count":3},{"id":"GO:0048172","count":2},{"id":"GO:0060079","count":2}]},{"hash":"2071010220170657163","title":"Condition-Dependent Transcriptional Activation","description":"The GO terms are dominated by positive regulation of transcription from RNA polymerase II promoter, across various nutrient- and condition-dependent contexts (nitrogen catabolite activation, regulation under nonfermentable carbon sources, and related DNA-templated transcription). A few terms touch on signaling or catabolic regulation, but the common thread is proteins that promote transcription in response to environmental/metabolic cues, rather than a single enzymatic function.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0035959","count":1},{"id":"GO:0001080","count":1},{"id":"GO:2001158","count":1},{"id":"GO:1901717","count":1}]},{"hash":"2127856730613530191","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0042594","count":5},{"id":"GO:0006207","count":4},{"id":"GO:0001889","count":4},{"id":"GO:0006508","count":4},{"id":"GO:0044205","count":4}]},{"hash":"1626447161751718265","title":"Unknown","description":"The top GO terms span transcription regulation, metabolism (oxidation-reduction, cellulose catabolic, antibiotic biosynthesis), sporulation, and even development/behavior in different organisms, with no clear single function tying all proteins together. The absence of a cohesive biological theme justifies an Unknown label.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0030245","count":3},{"id":"GO:0030435","count":3},{"id":"GO:0017000","count":3}]},{"hash":"1217697976372832547","title":"Lineage differentiation and transcriptional regulation","description":"The cluster centers on differentiation across multiple lineages (erythrocyte/megakaryocyte, endoderm, skeletal muscle, heart) and on transcriptional control (RNA polymerase II transcription, chromatin remodeling, DNA-templated transcription). This pattern suggests a group of proteins involved in guiding lineage specification and overarching transcriptional programs during development, rather than a single, specific pathway.","confidence":"Medium","size":21,"edges":129,"triangles":298,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045654","count":6},{"id":"GO:0071353","count":5},{"id":"GO:0006366","count":4},{"id":"GO:0043044","count":4},{"id":"GO:0003290","count":4}]},{"hash":"1070727210378761164","title":"Neural and endocrine development","description":"This cluster shows a mix of neural lineage differentiation signals (cerebral cortex GABAergic interneuron differentiation, subpallium neuron fate commitment, oligodendrocyte fate specification) along with endocrine organ development (pituitary gland development, endocrine pancreas development) and broader multicellular development, all tied to transcriptional regulation. The common theme is developmental differentiation across neural and endocrine tissues, suggesting a program of lineage specification rather than a single pathway. ","confidence":"Medium","size":21,"edges":57,"triangles":27,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0021983","count":5},{"id":"GO:0006366","count":4},{"id":"GO:0007275","count":4},{"id":"GO:2000648","count":4},{"id":"GO:0055114","count":4}]},{"hash":"2289267707854633315","title":"Developmental gene regulation and stem cell differentiation","description":"The cluster shows enrichment for transcriptional control and diverse developmental processes, including nervous system development, limb bud formation, forebrain radial glial differentiation, chondrocyte differentiation, and somatic stem cell maintenance/activation. While a couple of terms are outliers (IgA isotype switching and obsolete histone methylation), the dominant signal is coordinated gene regulation underlying developmental programs and stem cell\u2013driven tissue differentiation.","confidence":"Medium","size":21,"edges":18,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0070318","count":1},{"id":"GO:0007422","count":1},{"id":"GO:0060174","count":1},{"id":"GO:0035019","count":1}]},{"hash":"2006868854599363239","title":"Xenobiotic and Stress Response","description":"The top GO terms cluster around cellular responses to external chemicals and environmental stressors ( xenobiotic stimulus, ethanol, lipopolysaccharide, corticosterone) and associated metabolic adjustments (ubiquinone biosynthesis, antibiotic biosynthetic process). There are also hints of cytoskeletal remodeling (actin filament depolymerization) and development-related terms, suggesting a broad stress/metabolic response rather than a single pathway. With no observed edges among proteins, the label focuses on the general theme of environmental-response and metabolic adaptation.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0017000","count":4},{"id":"GO:0030435","count":4},{"id":"GO:0030042","count":3},{"id":"GO:0007275","count":3}]},{"hash":"1694522978996067739","title":"Amino acid, carbohydrate, nucleotide, and lipid biosynthesis","description":"GO terms indicate involvement in multiple biosynthetic pathways, including serine/cysteine/homocysteine metabolism, carbohydrate metabolism, GMP nucleotide synthesis, and fatty acid biosynthesis, with an additional note on protein tetramerization. This pattern points to a broad biosynthetic enzyme cluster rather than a single pathway, supporting a general \"biosynthesis\" theme.","confidence":"Medium","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0051289","count":10},{"id":"GO:0006565","count":10},{"id":"GO:0005975","count":10},{"id":"GO:0006535","count":10},{"id":"GO:0030071","count":10}]},{"hash":"567969562868070441","title":"DNA Replication, Repair, and Recombination","description":"The proteins cluster around core genome maintenance processes: DNA replication, error-free translesion synthesis, and cellular responses to DNA-damaging agents (cisplatin, gamma radiation, camptothecin), along with meiotic and mitotic recombination and their resolution, indicating a cohesive role in genome stability during replication and recombination.","confidence":"High","size":21,"edges":38,"triangles":19,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070987","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0072719","count":2},{"id":"GO:0071480","count":2},{"id":"GO:0072757","count":2}]},{"hash":"372586711822804589","title":"Embryonic Development and Morphogenesis","description":"The cluster is dominated by GO terms related to embryonic development, tissue morphogenesis, and organ specification. Terms like trophoblast giant cell differentiation, left/right pattern formation, EMT in endocardial cushion formation, cartilage morphogenesis, endocrine system and pancreatic cell development, and transcriptional regulation point to coordinated developmental programs governing tissue patterning and organ formation.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0060707","count":2},{"id":"GO:0060972","count":2},{"id":"GO:0003198","count":2},{"id":"GO:0035270","count":2}]},{"hash":"1218620045329044198","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":94,"triangles":230,"max_degree":17,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":6},{"id":"GO:0036494","count":5},{"id":"GO:0090084","count":5},{"id":"GO:0006458","count":5},{"id":"GO:0034975","count":5}]},{"hash":"2094640921058462929","title":"Stress-responsive mRNA processing and translation control","description":"This cluster centers on mRNA maturation and export (splicing, export, polyadenylation) and on translation initiation/reinitiation, including miRNA-mediated silencing and stress-related regulation of mRNA stability. The presence of terms for splice site recognition, mRNA export, preinitiation complex formation, eIF4F assembly, and translation reinitiation suggests a cohesive module coordinating RNA processing with translation control, particularly under stress. ","confidence":"High","size":21,"edges":194,"triangles":1059,"max_degree":20,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":6},{"id":"GO:0075525","count":4},{"id":"GO:0006376","count":4},{"id":"GO:0002188","count":4},{"id":"GO:1905663","count":4}]},{"hash":"437776229073754224","title":"Cardiac ion transport and T-tubule organization","description":"The cluster is enriched for metal and cation transport (Zn, Cd, Cu, K+, Na+) and ion homeostasis, plus GO terms linking to T-tubule organization and regulation of heart contraction/hypertrophy, implying a role in cardiac ion handling and excitation\u2013contraction coupling through T-tubule architecture.","confidence":"High","size":21,"edges":13,"triangles":1,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0071577","count":9},{"id":"GO:0070574","count":9},{"id":"GO:0030007","count":7},{"id":"GO:0036376","count":6},{"id":"GO:0097623","count":6}]},{"hash":"569503469661693119","title":"TNF-MAPK Immune Signaling and Cell Fate Regulation","description":"This cluster centers on TNF signaling, p38 MAPK cascade, T cell processes, autophagy, and apoptosis regulation, pointing to an immune stress-response module.","confidence":"Medium","size":21,"edges":19,"triangles":0,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0030488","count":1},{"id":"GO:0042098","count":1},{"id":"GO:0033209","count":1},{"id":"GO:0031086","count":1},{"id":"GO:0043029","count":1}]},{"hash":"714306390057523238","title":"Translation initiation and reinitiation regulation","description":"GO-term emphasis on translation initiation, preinitiation complex formation, and reinitiation (including viral IRES) suggests a cohesive function in initiating protein synthesis. Minor TOR signaling and amino acid response terms accompany, but do not override the core theme.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0075525","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0006511","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0006446","count":2}]},{"hash":"2204862644421273717","title":"Nutrient-responsive transcription regulation","description":"The top GO terms are dominated by DNA-templated transcription and regulation of transcription from RNA polymerase II promoter, with several entries indicating positive regulation by various metabolic cues (nonfermentable carbon source, oleic acid, glyoxylate cycle, leucine and pyrimidine biosynthesis). This pattern suggests a cluster of proteins that regulate transcription in response to nutrient/metabolic signals, rather than enzymes of metabolism themselves. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":10},{"id":"GO:0035959","count":7},{"id":"GO:2001158","count":7},{"id":"GO:0061414","count":7},{"id":"GO:1900399","count":7}]},{"hash":"1611198246807060374","title":"Nitrate and peptide transport with hormone signaling in plants","description":"The top GO terms cluster around nitrogen/nitrate uptake and assimilation (nitrate transport, nitrate assimilation, response to nitrate) and peptide transport (oligopeptide and dipeptide transport), suggesting a transport-focused module for nitrogen and peptide substrates. The presence of auxin-activated signaling and gibberellic acid homeostasis indicates coupling to plant hormone pathways, with additional general metabolism terms (isoprenoid biosynthesis, coenzyme A metabolic process) reflecting broader metabolic context. Overall, these terms point to a plant-specific nutrient-transport and hormone-signaling theme.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":2},{"id":"GO:0009635","count":1},{"id":"GO:0035672","count":1},{"id":"GO:0042938","count":1},{"id":"GO:0009734","count":1}]},{"hash":"835913402184673713","title":"Placental and embryonic morphogenesis","description":"This cluster centers on developmental processes, with terms referencing placental development and trophoblast differentiation, as well as embryonic tissue patterning and morphogenesis (left-right patterning, cartilage morphogenesis, EMT in heart development). Some GO terms touch on cellular logistics (Golgi ribbon formation, ER exit) that support protein processing during differentiation, suggesting a theme of developmental morphogenesis with placental emphasis. Confidence in this labeling is moderate because the terms span multiple related but distinct developmental axes.","confidence":"Medium","size":21,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0070863","count":2},{"id":"GO:0060707","count":1},{"id":"GO:0060972","count":1},{"id":"GO:0003198","count":1},{"id":"GO:0035270","count":1}]},{"hash":"676367989694461708","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0008286","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0051301","count":2},{"id":"GO:1903461","count":2}]},{"hash":"913511288523087404","title":"Skeletal muscle differentiation and development","description":"This cluster is dominated by GO terms tied to skeletal muscle biology, with explicit mentions of skeletal muscle cell differentiation (3) and skeletal muscle tissue development (2) suggesting a core muscle-development function. Other terms like swimming, membrane tubulation, and circadian regulation appear but are less central to the main theme, possibly reflecting broader regulatory or cross-species annotations. Overall, the strongest signal points to muscle differentiation and development as the defining function of this cluster.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035914","count":3},{"id":"GO:0097320","count":2},{"id":"GO:0051044","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0006351","count":2}]},{"hash":"2043622352556000309","title":"Phytochrome-driven light signaling and circadian regulation","description":"This cluster centers on red/far-red light signaling and phototransduction, plus regulation of circadian rhythm and DNA-templated transcription, pointing to light-controlled gene expression and clock control in plants; translation and cell-cycle terms appear as secondary related processes.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0010018","count":2},{"id":"GO:0042753","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0009585","count":2}]},{"hash":"1921778854207752692","title":"Unknown","description":"The listed GO terms are highly diverse, covering transcription, multiple amino acid and heme biosynthesis pathways, a glyoxylate cycle, insulin response, regulation of phospholipid biosynthesis and catabolism, and even neural cell migration/proliferation. There isn\u2019t a clear, single biological process or functional theme unifying these terms, so a cohesive label is not apparent.","confidence":"","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019878","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0006783","count":2},{"id":"GO:0032869","count":2},{"id":"GO:0071071","count":2}]},{"hash":"647099369288787933","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006370","count":3},{"id":"GO:0009236","count":3},{"id":"GO:0071051","count":2},{"id":"GO:0071035","count":2},{"id":"GO:0071042","count":2}]},{"hash":"1912980357311880577","title":"Developmental Regulation and Chromatin Modification","description":"The GO terms cluster around developmental processes (multicellular organism development, seminiferous tubule development, skin development) and chromatin-related regulation (histone acetylation), with some RNA maturation processes also present. This suggests a loose group of proteins involved in developmental gene expression control and chromatin/RNA processing, despite no network connectivity in this cluster. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006886","count":2},{"id":"GO:0043966","count":2},{"id":"GO:0070059","count":2},{"id":"GO:0072520","count":2},{"id":"GO:0043588","count":2}]},{"hash":"2109560692847763701","title":"DNA Maintenance and Cell Cycle Regulation","description":"The cluster shows GO terms centered on DNA repair (base-excision repair), DNA recombination, and cell cycle control (positive regulation of G1/S transition), plus a stress response (cellular response to hydrogen peroxide). Although there are some less-connected terms (phosphatidylinositol dephosphorylation and renal water transport), the dominant signals point to genome maintenance and coordination with the cell cycle under stress.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046856","count":3},{"id":"GO:0048681","count":2},{"id":"GO:0070301","count":2},{"id":"GO:0006310","count":2},{"id":"GO:1903507","count":2}]},{"hash":"1079525787723402608","title":"Ubiquitin-Proteasome-Mediated Protein Degradation","description":"The top GO terms point to ubiquitination and proteasomal or ubiquitin-dependent protein breakdown (SCF-dependent proteasomal ubiquitin-dependent catabolism, ubiquitin-dependent protein catabolic process, protein polyubiquitination, and positive regulation of polyubiquitination), indicating a cluster centered on protein turnover. Supplemental terms about circadian regulation and metal-response stress likely reflect broader cellular regulation, but the dominant theme is ubiquitin-mediated degradation.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":11},{"id":"GO:0000209","count":10},{"id":"GO:0042787","count":10},{"id":"GO:0000083","count":9},{"id":"GO:0046685","count":9}]},{"hash":"1014259203562649549","title":"Proteostasis-Linked Cell Cycle and DNA Replication Control","description":"This cluster is dominated by ubiquitin-proteasome\u2013related terms (ubiquitin-dependent proteolysis, SCF-dependent degradation, and protein polyubiquitination) with connections to circadian rhythm regulation, DNA replication initiation, and mitotic DNA damage checkpoints, plus related stress and synapse-associated terms. The overall pattern suggests a cohesive focus on proteostasis coordinating cell cycle and genome maintenance, with some neuronal/stress context.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":11},{"id":"GO:0031146","count":11},{"id":"GO:0042752","count":10},{"id":"GO:1902916","count":10},{"id":"GO:0000083","count":10}]},{"hash":"2143750615696470908","title":"Golgi trafficking and neural maturation regulation","description":"The cluster prominently features GO terms related to Golgi apparatus retention and Golgi-to-plasma membrane protein transport, indicating a core theme around Golgi trafficking. Other terms point to neural development, myelination, and neuron maturation, suggesting these trafficking functions may be relevant in neural contexts. A few terms relate to general stress responses (DNA damage checkpoints, gamma radiation response, mitophagy), which may reflect broader cellular processes but are less central to the cluster\u2019s main theme. Overall, the label emphasizes Golgi trafficking with a neural development context.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045053","count":2},{"id":"GO:0040014","count":1},{"id":"GO:0071480","count":1},{"id":"GO:0038028","count":1},{"id":"GO:0031641","count":1}]},{"hash":"1891718961018093031","title":"Translation Initiation and Protein Transport Regulators","description":"The cluster centers on translation-related processes (regulation of translational initiation, formation of translation preinitiation complex, viral termination-reinitiation) and on protein/vesicle transport (xenobiotic transmembrane transport, general protein transport, Golgi-to-ER retrograde transport). The presence of Rap signaling and GTPase activation hints at membrane-associated regulation that can modulate either translation or trafficking. Although these are distinct processes, the proteins may coordinate translation with intracellular transport in cellular signaling contexts, supporting a combined label focused on initiation and transport roles.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":2},{"id":"GO:0075525","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0032486","count":2}]},{"hash":"1900177850244771068","title":"Muscle differentiation and ubiquitin-mediated turnover","description":"The presence of GO terms for myotube development and skeletal muscle differentiation indicates a muscle development focus, while ubiquitin-dependent protein catabolic process and protein deubiquitination point to coordinated protein turnover through the ubiquitin system. Obsolete but informative terms related to histone modification and DNA-templated transcription suggest some regulatory roles, but the muscle differentiation and turnover signals provide a coherent functional theme for this cluster.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006511","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0061077","count":2},{"id":"GO:0051568","count":2},{"id":"GO:0033138","count":1}]},{"hash":"1939459466544021904","title":"Neuronal development and synapse formation","description":"This cluster centers on neural development signals, including CNS projection neuron axonogenesis, positive regulation of synapse assembly, and regulation of cell adhesion via integrins, suggesting a shared role in neuronal differentiation and synaptic connectivity. While a few terms (e.g., biofilm formation, meiosis spindle attachment) seem unrelated and may reflect broad regulatory annotations, the dominant themes point to neural development and synapse organization.","confidence":"Medium","size":20,"edges":177,"triangles":923,"max_degree":19,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000727","count":20},{"id":"GO:0001952","count":20},{"id":"GO:0006349","count":20},{"id":"GO:0021952","count":20},{"id":"GO:0090606","count":20}]},{"hash":"873604528625446951","title":"Developmental Transcription Regulators","description":"Most terms are about transcriptional regulation (DNA-templated transcription; regulation of transcription from RNA Pol II promoter) with several development-related terms (cartilage development, pituitary gland development) and related processes, suggesting the cluster is enriched for transcription factors/regulators driving development.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0007338","count":4},{"id":"GO:0007626","count":4},{"id":"GO:0051216","count":4},{"id":"GO:0021983","count":4}]},{"hash":"1254805614543019531","title":"Synaptic vesicle trafficking and exocytosis","description":"Based on the prominence of GO terms related to synaptic potentiation and postsynaptic excitation, SNARE complex assembly, and exocytic insertion of receptors, alongside vesicle transport between the ER and Golgi and Golgi ribbon formation, the cluster centers on secretory pathway processes that drive synaptic transmission and plasticity. This suggests a cohesive role in vesicle docking/fusion and receptor trafficking essential for synaptic signaling.","confidence":"High","size":20,"edges":55,"triangles":32,"max_degree":12,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0060291","count":10},{"id":"GO:0090161","count":8},{"id":"GO:0035493","count":8},{"id":"GO:2000463","count":8},{"id":"GO:0098967","count":8}]},{"hash":"1048311033021612563","title":"Secretory vesicle trafficking and neural development","description":"This cluster is dominated by GO terms tied to vesicle trafficking and secretory pathways (COPII-coated vesicle budding; retrograde Golgi-ER transport; regulation of synaptic vesicle exocytosis), plus brain development and multicellular growth signals. The overlap between neural development and secretory trafficking suggests a set of proteins mainly involved in processing and transport of vesicles critical for neuron function and growth. The presence of cell cycle and proliferation terms likely reflects general cellular growth context rather than a conflicting secondary role.","confidence":"High","size":20,"edges":113,"triangles":279,"max_degree":16,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007420","count":19},{"id":"GO:0010796","count":18},{"id":"GO:2000300","count":18},{"id":"GO:0031384","count":18},{"id":"GO:0090114","count":17}]},{"hash":"518595594413022351","title":"Mitochondrial Respiratory Chain & Complex Assembly","description":"The cluster is dominated by GO terms tied to mitochondrial electron transport and the assembly of respiratory chain complexes (e.g., mitochondrial electron transport, ATP synthase complex assembly, and Complex I assembly) as well as protein import into the mitochondrial matrix, indicating a cohesive module related to mitochondrial energy metabolism and biogenesis; the other terms appear peripheral.","confidence":"High","size":20,"edges":190,"triangles":1140,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0006123","count":4},{"id":"GO:0033615","count":2},{"id":"GO:0030150","count":2},{"id":"GO:0032981","count":2},{"id":"GO:0000087","count":1}]},{"hash":"192368474767889589","title":"Developmental transcriptional regulation","description":"The terms cluster around DNA-templated transcription and its regulation, plus multiple embryonic development processes (pancreatic development, neural crest migration, digestive tract morphogenesis, ureteric bud morphogenesis, megakaryocyte differentiation). This suggests a cohesive set of proteins that modulate gene expression during development across tissues.","confidence":"Medium","size":20,"edges":8,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0000122","count":6},{"id":"GO:0043046","count":6},{"id":"GO:0090190","count":5},{"id":"GO:0031018","count":5}]},{"hash":"349188097182671612","title":"Neural development and vesicle trafficking","description":"This cluster shows strong representation of neural development terms (nervous system development, brain development, negative regulation of axonogenesis) together with Rab protein signal transduction and regulation of synaptic vesicle exocytosis, plus protein transport. The convergence on neuronal growth and vesicle-mediated trafficking suggests a cohesive theme around neural development and synaptic function, despite a few non-neuronal or obsolete terms that may reflect annotation noise.","confidence":"High","size":20,"edges":23,"triangles":3,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":2},{"id":"GO:0050771","count":2},{"id":"GO:0032482","count":2},{"id":"GO:0015031","count":2},{"id":"GO:0007420","count":2}]},{"hash":"2228739630538718843","title":"Neural oxidative stress and amyloid metabolism","description":"This cluster centers on neural context with oxidative stress responses (reaction to hydrogen peroxide, ROS regulation), amyloid-beta metabolism and APP processing, and neural development signals (substantia nigra), plus proteostasis-related processes (deubiquitination, autoprocessing). The convergence of oxidative stress, amyloid metabolism, and brain development points to neurodegenerative\u2013relevant proteostasis and redox biology.","confidence":"Medium","size":20,"edges":80,"triangles":112,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:2000378","count":3},{"id":"GO:0042542","count":3},{"id":"GO:0014070","count":3},{"id":"GO:0021762","count":3},{"id":"GO:0016579","count":3}]},{"hash":"1115999505007548458","title":"Oxidative detoxification and metabolic stress response","description":"Reasoning: Top GO terms converge on detoxification of oxidants (cellular oxidant detoxification) and glutathione metabolism, with additional signals of toxin catabolism, starvation response, and DNA repair, suggesting a cluster focused on oxidative stress management and metabolic remodeling. A calcium-release regulation term is present but likely reflects broader signaling links rather than core function; overall, the cluster centers on detox and stress response pathways.","confidence":"Medium","size":20,"edges":189,"triangles":1122,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":14},{"id":"GO:0014810","count":10},{"id":"GO:0006749","count":10},{"id":"GO:0060316","count":10},{"id":"GO:2000255","count":10}]},{"hash":"381897030331822872","title":"DNA damage repair and meiotic recombination","description":"The top GO terms cluster around double-strand break repair, meiotic recombination, replication fork arrest, DNA damage signaling, and even immunoglobulin gene diversification, implying a group of proteins involved in genome maintenance, meiotic processes, and related DNA damage responses.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051096","count":2},{"id":"GO:0006302","count":2},{"id":"GO:0006311","count":2},{"id":"GO:0031573","count":2},{"id":"GO:0016446","count":2}]},{"hash":"1331735959077915737","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0000740","count":2},{"id":"GO:0036494","count":2},{"id":"GO:0090084","count":2},{"id":"GO:0006458","count":2}]},{"hash":"113356810947674067","title":"Ribosome biogenesis and rRNA maturation","description":"The top GO terms are dominated by maturation of rRNA species (5.8S, SSU, LSU) and ribosome biogenesis, with additional signals for translation initiation, transcription, and RNA processing. This points to a cluster of nucleolar proteins involved in ribosome assembly and rRNA maturation, with some linked RNA processing and cell-cycle functions.","confidence":"High","size":20,"edges":58,"triangles":34,"max_degree":11,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000463","count":4},{"id":"GO:0000724","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0000462","count":3},{"id":"GO:0000466","count":3}]},{"hash":"692930846062413917","title":"Regulation of muscle differentiation","description":"The top GO terms are dominated by regulation of muscle cell differentiation across cardiac, skeletal, and smooth muscle lineages (positive regulation of cardiac muscle cell differentiation; negative regulation of skeletal muscle cell differentiation; obsolete transcription-related terms tied to muscle precursors). This points to a core theme of modulating muscle lineage development, potentially involving signaling pathways like PDGFR-beta. While there are a few non-muscle-related terms (e.g., brain development), they appear peripheral to the main function. Therefore the label reflects the cluster\u2019s primary function.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000727","count":2},{"id":"GO:0032508","count":2},{"id":"GO:2000587","count":2},{"id":"GO:2001015","count":2},{"id":"GO:2000721","count":2}]},{"hash":"110789629869586779","title":"Ubiquitin-Dependent Protein Regulation","description":"Most terms center on deubiquitination (K48-linked and monoubiquitinated substrates) and ubiquitin-mediated control of protein fate, including proteolysis and chromatin-related deubiquitination. Additional terms reference cellular processes often regulated by ubiquitin signaling, such as GPCR pathway regulation, centrosome duplication, mitochondrial fission, spermatogenesis, and spliceosome assembly. Together, these indicate a cohesive theme of ubiquitin-dependent regulation of proteins and signaling.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":1},{"id":"GO:0000244","count":1},{"id":"GO:0008277","count":1},{"id":"GO:0007283","count":1},{"id":"GO:0071108","count":1}]},{"hash":"1076730452586388884","title":"Plant Growth Regulation and Phenylpropanoid Biosynthesis","description":"The top GO terms point to plant-specific processes: growth regulation (vegetative and seed growth), ABA response, and biosynthesis of flavonoids and lignin (flavonol, syringal lignin, sinapate esters). These together suggest a cluster tied to plant development and secondary metabolism. A couple terms are less aligned (sterol transport, viral process, telomeric D-loop disassembly) but do not override the dominant plant-development/metabolism theme. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032366","count":2},{"id":"GO:0061820","count":1},{"id":"GO:0009301","count":1},{"id":"GO:0016032","count":1},{"id":"GO:1905615","count":1}]},{"hash":"26500835610800667","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031915","count":2},{"id":"GO:0000467","count":1},{"id":"GO:0070481","count":1},{"id":"GO:0071032","count":1},{"id":"GO:0070651","count":1}]},{"hash":"1010999432190194331","title":"Innate antiviral defense and stress signaling","description":"The strongest signals are antiviral: defense response to virus, innate immune response, and positive regulation of interferon-beta production, indicating antiviral immune signaling. The presence of ripoptosome assembly linked to necroptosis supports a link to stress-induced cell death pathways. Some GO terms (RNA polymerase III transcription, tRNA transcription, CNS morphogenesis, ethanol response) appear less connected and may reflect annotation noise, but the core theme remains antiviral innate immunity.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051607","count":1},{"id":"GO:0032728","count":1},{"id":"GO:0006359","count":1},{"id":"GO:0042797","count":1},{"id":"GO:0045087","count":1}]},{"hash":"1962739352583465155","title":"Membrane remodeling and actin dynamics","description":"This cluster is enriched for terms linked to plasma membrane changes and actin-driven structures: plasma membrane tubulation, actin cytoskeleton organization, filopodium assembly, and clathrin coat assembly. The presence of small GTPase\u2013mediated signaling and regulation of membrane-related processes (e.g., membrane ectodomain proteolysis, IGF receptor signaling) suggests coordinated remodeling of the membrane and cytoskeleton, including protrusion formation and endocytic trafficking, rather than a single linear process. Some terms indicate regulatory roles in vascular remodeling or immune signaling, but the dominant theme centers on membrane dynamics and actin remodeling.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097320","count":3},{"id":"GO:0030036","count":2},{"id":"GO:0043314","count":2},{"id":"GO:0048009","count":2},{"id":"GO:0051489","count":2}]},{"hash":"609679607275325167","title":"Ubiquitin-Proteasome Regulation and Cell Cycle Control","description":"The cluster is dominated by GO terms for ubiquitin-dependent proteolysis and SCF-mediated proteasomal degradation (GO:0042787, GO:0031146, GO:1902916), indicating a proteostasis-focused group with links to cell cycle and DNA replication initiation (GO:0000083, GO:0030174, GO:1571). Additional terms point to circadian rhythm regulation and stress responses, suggesting broader regulation of protein turnover in proliferative and neuronal contexts. Overall, the common theme is ubiquitin-mediated protein degradation intertwined with cell cycle and DNA replication control.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":11},{"id":"GO:1903378","count":8},{"id":"GO:0031146","count":8},{"id":"GO:0042752","count":7},{"id":"GO:1902916","count":7}]},{"hash":"1793510820382131587","title":"Unknown","description":"The GO terms include antibiotic and biotin biosynthetic processes, together with multiple signaling and cytoskeletal regulation terms (insulin receptor signaling, Rac signaling, actin cytoskeleton organization, BMP secretion, stress fiber regulation, vascular permeability). This mix spans metabolism and cell signaling/cytoskeletal dynamics without a clear, cohesive functional theme, so there isn't a single interpretable function for this cluster.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":6},{"id":"GO:0009102","count":6},{"id":"GO:0046626","count":5},{"id":"GO:0043114","count":3},{"id":"GO:1904425","count":3}]},{"hash":"1217245989984253562","title":"Alcohol and aldehyde and sugar catabolism","description":"The top GO terms are dominated by catabolic processes for ethanol, formaldehyde, amino-acid\u2013to\u2013alcohol (Ehrlich pathway), and galactose via D-galactonate, plus related redox steps like NADH oxidation. This suggests a cluster of proteins involved in breaking down small carbon sources and managing redox state. While a few terms touch on immune or stress responses, the strongest theme is metabolic catabolism of alcohols, aldehydes, and sugars, so this label is representative and specific.","confidence":"Medium","size":19,"edges":168,"triangles":921,"max_degree":18,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0018119","count":18},{"id":"GO:0010430","count":18},{"id":"GO:0046294","count":18},{"id":"GO:0006116","count":18},{"id":"GO:0032496","count":18}]},{"hash":"284199639249638074","title":"Bacterial LPS and O-antigen polysaccharide biosynthesis","description":"The top GO terms are dominated by lipopolysaccharide and related surface polysaccharide biosynthesis (O antigen, colanic acid, dTDP-rhamnose, ADP-L-glycero-beta-D-manno-heptose, LPS biosynthetic), pointing to proteins involved in assembling bacterial cell envelope components. A few terms (transcription, cytolysis) are less specific, but the cohesive theme clearly centers on envelope polysaccharide construction.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006541","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0019835","count":4},{"id":"GO:0097171","count":3},{"id":"GO:0019305","count":3}]},{"hash":"1428591270966648510","title":"Adhesion signaling and neural development","description":"The cluster shows enrichment for regulation of cell adhesion (including integrin-mediated adhesion) and neural connectivity processes (axonogenesis and synapse assembly), plus signaling regulation such as phosphorylation. This suggests its proteins broadly participate in adhesion-dependent signaling pathways that guide neural development and connectivity, though a few terms appear peripheral (biofilm formation, meiosis regulation), indicating mixed functions with a primary neural adhesion focus.","confidence":"Medium","size":19,"edges":120,"triangles":348,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000727","count":19},{"id":"GO:0001952","count":19},{"id":"GO:0006349","count":19},{"id":"GO:0021952","count":19},{"id":"GO:0090606","count":19}]},{"hash":"2299891348278768753","title":"Cell Cycle and Transcriptional Stress Response","description":"This cluster centers on cell cycle progression and transcriptional regulation, with additional signals of stress responses, including ER unfolded protein response and xenobiotic/cocaine exposure, suggesting coordination of division with transcription control under stress.","confidence":"Medium","size":19,"edges":39,"triangles":18,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0035690","count":6},{"id":"GO:0051301","count":5},{"id":"GO:0030968","count":5},{"id":"GO:0000082","count":5}]},{"hash":"695247621697030275","title":"Ribosome Biogenesis and Translation Initiation","description":"The cluster\u2019s top GO terms cluster around ribosome assembly and the initiation of protein synthesis: translation reinitiation, formation of the translation preinitiation complex, ribosome biogenesis, and maturation of SSU-rRNA. These strongly indicate a shared role in producing and initiating translation. Some terms (e.g., DNA-templated transcription, histone methylation) appear as peripheral or noisy annotations, and a note about nutrient-response hints at broader regulatory links to translation. Overall, the core theme is ribosome biogenesis coupled with translation initiation.","confidence":"High","size":19,"edges":6,"triangles":0,"max_degree":4,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0002188","count":10},{"id":"GO:0001731","count":10},{"id":"GO:0007584","count":10},{"id":"GO:0043547","count":10},{"id":"GO:0000462","count":10}]},{"hash":"43806635027234451","title":"Nutrient-responsive transcription regulation","description":"The top GO terms cluster around DNA-templated transcription and its regulation by various nutrient signals (oleic acid, nonfermentable carbon sources, starvation), indicating a coordinated transcriptional response to nutrient status, especially in a fungal context. While some secondary metabolism terms appear, the dominant theme is transcriptional control in response to nutrients rather than a single metabolic pathway. ","confidence":"Medium","size":19,"edges":146,"triangles":608,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0061429","count":4},{"id":"GO:0035961","count":4},{"id":"GO:0061415","count":4},{"id":"GO:1904741","count":4}]},{"hash":"389860944843698510","title":"RNA processing and translation control","description":"This cluster is enriched for mRNA maturation processes (splicing via spliceosome, splice site recognition, export, and polyadenylation) alongside translation initiation/reinitiation steps (preinitiation complex formation, translation reinitiation) and miRNA-mediated translational silencing, with an added stress-regulation aspect. Together these terms point to a cohesive module coordinating RNA processing with initiation of translation, possibly adapting under stress or regulatory contexts. ","confidence":"High","size":19,"edges":159,"triangles":798,"max_degree":18,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":4},{"id":"GO:0010610","count":4},{"id":"GO:0075525","count":3},{"id":"GO:0006376","count":3},{"id":"GO:0002188","count":3}]},{"hash":"146480124655869580","title":"Actin Cytoskeleton Remodeling and Cell Adhesion","description":"This cluster centers on actin dynamics: terms for actin polymerization, filopodium assembly, and positive regulation of actin assembly, plus small GTPase signaling and cell spreading on extracellular matrix. ECM secretion and trafficking/ubiquitination further connect cytoskeletal rearrangements with adhesion sites and matrix remodeling. Overall, the theme is actin-driven cytoskeletal remodeling coupled to cell adhesion and matrix interactions.","confidence":"High","size":19,"edges":60,"triangles":75,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0030041","count":3},{"id":"GO:0030838","count":3},{"id":"GO:0070278","count":3},{"id":"GO:1900026","count":3},{"id":"GO:0007264","count":3}]},{"hash":"691245316675787856","title":"Golgi- and synaptic vesicle trafficking","description":"This cluster centers on Golgi-associated and vesicle trafficking processes: Golgi ribbon formation, SNARE complex assembly, intra-Golgi and ER-to-Golgi transport, vesicle docking/fusion, and exocytic insertion of receptors at the postsynaptic membrane, along with synaptic potentiation. Together they point to a cohesive role in neuronal secretory and vesicle delivery pathways. A few terms (cornified envelope assembly, apoptosis) are less directly related and may reflect broader multifunctionality.","confidence":"High","size":19,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090161","count":3},{"id":"GO:0035493","count":3},{"id":"GO:0006891","count":3},{"id":"GO:0060291","count":3},{"id":"GO:0048280","count":3}]},{"hash":"302441427283060420","title":"Vacuolar trafficking and autophagy","description":"The cluster shows several GO terms tied to vacuole function and autophagy: vacuolar transport, vacuole fusion, and microautophagy, plus polyphosphate biosynthesis linked to vacuolar storage in yeast. This suggests a coherent theme around vacuolar dynamics and autophagy, with other terms such as DNA replication and chromatin-related processes appearing as incidental annotations.","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070417","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0048016","count":2},{"id":"GO:0042144","count":2},{"id":"GO:0007034","count":2}]},{"hash":"35125793660461119","title":"Cell-cycle and gene-expression machinery","description":"This cluster is dominated by GO terms for mitotic cell cycle, cell division, ribosome biogenesis, transcription, and translation initiation, indicating involvement in core cellular growth and protein-synthesis processes. Ubiquitination (protein turnover) further supports a link to regulated protein machinery. The neuron projection development term is an outlier but may reflect shared/general cellular machinery used in neural differentiation. Overall, the proteins point to fundamental cellular growth and gene-expression processes rather than a single specialized function.","confidence":"Medium","size":19,"edges":16,"triangles":0,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":11},{"id":"GO:0031175","count":11},{"id":"GO:0000278","count":11},{"id":"GO:0000747","count":9},{"id":"GO:0042254","count":9}]},{"hash":"2262616422209518940","title":"Unknown","description":"The top GO terms span a wide range of processes (DNA replication, post-translational targeting to membranes, iron-sulfur cluster assembly, karyogamy, beta-glucan biosynthesis, and more). With no evident shared pathway and no edges connecting the proteins, there isn\u2019t a single cohesive function that ties these proteins together. Therefore, Unknown is the most appropriate label with no confidence in a common function.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0031204","count":1},{"id":"GO:1903751","count":1},{"id":"GO:0000742","count":1},{"id":"GO:0006880","count":1}]},{"hash":"1604812251540435326","title":"ER-Golgi vesicle transport and ubiquitination","description":"The top terms cluster around vesicle trafficking between the ER and Golgi (including ER-to-Golgi and Golgi-to-ER transport) and endocytosis, with ubiquitination and GTPase activity regulation linked to trafficking and signaling, pointing to an integrated vesicle transport and post-translational modification theme.","confidence":"Medium","size":19,"edges":8,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0033138","count":2},{"id":"GO:0006623","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0070374","count":2},{"id":"GO:0006890","count":2}]},{"hash":"987385702038497262","title":"ER Signaling and Splicing Regulation","description":"The Top Terms include regulation of intracellular estrogen receptor signaling and regulation of splicing via the spliceosome, with additional terms for protein modification (ufmylation) and proteasomal degradation. This points to a cluster of regulators that influence gene expression and protein homeostasis, with prominent RNA processing and ER signaling themes; the lack of direct interaction edges suggests a loose association, but the two strongest themes are ER signaling and RNA splicing.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033146","count":2},{"id":"GO:0032436","count":1},{"id":"GO:1905050","count":1},{"id":"GO:1905552","count":1},{"id":"GO:1905636","count":1}]},{"hash":"1802614425109888581","title":"Histone Modification and Chromatin Regulation","description":"Most terms point to histone modification and chromatin regulation (acetylation/deacetylation, heterochromatin control), with ancillary links to development and endocytosis; overall, the cluster seems centered on epigenetic regulation rather than a single signaling pathway.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010923","count":2},{"id":"GO:0030097","count":2},{"id":"GO:0048538","count":2},{"id":"GO:0061188","count":2},{"id":"GO:0016575","count":2}]},{"hash":"1929162000323412802","title":"Diverse solute transmembrane transporters","description":"This cluster is dominated by GO terms for transmembrane transport of a wide range of substrates: ions (sodium, potassium), small molecules (arabinose, fucose, vitamins), nitrite/nitrate, xenobiotics, and even neurotransmitter loading into vesicles. The unifying theme is membrane transport of diverse solutes rather than a single substrate, indicating a group of transport proteins with broad substrate specificity.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":1},{"id":"GO:0035725","count":1},{"id":"GO:0015751","count":1},{"id":"GO:0006004","count":1},{"id":"GO:0006855","count":1}]},{"hash":"1086416692758927538","title":"Development and morphogenesis","description":"GO term patterns point to tissue development and morphogenesis across multiple contexts (PNS development, epidermis development, eye morphogenesis, interneuron differentiation, axis patterning), with some generic cellular processes like Golgi to plasma membrane transport appearing as ancillary. This suggests the proteins collectively participate in developmental regulation and morphogenetic events rather than a single molecular function.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006893","count":2},{"id":"GO:0007253","count":2},{"id":"GO:0007422","count":1},{"id":"GO:0071392","count":1},{"id":"GO:0031659","count":1}]},{"hash":"1767427033001743768","title":"Membrane peptide and xenobiotic exporters","description":"The top GO terms cluster around transport across membranes, including amino acid and vitamin transmembrane transport, xenobiotic export, oligopeptide export from mitochondrion, doxorubicin transport, and peptide pheromone export. This suggests a group of membrane transporter/exporter proteins handling small molecules, peptides, and xenobiotics. Some terms (SOS response, bacteriocin immunity, androgen metabolism, stem cell proliferation) are less directly aligned and may reflect broader annotation, but the dominant theme is membrane transport/export. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008209","count":2},{"id":"GO:0003333","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0046618","count":2},{"id":"GO:0009432","count":2}]},{"hash":"932343958326185493","title":"Embryonic development and tissue differentiation","description":"This cluster is dominated by GO terms related to developmental processes across tissues (placenta, heart via EMT, pancreas/endocrine development) and patterning (left-right), plus cell migration and small GTPase signaling that drive morphogenesis and cell movements during development. The terms point to a cohesive theme of developmental differentiation and tissue morphogenesis rather than a single pathway.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":2},{"id":"GO:1903527","count":2},{"id":"GO:0007264","count":2},{"id":"GO:0061000","count":2},{"id":"GO:0060707","count":2}]},{"hash":"2069599300691993717","title":"Unknown","description":"These terms span transcription regulation (RNA polymerase II transcription and preinitiation complex assembly) and chromatin modification (histone acetylation/deubiquitination), but also include diverse, organism-specific processes such as axon target recognition, pseudohyphal/invasive growth, endosperm development, and iron response. The lack of a coherent functional theme across the top terms\u2014and the absence of edges linking proteins\u2014suggests there is no unambiguous single function that characterizes this cluster. Therefore, Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007412","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0051123","count":1},{"id":"GO:0007124","count":1},{"id":"GO:0043966","count":1}]},{"hash":"287715032789368397","title":"Unknown","description":"The top terms are highly diverse, spanning phosphate transport, muscle development, cell cycle localization, tRNA modification, and more, with only one term per protein and no connecting edges. This suggests no single cohesive function or pathway characterizes the cluster, making it inappropriate to assign a specific biological theme beyond Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006817","count":1},{"id":"GO:2000185","count":1},{"id":"GO:0051604","count":1},{"id":"GO:0007519","count":1},{"id":"GO:0036268","count":1}]},{"hash":"2223409407798440025","title":"Golgi\u2013ER\u2013Vacuole Vesicle Trafficking","description":"The set centers on vesicle trafficking within the Golgi-ER-vacuole network (Golgi-to-vacuole, ER-to-Golgi, endocytosis, and vacuole targeting), indicating a common intracellular transport role. Some neuronal phenotype terms appear but are secondary to the trafficking motif.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006896","count":1},{"id":"GO:0008344","count":1},{"id":"GO:0051645","count":1},{"id":"GO:0016185","count":1},{"id":"GO:0006890","count":1}]},{"hash":"1109884626106749365","title":"Fungal septation and chitin biosynthesis","description":"This cluster\u2019s top GO terms point to fungal cell wall formation (chitin biosynthetic process, cell wall organization) and cytokinesis-related events (division septum site selection, actomyosin contractile ring contraction, septum digestion after cytokinesis), suggesting a cohesive group of proteins involved in fungal cell division and cell-wall construction. Some terms are insect- or obsolete-linked, but the dominant pattern aligns with fungal septation and chitin synthesis.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051568","count":2},{"id":"GO:0001744","count":1},{"id":"GO:0034217","count":1},{"id":"GO:0007299","count":1},{"id":"GO:0075015","count":1}]},{"hash":"926115399816018469","title":"Neuronal development and synapse formation","description":"This cluster is driven by terms related to neural development and connectivity, including CNS projection neuron axonogenesis, synapse assembly, and regulation of cell adhesion (integrin-mediated). It also includes kinase signaling and regulatory processes relevant to developmental signaling. A few terms (biofilm formation, meiosis kinetochore regulation, imprinting) are outliers, but the dominant theme centers on neural development and synaptic organization.","confidence":"Medium","size":18,"edges":67,"triangles":85,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000727","count":17},{"id":"GO:0001952","count":17},{"id":"GO:0006349","count":17},{"id":"GO:0021952","count":17},{"id":"GO:0090606","count":17}]},{"hash":"349618658098175903","title":"Chromatin remodeling and transcription regulation","description":"The proteins are enriched for chromatin-related processes and transcription control, including negative regulation of RNA Pol II transcription, histone acetylation, chromatin remodeling during transcription initiation, heterochromatin formation (rDNA), and chromatin assembly. Together these indicate a shared role in regulating chromatin state to modulate transcription; a few terms like brain development or mating-type silencing may reflect broader chromatin functions rather than cluster-specific activities.","confidence":"High","size":18,"edges":130,"triangles":534,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":8},{"id":"GO:0043966","count":6},{"id":"GO:0051290","count":6},{"id":"GO:0045815","count":6},{"id":"GO:0000183","count":6}]},{"hash":"306321430367543323","title":"ER Stress and UPR Transcriptional Regulation","description":"Primarily driven by transcription-related GO terms (transcription by RNA polymerase II; positive regulation of transcription) and unfolded protein response pathways (PERK-mediated UPR, ER stress), suggesting these proteins function in ER stress\u2013induced transcriptional regulation. Additional terms such as cellular response to calcium, oxidative stress, and apoptotic signaling align with stress-responsive signaling networks that connect ER stress to broader cellular outcomes. While a few terms (e.g., synaptic assembly, abscisic acid response) are peripheral, the dominant theme is ER stress\u2013triggered transcriptional control.","confidence":"High","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":12},{"id":"GO:0006990","count":9},{"id":"GO:1990440","count":9},{"id":"GO:0071277","count":8},{"id":"GO:0035470","count":7}]},{"hash":"954089213379158577","title":"RNA Pol II Transcriptional Regulation in Development","description":"Based on the top GO term, transcription by RNA polymerase II, the cluster likely contains proteins involved in controlling gene expression. The presence of multiple development-related terms\u2014oligodendrocyte development, astrocyte differentiation, Notch signaling in heart induction, endocardial cushion mesenchymal transition, pancreatic cell development, and regulation of differentiation\u2014suggests a theme of transcriptional regulators shaping cell fate during development. The mix of neural, cardiac, and skeletal development terms indicates a broad role for transcriptional control in diverse lineage specification. Some terms are marked obsolete in GO, but the core signal remains transcriptional regulation linked to development.","confidence":"High","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":14},{"id":"GO:0048712","count":8},{"id":"GO:2001038","count":8},{"id":"GO:0006990","count":8},{"id":"GO:1990440","count":8}]},{"hash":"1861018260788470239","title":"Translation Machinery and Regulation","description":"This cluster is dominated by GO terms tied to protein synthesis and ribosomal function across compartments: cytoplasmic and mitochondrial translation, initiation/elongation/termination, and selenocysteine incorporation, with supporting signals from mRNA decay and regulation of translation, indicating a cohesive set of translation-related proteins.","confidence":"High","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":14},{"id":"GO:0046677","count":7},{"id":"GO:0002181","count":6},{"id":"GO:0000288","count":4},{"id":"GO:0014009","count":4}]},{"hash":"721197194553990562","title":"Plant lipid metabolism and redox processes","description":"This cluster features several GO terms tied to lipid catabolism (triglyceride catabolic process, phospholipid dephosphorylation) and redox-related activities (oxidation-reduction process, cellular oxidant detoxification), plus pathways like epoxygenase P450 and strigolactone biosynthesis, and even stilbene metabolism. Together, they suggest a group of plant enzymes involved in lipid remodeling, oxidative metabolism, and related detox/secondary metabolism. Confidence: Medium","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0046272","count":4},{"id":"GO:0097755","count":4},{"id":"GO:0046839","count":4},{"id":"GO:0009086","count":4}]},{"hash":"828502890967258263","title":"RNA processing and translation regulation","description":"The cluster centers on RNA metabolism and control of gene expression at the level of RNA processing, export, splicing recognition, and translation initiation/reinitiation, with miRNA-mediated translational inhibition and related translation events, plus some proteolysis signals. This pattern suggests a cohesive role in mRNA maturation and control of protein synthesis.","confidence":"High","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":2},{"id":"GO:0075525","count":1},{"id":"GO:0006376","count":1},{"id":"GO:0002188","count":1},{"id":"GO:1905663","count":1}]},{"hash":"679463708139021040","title":"Plant Growth Signaling and Vacuolar Transport","description":"Most of the top GO terms are plant-specific, including brassinosteroid signaling, circadian rhythm regulation, and flower development, along with transmembrane transport of amino acids into and out of the vacuole. This suggests a coherent theme of plant growth regulation and vacuolar metabolism, with a few terms (germinal center formation, B cell receptor signaling) likely annotation noise or cross-ontology misannotations. Overall, the label helps capture the dominant plant-focused functions in the cluster.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0002467","count":2},{"id":"GO:0009742","count":2},{"id":"GO:0042752","count":2},{"id":"GO:0009911","count":2}]},{"hash":"842986875722392606","title":"N-terminal acetylation and chromatin regulation","description":"This cluster is dominated by terms involving N-terminal acetylation/propionylation of proteins, plus chromatin-related processes such as histone acetylation, subtelomeric heterochromatin formation, and centromeric cohesion, indicating a common theme of protein modification affecting chromatin state and regulation.","confidence":"High","size":18,"edges":152,"triangles":800,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0061606","count":17},{"id":"GO:0017196","count":17},{"id":"GO:0043967","count":17},{"id":"GO:0060358","count":17},{"id":"GO:0017198","count":17}]},{"hash":"2185889096817173327","title":"Transmembrane transporter proteins","description":"The cluster is dominated by transmembrane transport GO terms (GO:0055085) and substrate-specific transport (citrate, malate, succinate, arsenite, K+, Na+, monoatomic anions), plus regulation of phosphate transport, suggesting a group of membrane transport proteins moving ions and metabolites across membranes.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"transmembrane transport","top_go_terms":[{"id":"GO:0051260","count":4},{"id":"GO:2000185","count":4},{"id":"GO:0055085","count":4},{"id":"GO:0015746","count":4},{"id":"GO:0098656","count":4}]},{"hash":"403773821923063673","title":"Actin Cytoskeleton Remodeling","description":"The top GO terms are strongly centered on actin dynamics, notably positive regulation of Arp2/3-mediated actin nucleation and actin filament depolymerization, which point to cytoskeletal remodeling as the main theme. Additional terms touch on signaling and regulation (tyrosine phosphorylation, ubiquitin ligase activity, mitochondria-nucleus signaling) and even brain development, which can relate to cytoskeletal roles in neurons and cardiac tissues, supporting a cohesive, actin-centric cluster. However, some terms are peripheral to this theme (e.g., translation reinitiation), so the overall connection is plausible but not exclusive, yielding a Medium confidence.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:2000601","count":6},{"id":"GO:0050731","count":6},{"id":"GO:0072432","count":5},{"id":"GO:0030042","count":5},{"id":"GO:0010659","count":5}]},{"hash":"1121376218078923433","title":"Diverse substrate transmembrane transporters","description":"The GO terms show transport across membranes for a wide range of substrates (vitamins, sugars like galactose and arabinose, ions such as potassium and phosphate, nitrite/nitrate assimilation, and even neurotransmitter loading). This suggests the cluster comprises transporter proteins with broad or varied substrate specificities rather than a single substrate, hence a label of diverse transmembrane transport activity. Confidence is moderate due to substrate diversity and limited connectivity among proteins.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":2},{"id":"GO:0042891","count":2},{"id":"GO:0015757","count":2},{"id":"GO:0015707","count":2},{"id":"GO:0042128","count":2}]},{"hash":"1440733344775640399","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":76,"triangles":128,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":3},{"id":"GO:0000472","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0006368","count":2},{"id":"GO:0032968","count":2}]},{"hash":"1339287714568189679","title":"ER Stress and Protein Trafficking","description":"The cluster\u2019s terms center on endoplasmic reticulum processes: ER\u2013Golgi transport, unfolded protein response, and retrograde ER-to-cytosol proteolysis, with associated oxidative-stress\u2013driven apoptotic signaling. This suggests a cohesive theme of ER stress\u2013related protein handling and quality control, despite a few outlier terms tied to development or immune processes that may reflect broader multifunctionality or annotation spillover. Confidence: Medium","confidence":"","size":18,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010917","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0002037","count":1},{"id":"GO:0008631","count":1},{"id":"GO:0048515","count":1}]},{"hash":"1488634353942622774","title":"Membrane Ion Transporters and pH Homeostasis","description":"The cluster is dominated by transmembrane transport terms for various ions (chloride, sulfate, bicarbonate, oxalate) and related processes like regulation of membrane potential and intracellular pH, suggesting a shared role in ion transport and ionic balance. A few outlier terms (transcription regulation, sensory perception of sound, sperm capacitation) are less consistent with this theme, but the transporter/is ion homeostasis signal is strong enough to name the group accordingly.","confidence":"Medium","size":18,"edges":4,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0089712","count":3},{"id":"GO:0019532","count":3},{"id":"GO:0051454","count":3},{"id":"GO:0007605","count":3}]},{"hash":"51462695962210553","title":"Receptor-mediated endocytosis and cholesterol transport regulation","description":"Top GO terms cluster around negative regulation of receptor recycling, receptor-mediated endocytosis involved in cholesterol transport, and LDL receptor catabolic processes, suggesting a shared theme of controlling how cells take up and process lipid-associated receptors. While some terms touch on peptide processing or reproductive processes, the dominant signal is regulation of receptor trafficking and cholesterol handling. Therefore, a label focused on endocytosis and lipid transport regulation captures the main function inferred for this cluster.","confidence":"Medium","size":18,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0061096","count":1},{"id":"GO:0034230","count":1},{"id":"GO:0048240","count":1},{"id":"GO:0090472","count":1},{"id":"GO:0032805","count":1}]},{"hash":"218191605526042935","title":"Mitochondrial Metabolite Transport","description":"The set of GO terms centers on transport of diverse metabolites across the mitochondrial membrane (ATP, Mn2+, \u03b1-ketoglutarate, thiamine pyrophosphate, pyrimidine nucleotides) and related processes like the malate-aspartate shuttle, mitochondrial localization during fission, and apoptotic mitochondrial changes. This cohesive pattern suggests proteins functioning as mitochondrial transporters and mediators of metabolic exchange, hence the label.","confidence":"High","size":18,"edges":18,"triangles":1,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:1990544","count":4},{"id":"GO:0006828","count":4},{"id":"GO:0090152","count":4},{"id":"GO:0008637","count":4},{"id":"GO:0060546","count":4}]},{"hash":"1161609172113325056","title":"Unknown","description":"The top GO terms span immune regulation (negative regulation of NK cell cytotoxicity, IL-4 production), apoptosis, GTPase and Ras signaling, vesicle trafficking, cell polarity, and membrane-related processes, with no single coherent function or pathway dominating the set. Given the lack of a unifying biological theme and the absence of edges, the cluster does not map to a specific shared function, so Unknown is the most appropriate label.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045953","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0001878","count":2},{"id":"GO:0090162","count":2}]},{"hash":"217546030756616167","title":"Unknown","description":"The top GO terms span mitochondrial import, iron starvation response, ubiquitination, RNA splicing, telomere maintenance, and regulation of helicase activity, with several obsolete annotations. There are no edges or meaningful connections among proteins (no shared pathway or process), making it hard to derive a single coherent biological theme for the cluster. Therefore, Unknown with None confidence. ","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045041","count":1},{"id":"GO:0010106","count":1},{"id":"GO:1901485","count":1},{"id":"GO:0016567","count":1},{"id":"GO:0051096","count":1}]},{"hash":"532737839050299391","title":"Ubiquitin-Proteasome\u2013Mediated Cell Cycle Control","description":"The proteins are enriched for ubiquitin-dependent proteolysis and proteasomal catabolic processes, with strong ties to cell cycle regulation (G1/S, spindle assembly) and microtubule dynamics. While some terms touch circadian rhythm and stress-induced apoptosis, the dominant theme is protein turnover via ubiquitin\u2013proteasome pathways that govern cell cycle progression and spindle function.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":5},{"id":"GO:0008285","count":4},{"id":"GO:0042752","count":4},{"id":"GO:0000083","count":4},{"id":"GO:1903378","count":4}]},{"hash":"1875133395213075927","title":"Ubiquitin-Dependent Protein Degradation","description":"The top GO terms are dominated by ubiquitination and degradation processes (protein ubiquitination, polyubiquitination, ubiquitin-dependent ERAD, ubiquitin-dependent proteolytic/protein catabolic processes). This points to a coherent theme: these proteins function in tagging substrates with ubiquitin and directing them to degradation pathways, with some links to TNF signaling and growth regulation via ubiquitin-mediated control. Confidence: High","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033280","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0030433","count":3},{"id":"GO:1903265","count":3},{"id":"GO:0000209","count":3}]},{"hash":"1942775911446633954","title":"Nuclear envelope\u2013chromosome dynamics","description":"The cluster\u2019s top GO terms revolve around meiosis and chromosome organization relative to the nuclear envelope\u2014spermatogenesis; homologous chromosome pairing at meiosis; meiotic attachment of telomere to nuclear envelope; centromere clustering at the nuclear envelope; nucleokinesis and nuclear migration along microfilaments; centrosome localization. These points suggest a shared theme of nuclear envelope\u2013mediated chromosome dynamics and intracellular movement during development and cell division. A few terms (osteoblast differentiation, bone remodeling) are less connected, acting as minor outliers. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007283","count":1},{"id":"GO:0007129","count":1},{"id":"GO:0045669","count":1},{"id":"GO:0072766","count":1},{"id":"GO:0021817","count":1}]},{"hash":"1323271575765204608","title":"Intracellular signaling and vesicle trafficking","description":"The cluster centers on intracellular signal transduction along with vesicular trafficking functions, including endosome organization and Golgi-to-plasma membrane transport, plus related signaling pathways (Wnt, GPCR-related) and polarity establishment, suggesting proteins coordinating signaling with membrane trafficking and cell polarity.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":3},{"id":"GO:0007032","count":2},{"id":"GO:0006893","count":2},{"id":"GO:0045083","count":2},{"id":"GO:0090162","count":2}]},{"hash":"1546103726738218492","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016554","count":1},{"id":"GO:0031426","count":1},{"id":"GO:1905639","count":1},{"id":"GO:0031425","count":1},{"id":"GO:0001682","count":1}]},{"hash":"1840074988183303335","title":"Unknown","description":"The GO terms in this cluster span very diverse processes (thrombin signaling, LPS biosynthesis, glucose import regulation, bone remodeling, neuroblast division, GTPase regulation, balance sensation, actin-myosin contractile ring assembly, and VEGF-driven cell migration) with little apparent shared function or pathway. There\u2019s no single overarching theme linking these proteins, so a generic \u201cUnknown\u201d label with no strong confidence is appropriate.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070493","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0046325","count":2},{"id":"GO:0046849","count":2},{"id":"GO:1902405","count":1}]},{"hash":"1144614334041723174","title":"Neural development and glial signaling","description":"The top terms point to nervous system development (neural tube closure, multicellular organism development, astrocyte activation) and associated signaling pathways (Wnt/calcium modulating, GPCR signaling) with supporting cellular processes like hypoxia response and vesicle dynamics, suggesting a cluster of proteins involved in neural development and glial signaling rather than a single enzymatic function. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008584","count":2},{"id":"GO:0048143","count":2},{"id":"GO:0001843","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0007223","count":2}]},{"hash":"787612787285352191","title":"Rho GTPase Signaling Regulation","description":"The cluster is defined by GO terms centered on regulation and activation of GTPases, especially Rho family signaling (positive regulation of GTPase activity; regulation of Rho protein signal transduction). Other terms like phosphorylation, cell proliferation, and DNA repair appear but are broader; overall the core theme is cytoskeletal signaling control via Rho GTPases. Some GO terms are obsolete, reflecting annotation drift rather than a different function.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0007584","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0035023","count":2}]},{"hash":"291252047386438063","title":"Mitochondrial and Chloroplast Protein Import","description":"The cluster\u2019s top GO terms point strongly to protein import into chloroplast stroma and mitochondrial matrix, plus insertion into the mitochondrial inner membrane, which together indicate a shared function in targeting and assembling proteins within plant organelles. Some peripheral terms (cell wall biogenesis, beta-glucan biosynthesis, response to food) are less central but may reflect broader plant physiology; overall the core signal is organelle protein import and membrane insertion.","confidence":"Medium","size":17,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":2},{"id":"GO:0045037","count":2},{"id":"GO:0030150","count":2},{"id":"GO:0045039","count":2},{"id":"GO:0032094","count":2}]},{"hash":"280480712433753094","title":"Unknown","description":"The terms are scattered across immune signaling, ER stress\u2013related apoptosis, peroxisomal import, development, and tissue regeneration, with several obsolete entries. There is no single, cohesive function tying the proteins together, so a precise label cannot be determined.","confidence":"","size":17,"edges":39,"triangles":45,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0071353","count":3},{"id":"GO:0030433","count":2},{"id":"GO:0016558","count":2},{"id":"GO:1990440","count":2},{"id":"GO:0001080","count":2}]},{"hash":"1114283809815562655","title":"Macrophage transcriptional regulation and ER stress response","description":"Top GO terms center on transcription by RNA polymerase II and macrophage biology (macrophage differentiation, MHC class II biosynthesis), with additional signals of endoplasmic reticulum stress and nitrosative stress\u2013related apoptosis. This pattern suggests a cluster of proteins involved in regulating gene expression in macrophages, linked to immune antigen presentation and stress responses. The mix of transcriptional control and immune-related processes supports a cohesive theme around macrophage immune regulation under cellular stress.","confidence":"Medium","size":17,"edges":133,"triangles":636,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":12},{"id":"GO:0030225","count":7},{"id":"GO:0006990","count":7},{"id":"GO:0045348","count":7},{"id":"GO:0044324","count":7}]},{"hash":"902676368268362679","title":"RNA Splicing and Translation Regulation","description":"The cluster is enriched for mRNA processing (splicing, export, stability) and translation control (preinitiation complex formation, reinitiation, miRNA-mediated silencing), suggesting a cohesive role in RNA maturation and subsequent translation regulation.","confidence":"High","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":13},{"id":"GO:0045292","count":13},{"id":"GO:0010610","count":12},{"id":"GO:0075525","count":10},{"id":"GO:0006376","count":10}]},{"hash":"2142523328606339104","title":"Cell wall biogenesis and septation","description":"The cluster\u2019s top GO terms are dominated by cell wall-related processes (mycolate cell wall layer assembly, capsule polysaccharide biosynthesis, cell wall organization) and cytokinesis/septation (division septum site selection, septum digestion after cytokinesis), pointing to a cohesive theme of cell envelope construction and division. A few terms are unrelated or obsolete, but the prevalent pattern supports labeling this cluster as related to cell wall biogenesis and septation.","confidence":"Medium","size":17,"edges":52,"triangles":53,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0001744","count":1},{"id":"GO:0071769","count":1},{"id":"GO:0034217","count":1},{"id":"GO:0045227","count":1}]},{"hash":"387236714781518235","title":"Ubiquitin-Mediated Degradation and Actin Dynamics","description":"The cluster highlights ubiquitin-dependent protein degradation (ERAD) alongside multiple actin-related processes (polymerization, nucleation, barbed-end capping, and bundle assembly) and COPII vesicle loading, suggesting a shared theme of proteostasis coupled with cytoskeletal remodeling and trafficking. An outlier term for DNA replication is noted but does not override the prevailing link between protein quality control and actin dynamics.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0042787","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0006469","count":3},{"id":"GO:0046328","count":3}]},{"hash":"214971601437261967","title":"RNA Pol II Transcription Regulation","description":"These proteins appear to function mainly as transcription regulators, with GO terms centered on regulation of RNA polymerase II\u2013mediated transcription, including preinitiation complex assembly and negative regulation. The cluster also touches on promoter-specific transcription control and chromatin-associated processes, reinforcing a shared role in modulating Pol II\u2013dependent transcription rather than enzymatic activity.","confidence":"High","size":17,"edges":13,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:1900446","count":1},{"id":"GO:0043966","count":1},{"id":"GO:0000436","count":1},{"id":"GO:0043457","count":1}]},{"hash":"2290505241286428983","title":"Lymphoid development and T cell signaling","description":"This cluster is best described by terms like thymus development, hematopoietic progenitor differentiation, and T cell receptor signaling, which point to lymphoid/immune development and adaptive immune signaling. While there are a couple of cardiovascular development terms in the mix, those appear less central to the core theme of this cluster.","confidence":"High","size":17,"edges":19,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0018298","count":2},{"id":"GO:0033160","count":2},{"id":"GO:0001568","count":2},{"id":"GO:0050852","count":2},{"id":"GO:0007507","count":2}]},{"hash":"1696496890829272251","title":"Detox and oxidative stress signaling cluster","description":"The top GO terms point to cellular responses to oxidative stress (hydrogen peroxide, methylglyoxal), and drug/ xenobiotic metabolism (doxorubicin, daunorubicin), coupled with signaling pathway regulation (JAK-STAT, retinoic acid receptor). Endothelial apoptosis regulation and renal water homeostasis add a stress/homeostasis dimension, suggesting a cohesive theme around cellular stress responses and associated signaling rather than a single linear function. Confidence: Medium.","confidence":"","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:2000353","count":17},{"id":"GO:0019853","count":17},{"id":"GO:0044598","count":17},{"id":"GO:0046427","count":17},{"id":"GO:0097238","count":17}]},{"hash":"1605107061711352616","title":"Fungal cell wall biosynthesis and stress response","description":"The top GO terms point to fungal-specific processes like beta-glucan cell wall biosynthesis and karyogamy, alongside general stress and proteostasis responses (unfolded protein response, heat response, protein targeting). This suggests a cluster of proteins involved in building/maintaining the fungal cell wall while coping with cellular stress, rather than a single isolated function.","confidence":"Medium","size":17,"edges":135,"triangles":665,"max_degree":16,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000742","count":12},{"id":"GO:0031204","count":9},{"id":"GO:1903751","count":9},{"id":"GO:0006880","count":9},{"id":"GO:0090084","count":9}]},{"hash":"1299777368673867478","title":"Chromatin regulation and DNA repair","description":"The terms center on transcription regulation through chromatin remodeling (DNA-templated transcription, SAGA complex localization, histone deubiquitination), alongside DNA repair pathways (homologous recombination, nucleotide-excision repair regulation) and related processes like mRNA export and proteasome assembly, suggesting a cluster of nuclear processes linking transcription control with genome maintenance. Some developmental terms appear peripheral and do not define the main theme. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006406","count":1},{"id":"GO:0040025","count":1},{"id":"GO:0030447","count":1},{"id":"GO:0035753","count":1}]},{"hash":"620132591800378086","title":"Transmembrane nutrient transport","description":"The top GO terms cluster around transport across the plasma membrane for vitamins, sugars, and ions (e.g., vitamin transmembrane transport, galactose transport, phosphate and nitrite transport, selenite transport, and ascorbic acid metabolism). While a couple regulatory terms appear, the dominant theme is membrane-based transport of nutrients/ions, justifying a single cohesive label.","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":3},{"id":"GO:1904728","count":3},{"id":"GO:0042891","count":3},{"id":"GO:0043252","count":3},{"id":"GO:0097080","count":3}]},{"hash":"1729842714177726740","title":"Membrane-cortex assembly and localization","description":"GO terms point to membrane-associated assembly and cytoskeletal dynamics (autophagosome, ruffle, focal adhesion) and protein localization to the plasma membrane, with PI signaling involvement; a few terms appear obsolete or unrelated, indicating annotation noise but the common theme remains membrane organization.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000786","count":1},{"id":"GO:0097178","count":1},{"id":"GO:0042070","count":1},{"id":"GO:1902635","count":1},{"id":"GO:0048041","count":1}]},{"hash":"1319561185769394702","title":"Unknown","description":"The GO terms are diverse, including CNS myelination, vesicle transport between ER and Golgi, various transmembrane transport processes (amino acids and ions), transcription regulation, and a fungal differentiation term. No single, coherent function dominates the cluster, so a specific, representative label cannot be reliably assigned.","confidence":"","size":17,"edges":15,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0060628","count":1},{"id":"GO:0060576","count":1},{"id":"GO:0022010","count":1},{"id":"GO:0032286","count":1},{"id":"GO:0031643","count":1}]},{"hash":"2126488301842792719","title":"Ubiquitin-Proteasome\u2013Mediated Protein Degradation","description":"The cluster is dominated by ubiquitination and proteasomal degradation terms, including ubiquitin-dependent protein catabolic process, SCF-dependent proteasomal ubiquitin-dependent protein catabolic process, protein polyubiquitination, autoubiquitination, and K6-linked ubiquitination. While there are secondary terms related to signaling and circadian rhythm, the strongest common theme is ubiquitin-proteasome\u2013driven protein turnover.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:0031146","count":5},{"id":"GO:0000209","count":4},{"id":"GO:1903378","count":4},{"id":"GO:0051865","count":4}]},{"hash":"88546324267422124","title":"Transcription Regulation and RNA Processing","description":"The GO terms emphasize transcription regulation by RNA Pol II and chromatin modification (histone deacetylation), alongside RNA processing and silencing activities (tRNA splicing, RISC assembly, mRNA cleavage). The cerebellar cortex development term is an outlier but does not overwhelm the core theme of gene-expression control.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016575","count":2},{"id":"GO:0042795","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0006367","count":1},{"id":"GO:0016310","count":1}]},{"hash":"1275033199286576597","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0001731","count":5},{"id":"GO:0002188","count":4},{"id":"GO:0075525","count":4},{"id":"GO:0075522","count":4},{"id":"GO:0006446","count":4}]},{"hash":"2019096768162888747","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034476","count":1},{"id":"GO:0071033","count":1},{"id":"GO:1901917","count":1},{"id":"GO:0071039","count":1},{"id":"GO:0071035","count":1}]},{"hash":"2273575532409115463","title":"Plant defense and RNA silencing","description":"The GO terms cluster around plant immune signaling (ethylene-activated pathway, defense against fungus) and RNA silencing processes (ta-siRNA processing), with heat/stress\u2013responsive mRNA export also present, suggesting a theme of plant defense coupled with RNA regulatory mechanisms. A few terms appear unrelated (e.g., IgA isotype switching, DNA damage checkpoint) and may reflect annotation noise.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046784","count":2},{"id":"GO:0051841","count":1},{"id":"GO:0010267","count":1},{"id":"GO:0031990","count":1},{"id":"GO:0050832","count":1}]},{"hash":"390683081459829594","title":"Mitochondrial protein import and inner membrane insertion","description":"The dominant GO terms are protein import into the mitochondrial matrix and protein insertion into the mitochondrial inner membrane, each with multiple occurrences, which points to a cluster enriched for components of the mitochondrial import machinery and inner membrane integration. The other terms (lignan biosynthesis/catabolism, transcription-related) appear less connected and may reflect noise or incidental annotations, but do not override the clearly supported mitochondrial import theme.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030150","count":3},{"id":"GO:0045039","count":3},{"id":"GO:1902132","count":1},{"id":"GO:1901006","count":1},{"id":"GO:0001081","count":1}]},{"hash":"1364756732897938665","title":"Mitochondrial Transporters and Metabolic Exchange","description":"The proteins cluster around mitochondrial transport and metabolism, as shown by GO terms for ATP transmembrane transport, manganese and other metabolite imports (e.g., alpha-ketoglutarate, pyrimidine, thiamine pyrophosphate), the malate-aspartate shuttle, and mitochondrial apoptotic changes. This suggests a cohesive function in mitochondrial metabolite exchange and energy-related transport, rather than cytosolic processes.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1990544","count":15},{"id":"GO:0006828","count":15},{"id":"GO:0090152","count":15},{"id":"GO:0008637","count":15},{"id":"GO:0060546","count":15}]},{"hash":"1422633637308769459","title":"Mitochondrial outer membrane protein import","description":"The majority of terms point to mitochondrial membrane biology: assembly of the outer membrane translocase, insertion of proteins into the outer membrane, and mitochondrial inheritance, plus ER\u2013mitochondria tethering, all aligning with mitochondrial protein import and outer-membrane biogenesis. A few entries (pinocytosis, IL-12 regulation, chloroplast thylakoid import) seem less related or cross-organellar annotations, contributing some noise to the cluster.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":2},{"id":"GO:0048549","count":2},{"id":"GO:0000002","count":1},{"id":"GO:0070096","count":1},{"id":"GO:0000001","count":1}]},{"hash":"792689177970989057","title":"Cell Cycle and Transcription Regulators","description":"The top GO terms center on core cell-cycle processes (cell division, mitotic spindle assembly) and transcriptional control (DNA-templated transcription, chromatin remodeling, transcription initiation), suggesting a group of proteins that coordinate proliferation with gene expression. The presence of broad developmental terms (gonad development, seed dormancy, neuron development) indicates roles across development, but the shared theme remains regulation of cell-cycle\u2013linked transcription. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0008584","count":2},{"id":"GO:0046855","count":1}]},{"hash":"264159520927002457","title":"Ubiquitin-Proteasome Regulation in DNA Replication and Stress","description":"The cluster is dominated by ubiquitin-dependent protein catabolic processes (including SCF-dependent proteasomal degradation), indicating core activity in proteasome-mediated protein turnover. Additional GO terms tie to DNA replication initiation, G1/S cell-cycle regulation, and DNA damage checkpoints, suggesting a role in cell-cycle control. Stress-response terms (heavy metal and oxidative stress) point to coordinated regulation under stress. Together, these imply a proteasome-centric cluster linking replication/cell-cycle control with stress responses.","confidence":"High","size":17,"edges":55,"triangles":17,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:1902564","count":7},{"id":"GO:0042787","count":7},{"id":"GO:0031146","count":7},{"id":"GO:0071276","count":7},{"id":"GO:0042752","count":6}]},{"hash":"2078308975741574240","title":"Unknown","description":"The top GO terms span apoptosis, neurotransmitter and insulin secretion, NF-kappaB signaling, immune response, and developmental processes, with no clear single function tying all proteins together. Because of this heterogeneity, there isn\u2019t a coherent theme to assign a precise label.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":3},{"id":"GO:0007269","count":2},{"id":"GO:0032024","count":2},{"id":"GO:1901223","count":2},{"id":"GO:0000272","count":2}]},{"hash":"940449454457022383","title":"Neural and Muscle Development Signaling","description":"This cluster\u2019s top GO terms are dominated by nervous system development and muscle development (including CNS axonogenesis, skeletal and cardiac muscle differentiation) and related signaling/adhesion processes (e.g., calcineurin-NFAT signaling, cell-matrix adhesion). While a few terms appear as outliers (immune signaling, meiosis spindle regulation, biofilm), the prevalent theme is developmental signaling guiding neural and muscular differentiation and connectivity, making this a concise label for the cluster.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051534","count":3},{"id":"GO:0050853","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0007519","count":3},{"id":"GO:2000727","count":2}]},{"hash":"238860885428825782","title":"Unknown","description":"The GO terms are scattered across transcription, cell division, development (brain, visual, cardiac), DNA damage response, cytoskeleton remodeling, ubiquitin ligase regulation, and even innate defense, with no single coherent theme tying them together. This makes it hard to assign a focused, intuitive label to the cluster.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006349","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0007601","count":2}]},{"hash":"1262920980298972403","title":"Developmental transcriptional regulators","description":"This cluster is dominated by GO:0006366 (transcription by RNA polymerase II) and GO:0000122 (negative regulation of transcription by RNA polymerase II), suggesting core transcriptional control. The breadth of development-related terms (lung morphogenesis, ureteric bud formation, male gonad development, pancreatic cell differentiation, eye development, forebrain proliferation, uterus development, inner ear morphogenesis) points to transcriptional regulators governing diverse organogenesis programs. Hence, a label like Developmental transcriptional regulators fits best.","confidence":"Medium","size":16,"edges":117,"triangles":520,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":7},{"id":"GO:0000122","count":6},{"id":"GO:0060441","count":6},{"id":"GO:0072107","count":5},{"id":"GO:0008584","count":5}]},{"hash":"773261684326095902","title":"Gonad and Kidney/Urinary Tract Development","description":"This cluster is dominated by GO terms tied to reproductive organ development (male gonad, uterus) and kidney-associated morphogenesis (mesenchymal-to-epithelial transition, ureteric bud formation), suggesting a cohesive theme around genital and renal tract organogenesis. EMT is a key shared process in development, aligning with these terms. A few terms (norepinephrine, IL-5, pancreatic differentiation) may reflect broader regulatory roles or annotation noise, but the core signal points to genital and kidney/urinary tract development.","confidence":"Medium","size":16,"edges":41,"triangles":38,"max_degree":15,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0008584","count":7},{"id":"GO:0060065","count":5},{"id":"GO:0060231","count":4},{"id":"GO:0072107","count":4},{"id":"GO:2000734","count":4}]},{"hash":"1640277265027349687","title":"Embryogenesis and organogenesis","description":"This cluster shows GO terms spanning DNA-templated transcription and multiple organ-development processes (placental, pancreatic, cartilage, right/left patterning, EMT in heart development, endocrine tissue formation). The common thread is embryonic development and tissue morphogenesis across diverse lineages, indicating a developmental program governing differentiation and organ formation.","confidence":"High","size":16,"edges":30,"triangles":5,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0060707","count":5},{"id":"GO:0060972","count":5},{"id":"GO:0003198","count":5},{"id":"GO:0035270","count":5}]},{"hash":"1830020283261453071","title":"Transmembrane transport of vitamins and xenobiotics","description":"The cluster is dominated by GO terms for transmembrane transport across membranes, including vitamin transport, xenobiotic transport, and various ion and small-molecule transport processes (e.g., potassium, phosphate, organic anions, selenite, and L-ascorbic acid). This suggests a cohesive group of membrane transport proteins handling nutrients and xenobiotics, with one outlier term possibly reflecting broader regulatory roles or annotation noise. Overall, the label captures the core function represented by the top terms.","confidence":"High","size":16,"edges":58,"triangles":79,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":16},{"id":"GO:0006855","count":16},{"id":"GO:0071805","count":13},{"id":"GO:0042908","count":13},{"id":"GO:0042891","count":12}]},{"hash":"1602052240107873806","title":"Fungal protein maturation and stress response","description":"This cluster includes GO terms pointing to membrane-targeting and protein processing (post-translational targeting to membrane, unfolded protein response, regulation of inclusion body assembly) and cofactors like iron-sulfur cluster assembly, suggesting a shared theme of protein maturation and quality control. It also contains fungus-specific processes (beta-glucan biosynthesis) and mating-related karyogamy, plus stress-related responses (response to hydrogen peroxide, response to heat), which together reflect fungal cellular maintenance under stress and membrane-associated processes, with some mating-related functions represented.","confidence":"Medium","size":16,"edges":36,"triangles":32,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0031204","count":6},{"id":"GO:1903751","count":6},{"id":"GO:0000742","count":6},{"id":"GO:0006880","count":6},{"id":"GO:0090084","count":6}]},{"hash":"2080024206030012948","title":"Stress-Response and Developmental Morphogenesis","description":"This cluster is enriched for unfolded protein response and oxidative stress terms (e.g., PERK-mediated UPR, response to oxidative stress) together with multiple morphogenesis/development terms (dorsal closure, outflow tract morphogenesis, eye morphogenesis, neuromuscular junction assembly). The combination suggests proteins that participate in stress signaling while modulating developmental processes.","confidence":"Medium","size":16,"edges":116,"triangles":507,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0036091","count":5},{"id":"GO:0036499","count":5},{"id":"GO:0051124","count":5},{"id":"GO:0009737","count":5},{"id":"GO:1903984","count":5}]},{"hash":"1792418289609920708","title":"Proteolysis and peptide hormone maturation","description":"This cluster centers on proteolytic processing of peptides and proteins, including general proteolysis and protein catabolic processes, as well as maturation of peptide hormones like angiotensin. Amyloid precursor protein processing and amyloid-beta metabolism reinforce the proteolysis theme, while immune-related terms (antigen processing via MHC II and antibacterial peptide production) reflect peptide handling in immunity. Overall, the shared theme is proteolysis-driven peptide processing across endocrine, neural, and immune contexts.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0002016","count":5},{"id":"GO:0042985","count":5},{"id":"GO:0016540","count":5},{"id":"GO:0050435","count":5},{"id":"GO:0002803","count":5}]},{"hash":"604097038227905088","title":"Ribosome biogenesis and chromatin-driven cell division","description":"The cluster is enriched for nuclear processes: ribosome assembly, chromatin organization, and mitotic cell cycle/division, with supportive terms on protein stabilization and proteolysis, suggesting coordinated production and turnover of nuclear proteins during cell growth and division. Some outlier terms (collagen catabolic process, glomerular filtration) may reflect background noise or broader protein turnover annotations.","confidence":"High","size":16,"edges":72,"triangles":169,"max_degree":14,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":5},{"id":"GO:0034396","count":4},{"id":"GO:0034724","count":4},{"id":"GO:0035551","count":4},{"id":"GO:0030574","count":4}]},{"hash":"2098883969661891507","title":"Innate Immune Signaling and Cytokine Production","description":"These proteins appear enriched for innate immune signaling and cytokine-related functions, with top terms including positive regulation of TLR3 signaling and interleukin-2 production, plus membrane raft localization that supports signaling platforms and excretion of secreted factors. While some older terms touch on proteolysis and organelle morphogenesis, the core theme centers on immune receptor signaling, cytokine regulation, and related cell interactions, suggesting a cluster focused on innate immune signaling and cytokine production.","confidence":"Medium","size":16,"edges":81,"triangles":223,"max_degree":15,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0030433","count":6},{"id":"GO:0070584","count":5},{"id":"GO:1903044","count":5},{"id":"GO:0045861","count":5},{"id":"GO:0034141","count":5}]},{"hash":"903520380602227161","title":"Podosome-driven cell migration and polarity","description":"The cluster is dominated by cytoskeleton and migration signals: positive regulation of podosome assembly, cell migration, and establishment of epithelial cell polarity, with accompanying small GTPase signaling. Other terms (innate immune response, lysosome localization, and translation-related processes) may reflect additional functional connections, but the core theme is actin remodeling and movement.","confidence":"High","size":16,"edges":15,"triangles":7,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0071803","count":3},{"id":"GO:0090162","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0007264","count":3}]},{"hash":"2244832315468757458","title":"Biosynthesis, catabolism, and ubiquitin-proteasome turnover","description":"The top GO terms span multiple biosynthetic processes (antibiotic, clavulanic acid, carnitine) and several catabolic and degradation-related terms (xanthine catabolic process, herbicide degradation) along with ubiquitin-dependent proteolysis (SCF-dependent proteasomal degradation and protein polyubiquitination) and a stress-related cadmium response. This mixture points to a cluster of proteins involved in metabolic processing and protein quality control, rather than a single, narrow function. Confidence: Medium","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0031146","count":4},{"id":"GO:0000209","count":4},{"id":"GO:0006151","count":3}]},{"hash":"557931472938571820","title":"Unknown","description":"The top GO terms span plants (anthocyanin biosynthesis), bacteria (colanic acid biosynthesis), general metabolism (nitrate assimilation), protein structure (homotetramerization), and various vertebrate development and signaling processes (osteoblast differentiation, kidney development, vitamin A/C responses, growth factor signaling). This cross-kingdom, multi-process mix shows no single coherent function or pathway tying the proteins together, and even includes an obsolete term, suggesting the cluster is not functionally cohesive. ","confidence":"","size":16,"edges":12,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0009718","count":3},{"id":"GO:0009242","count":3},{"id":"GO:0042128","count":3},{"id":"GO:0051289","count":3}]},{"hash":"2139566278077806801","title":"Ribosome biogenesis and translation regulation","description":"The cluster is dominated by GO terms for translation, ribosomal subunit assembly, and ribosome biogenesis, with additional terms tying translation regulation to transcription elongation and DNA damage/UV responses, indicating coordinated control of ribosome production and protein synthesis under stress.","confidence":"High","size":16,"edges":119,"triangles":546,"max_degree":15,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":13},{"id":"GO:0000027","count":4},{"id":"GO:0042254","count":4},{"id":"GO:1902164","count":3},{"id":"GO:0006977","count":3}]},{"hash":"1190507197533307144","title":"Ubiquitin-Dependent Proteostasis and ERAD","description":"The cluster\u2019s top GO terms center on ubiquitin-dependent protein catabolic processes and ubiquitin recycling, along with deubiquitination and ER-associated degradation (ERAD). This points to a cohesive theme of protein ubiquitination controlling turnover and quality control, with additional signals related to transcription and chromatin that may reflect broader nuclear roles or pleiotropy. Overall, a label focusing on ubiquitin-mediated proteostasis best represents the shared function among the proteins.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034729","count":1},{"id":"GO:0048149","count":1},{"id":"GO:1901026","count":1},{"id":"GO:0021551","count":1},{"id":"GO:0006511","count":1}]},{"hash":"1508101272417802885","title":"Ribosome biogenesis and RNA processing","description":"The top terms point to nucleic-acid\u2013related processes, especially ribosome assembly signals like ribosomal small subunit export from the nucleus and rRNA modification, as well as arginine methylation involved in RNA-binding protein regulation. While there are outliers (DNA replication, developmental signaling), the strongest cohesive theme is ribosome biogenesis and RNA processing, with supporting links to protein modification. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0030433","count":2},{"id":"GO:0071374","count":2},{"id":"GO:0070389","count":2},{"id":"GO:1901621","count":2}]},{"hash":"1091282821036283144","title":"Chromatin Modification and Remodeling","description":"The top GO terms are dominated by histone acetylation and transcription initiation\u2013coupled chromatin remodeling, indicating a cluster centered on chromatin-level regulation of transcription. While some terms are obsolete or unrelated, the recurring theme is chromatin modification processes that influence transcriptional control.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043969","count":1},{"id":"GO:0018076","count":1},{"id":"GO:1903699","count":1},{"id":"GO:0045815","count":1},{"id":"GO:0001207","count":1}]},{"hash":"687428171305665069","title":"Actin cytoskeleton remodeling and cell motility","description":"The top GO terms cluster around lamellipodium and filopodium assembly, activation of Rho GTPase and regulation of Rho signaling, and substrate adhesion-dependent cell spreading, all of which point to actin cytoskeleton dynamics driving cell movement and adhesion. Developmental processes like midbrain morphogenesis and blood vessel remodeling fit emerging roles of cytoskeletal remodeling in morphogenesis. A single term related to autophagy is likely incidental. Overall, the cluster likely represents actin-driven cytoskeletal remodeling and cell migration.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904693","count":2},{"id":"GO:0030032","count":2},{"id":"GO:1900026","count":2},{"id":"GO:0043314","count":2},{"id":"GO:0090630","count":2}]},{"hash":"1381483726018046826","title":"Rho/Rac-mediated actin cytoskeleton remodeling","description":"This cluster\u2019s GO terms cluster around actin dynamics and cell movement: lamellipodium and filopodium assembly, substrate adhesion-dependent cell spreading, and signaling through Rho and Rac GTPases, including activation of GTPase activity. These points indicate a core function in actin cytoskeleton remodeling that drives protrusion formation and migration. Some terms like midbrain morphogenesis or blood vessel remodeling are broader developmental contexts and less central to the primary theme. ","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904693","count":3},{"id":"GO:0030032","count":3},{"id":"GO:1900026","count":3},{"id":"GO:0043314","count":3},{"id":"GO:0090630","count":3}]},{"hash":"1257199345296321211","title":"Amino acid and D-amino acid transport","description":"This cluster is dominated by GO terms for import/transport of multiple amino acids across the plasma membrane (arginine, ornithine, methionine, lysine, D-alanine, D-serine), pointing to a membrane transport function for amino acids. The linked arginine catabolic process and nitric oxide production fit with arginine metabolism, but two outlier terms (germinal center formation and brassinosteroid signaling) suggest some noise or cross-kingdom annotations. Medium","confidence":"","size":16,"edges":10,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006527","count":2},{"id":"GO:0044690","count":2},{"id":"GO:0097640","count":2},{"id":"GO:0097638","count":2},{"id":"GO:0002537","count":2}]},{"hash":"2274744945891456348","title":"Proteasome-Dependent Protein Degradation and Cell Cycle Control","description":"The dominant GO terms point to ubiquitin-proteasome\u2013mediated protein degradation (SCF-dependent) and cell cycle regulation (G1/S transcription, DNA damage checkpoint, DNA replication initiation). Additional terms reflect stress and metal responses, which can influence proteostasis, with a few items hinting at broader regulatory roles (circadian rhythm, synapse assembly). Overall, the core theme is proteolysis-driven control of the cell cycle and stress responses.","confidence":"High","size":16,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":8},{"id":"GO:0031146","count":8},{"id":"GO:0042752","count":7},{"id":"GO:0000083","count":7},{"id":"GO:1903378","count":7}]},{"hash":"2045587794685567838","title":"Unknown","description":"The top GO terms across the cluster are highly heterogeneous, spanning skeletal muscle and nervous system development, kidney morphogenesis, plant-specific metabolism, tRNA wybutosine biosynthesis, and even immune signaling, with no clear unifying biological function. This makes it impossible to assign a concise, representative label for the cluster beyond Unknown.","confidence":"","size":16,"edges":73,"triangles":158,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0007519","count":2},{"id":"GO:0036268","count":2},{"id":"GO:0072156","count":2},{"id":"GO:0031591","count":2},{"id":"GO:0035914","count":2}]},{"hash":"2008414674330411538","title":"Copper Ion Transport and Homeostasis","description":"The top GO terms are dominated by copper-related processes: copper ion import across the plasma membrane, regulation of copper ion transmembrane transport, and intracellular copper ion homeostasis, which together indicate a copper-centered transport/homeostasis theme for this cluster. Other terms present (xenobiotic transport, cholesterol biosynthesis, DNA-templated transcription, centrosome cycle, visual learning) may reflect broader annotation or secondary associations, but the strongest signal is copper handling across membranes.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0007098","count":2},{"id":"GO:0008542","count":2},{"id":"GO:0006695","count":2}]},{"hash":"945783339932030372","title":"Neural development and transcription regulation","description":"Top GO terms show DNA-templated transcription and neural development (brain, retina), plus RNA methylation and transcriptional control, indicating proteins involved in gene expression programs guiding neural development. A few inflammatory cytokine terms appear but seem peripheral to the main theme. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0007420","count":4},{"id":"GO:0035948","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0060041","count":3}]},{"hash":"99556415003623856","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":98,"triangles":374,"max_degree":14,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0042254","count":3},{"id":"GO:0000028","count":3},{"id":"GO:0000398","count":2},{"id":"GO:0000462","count":2}]},{"hash":"1700297665338380788","title":"Epigenetic Regulation of Differentiation","description":"The terms cluster around chromatin-level control (chromatin binding regulation, histone deacetylation) and differentiation programs (stem cell proliferation, neuron maturation, megakaryocyte differentiation, gamete-related processes), with metabolism (tetrahydrofolate) supporting proliferative/differentiation needs. Some terms appear peripheral or obsolete, but the central theme is epigenetic regulation driving cell fate decisions.","confidence":"Medium","size":15,"edges":63,"triangles":162,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0045654","count":7},{"id":"GO:0043046","count":7},{"id":"GO:0048240","count":6},{"id":"GO:0035563","count":6},{"id":"GO:0046886","count":6}]},{"hash":"2281354071597042509","title":"Amino acid metabolism cluster","description":"This cluster is strongly enriched for amino acid-related processes (L-kynurenine and L-alanine catabolism, L-aspartate biosynthesis, lysine biosynthetic pathways) with additional related biosynthetic activities (porphyrinogen, sphinganine). While other terms (Notch signaling, systemic acquired resistance) appear, the majority point to amino acid metabolism and linked biosynthetic pathways, making this an appropriate representative label despite some noise. ","confidence":"Medium","size":15,"edges":91,"triangles":364,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0097053","count":8},{"id":"GO:0042853","count":8},{"id":"GO:0007219","count":8},{"id":"GO:0019878","count":6},{"id":"GO:0009862","count":5}]},{"hash":"281354604815290776","title":"Proteostasis and Stress Response","description":"The top GO terms center on protein quality control and stress signaling: peptidyl-prolyl isomerization and ubiquitin-dependent proteolysis point to proteome maintenance, while ER stress\u2013related translation upregulation, oxidative (hydrogen peroxide) and interferon responses indicate cellular stress signaling. A few tissue-specific terms appear, but the prevailing theme ties together folding, degradation, and stress-response pathways. ","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000413","count":4},{"id":"GO:0042787","count":4},{"id":"GO:0048709","count":3},{"id":"GO:0060743","count":3},{"id":"GO:0031400","count":3}]},{"hash":"237422639561970107","title":"Embryo and Placental Development Transcription Regulation","description":"The prevalent GO terms combine transcriptional control (DNA-templated transcription and negative regulation of transcription by RNA Pol II) with several embryonic and placental development processes (trophoblast giant cell differentiation, placental and embryonic development, left-right pattern formation, EMT in heart cushion formation, brain and cartilage development, endocrine system development, etc.), suggesting a cohesive theme of transcription-driven developmental programs in embryo and placenta formation.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0000122","count":3},{"id":"GO:0060707","count":3},{"id":"GO:0060972","count":3},{"id":"GO:0003198","count":3}]},{"hash":"272771033443672890","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006364","count":3},{"id":"GO:0030420","count":3},{"id":"GO:0031126","count":3},{"id":"GO:0034414","count":3},{"id":"GO:0017001","count":3}]},{"hash":"434201374367759048","title":"Nuclear ribosome biogenesis and export","description":"This cluster is dominated by GO terms for ribosome biogenesis and nuclear export of ribosomal components (ribosome biogenesis; ribosomal large subunit export from nucleus) along with RNA export (mRNA export) and cell cycle-related processes (DNA replication, kinetochore localization). The oxidative stress and ethanol response terms are present but less central, suggesting a module focused on assembling/exporting ribosomal machinery and coordinating with cell division.","confidence":"High","size":15,"edges":91,"triangles":328,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006406","count":5},{"id":"GO:0030433","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0034599","count":3},{"id":"GO:0006260","count":3}]},{"hash":"383238718805274935","title":"Glycolipid and membrane lipid biosynthesis","description":"The top GO terms cluster around glycolipid biosynthetic process, phosphatidylinositol metabolism, and GPI anchor biosynthesis, all pointing to membrane lipid/glycan assembly. While there are some sugar-response terms (sucrose/mannitol), the predominant theme is lipid and glycan biosynthesis related to membrane components, supporting a membrane-lipid biosynthesis label.","confidence":"High","size":15,"edges":24,"triangles":26,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0009744","count":2},{"id":"GO:0009247","count":2},{"id":"GO:0046488","count":2},{"id":"GO:0009405","count":2},{"id":"GO:0071793","count":2}]},{"hash":"944105605396554721","title":"Cell Cycle Regulation and Telomere Maintenance","description":"This cluster centers on cell cycle control, chromosome segregation, and telomere maintenance (telomerase-related), with supporting signals like protein kinase activity and protein binding. These terms suggest a cohesive theme around cell division regulation and telomere biology, common in development. A few peripheral terms ( xenobiotic response, light detection) may reflect broader signaling roles or annotations, but do not override the main theme.","confidence":"High","size":15,"edges":104,"triangles":442,"max_degree":14,"top_function":"protein folding","top_go_terms":[{"id":"GO:0071902","count":5},{"id":"GO:0032516","count":4},{"id":"GO:0035690","count":4},{"id":"GO:0007275","count":3},{"id":"GO:0007059","count":3}]},{"hash":"432099272197884572","title":"Golgi\u2013Endosome Trafficking and Vacuolar Targeting","description":"Most terms describe trafficking and sorting within the endomembrane system: Golgi-to-endosome and early endosome-to-Golgi transport, endocytosis, and targeting proteins to the vacuole, plus multivesicular body sorting. Ubiquitination is a key regulator of endosomal cargo sorting, linking these processes; a few terms suggest signaling cross-talk with trafficking. Overall, the cluster centers on vesicle trafficking within the Golgi\u2013endosome\u2013vacuole pathway.","confidence":"High","size":15,"edges":50,"triangles":80,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006895","count":5},{"id":"GO:0034498","count":5},{"id":"GO:0006897","count":5},{"id":"GO:0006623","count":5},{"id":"GO:0071985","count":5}]},{"hash":"923036714019067089","title":"Bacterial cell envelope polysaccharide biosynthesis","description":"This cluster is dominated by GO terms for biosynthesis of surface polysaccharides and related envelope components (lipopolysaccharide, O antigen, colanic acid, lipoteichoic acid) along with sugar precursor pathways (ADP-L-glycero-beta-D-manno-heptose, dTDP-rhamnose) and even storage polymer biosynthesis (poly-hydroxybutyrate). The shared theme is production of cell surface polysaccharides and envelope-associated molecules, suggesting a cohesive functional role in assembling bacterial outer membranes or capsules.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":7},{"id":"GO:0009103","count":7},{"id":"GO:0097171","count":5},{"id":"GO:0019305","count":5},{"id":"GO:0009718","count":5}]},{"hash":"412744750358466068","title":"Bacterial Energy and Envelope Biosynthesis","description":"The cluster centers on energy-related metabolism (menaquinone and phylloquinone biosynthesis, fatty acid beta-oxidation, valine/phenylacetate catabolism) and cell-surface/envelope construction (O antigen and lipopolysaccharide biosynthesis), with an antibiotic biosynthetic process term reflecting secondary metabolism potential. Together these terms suggest a cohesive theme of bacterial metabolism linked to energy production and outer-membrane component biosynthesis.","confidence":"High","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":11},{"id":"GO:0006574","count":8},{"id":"GO:0009234","count":8},{"id":"GO:0042372","count":8},{"id":"GO:0006635","count":8}]},{"hash":"2014061610625786285","title":"Transmembrane Transport of Ions and Nutrients","description":"These proteins collectively participate in moving a broad range of substrates across membranes, including ions (Na+, K+), nitrite/nitrate, sugars (arabinose, fucose), vitamins, and xenobiotics, with a note of neurotransmitter packaging into synaptic vesicles. The pervasive theme is transmembrane transport rather than a single substrate or pathway, so this umbrella label is apt.","confidence":"High","size":15,"edges":14,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":7},{"id":"GO:0006004","count":6},{"id":"GO:0042128","count":6},{"id":"GO:0035725","count":5},{"id":"GO:0015751","count":5}]},{"hash":"2240381589464373023","title":"Endosomal trafficking and Golgi\u2013endosome transport","description":"The cluster is dominated by GO terms related to endocytosis, Golgi-to-endosome transport, multivesicular body sorting, and early endosome\u2013to\u2013Golgi routing, plus protein targeting to vacuole, which together point to a cohesive vesicle trafficking/endomembrane system function. Some terms (DNA-templated transcription, viral RNA genome replication, spermatid development) are less clearly connected and may reflect multifunctional proteins or noise, but the central theme remains endosomal trafficking.","confidence":"Medium","size":15,"edges":69,"triangles":197,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0039694","count":2},{"id":"GO:0006268","count":2},{"id":"GO:0006897","count":2},{"id":"GO:0006623","count":2}]},{"hash":"1915084026682027762","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070898","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0035914","count":2},{"id":"GO:0030010","count":1},{"id":"GO:0000472","count":1}]},{"hash":"1612354862850216812","title":"COPII-Mediated ER Export","description":"The GO terms are dominated by COPII-coated vesicle budding, vesicle transport from the ER, and ER exit-site localization, all pointing to COPII-dependent trafficking from the endoplasmic reticulum to the Golgi. This theme is reinforced by terms for ER organization and protein localization to ER exit sites, suggesting the cluster centers on ER-to-Golgi transport machinery. A few outlier terms (peroxisome fission, vitamin transport) exist but do not override the main ER trafficking signal. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090114","count":1},{"id":"GO:0016192","count":1},{"id":"GO:0016559","count":1},{"id":"GO:0007029","count":1},{"id":"GO:0070973","count":1}]},{"hash":"1887890095376615322","title":"Unknown","description":"The top GO terms are very diverse (actin cytoskeleton regulation, insulin signaling, STAT phosphorylation, response to yeast, NK cell regulation, epithelial polarity, synaptic vesicle uncoating, cell fusion, caveola assembly, IL-6 signaling), showing no single cohesive function or pathway. With zero edges among proteins, there\u2019s no clear common theme to name a specific cluster function beyond Unknown.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000251","count":2},{"id":"GO:0038028","count":1},{"id":"GO:0042503","count":1},{"id":"GO:0001878","count":1},{"id":"GO:0045953","count":1}]},{"hash":"705613586463568861","title":"Nuclear transcription and mitosis regulation","description":"The strongest GO signals center on DNA-templated transcription, mitotic cell cycle, mitotic spindle assembly, protein polyubiquitination, and histone H3-K9 methylation, pointing to a core theme of transcriptional/chromatin regulation associated with cell division. While there are additional terms related to vesicle transport, development, and oxidative stress, these are less dominant and may reflect pleiotropy or broader roles of shared proteins. Overall, the cluster seems to unify chromatin/conduct of transcription with mitotic control and protein turnover. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0031954","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0000209","count":2}]},{"hash":"706712618279557204","title":"Autophagy and organelle turnover","description":"The top GO terms are dominated by autophagy-related processes: macroautophagy, autophagosome assembly, autophagy of mitochondrion, and nucleophagy (piecemeal microautophagy of the nucleus). Positive regulation of TORC1 signaling and protein catabolic processes further connect to autophagy regulation. Some rRNA processing terms appear as noise, but the strongest signal is autophagy, supporting a label focused on cellular component turnover via autophagy pathways.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0000447","count":2},{"id":"GO:1904263","count":2},{"id":"GO:0045732","count":1},{"id":"GO:0051697","count":1}]},{"hash":"1853960217394707985","title":"Cytoskeletal organization and adhesion signaling","description":"The cluster\u2019s top GO terms point to cytoskeletal and structural organization (sarcomere), focal adhesion assembly, and signaling pathways that regulate cell shape and movement (Rho signaling, EGFR and IL-6 responses, thrombin receptor signaling). While a couple of terms touch on cell wall biosynthesis, the dominant theme centers on cytoskeletal dynamics, cell\u2013ECM adhesion, and growth-factor\u2013mediated signaling, suggesting a cohesive functional module around cytoskeleton remodeling and signaling. ","confidence":"Medium","size":15,"edges":12,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0045214","count":3},{"id":"GO:0071364","count":3},{"id":"GO:0045792","count":3},{"id":"GO:0006606","count":3},{"id":"GO:0006078","count":2}]},{"hash":"689842770569310739","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":93,"triangles":322,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0016554","count":2},{"id":"GO:0031426","count":2},{"id":"GO:1905639","count":2},{"id":"GO:0031425","count":2},{"id":"GO:0001682","count":2}]},{"hash":"1965129173027575399","title":"ER-Golgi vesicle trafficking and SNARE assembly","description":"The cluster shows terms centered on vesicle transport between the ER and Golgi (ERGIC membrane fusion, Golgi ribbon formation) and SNARE complex assembly, pointing to a cohesive role in Golgi-ER trafficking and SNARE-mediated fusion. Some mitochondrial-related terms and secretion-related terms appear as outliers, which may reflect dual-targeting annotations or noise, but the strongest signal is ER-Golgi trafficking and Golgi organization. ","confidence":"Medium","size":15,"edges":7,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":3},{"id":"GO:0045039","count":1},{"id":"GO:0006626","count":1},{"id":"GO:0072321","count":1},{"id":"GO:0090161","count":1}]},{"hash":"1818721596294888918","title":"APC/C-Mediated Mitosis and Ubiquitination","description":"The cluster is dominated by mitosis-related terms: mitotic cell cycle, anaphase-promoting complex\u2013dependent catabolic process, and K11-linked ubiquitination, all pointing to APC/C-driven proteolysis that governs mitotic progression. Other terms like RNA methylation and cadmium response appear less central, but do not override the core cell-cycle signal.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0070979","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0000278","count":2}]},{"hash":"6763080969366540","title":"Glycan and Polysaccharide Biosynthesis","description":"Top GO terms cluster around glycan and carbohydrate biosynthesis (UDP-D-galactose metabolic process; glucosylceramide biosynthetic process; cell wall polysaccharide biosynthetic process), as well as terms related to insect follicle epithelium development (follicle cell adhesion and polarity) and eye primordium formation. This suggests a shared theme of carbohydrate-based biosynthesis and extracellular matrix components that support tissue morphogenesis. Some terms (mycolate cell wall layer assembly; capsule polysaccharide biosynthetic process) appear cross-species or noisy, but the dominant signal points to glycan assembly pathways. Therefore, a label like Glycan and Polysaccharide Biosynthesis captures the main functional trend.","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001744","count":2},{"id":"GO:0071769","count":2},{"id":"GO:0045227","count":2},{"id":"GO:0007299","count":2},{"id":"GO:0075015","count":2}]},{"hash":"1219554151546190231","title":"Insulin/IGF signaling and cytoskeletal regulation","description":"The top GO terms cluster around regulation of insulin receptor and insulin-like growth factor signaling, together with small GTPase\u2013mediated signal transduction and actin cytoskeleton organization, suggesting a module where growth factor signals drive cytoskeletal remodeling via GTPases. A pair of meiosis-related terms appears but is not central to the main theme. This label reflects the dominant functional pattern in the cluster.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046626","count":2},{"id":"GO:1990758","count":2},{"id":"GO:0030036","count":2},{"id":"GO:0043314","count":2},{"id":"GO:0043547","count":2}]},{"hash":"24530276044521184","title":"Unknown","description":"The top GO terms are scattered across development (fat pad, brain, cardiac muscle) and cytoskeletal/translation processes (actin depolymerization, translation reinitiation), with some terms obsolete and no clear single theme. There are no network connections to suggest a cohesive function, making it impossible to assign a concise, representative label. ","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061087","count":2},{"id":"GO:0060613","count":2},{"id":"GO:0072432","count":1},{"id":"GO:0030042","count":1},{"id":"GO:0010659","count":1}]},{"hash":"429786888435554347","title":"Developmental morphogenesis and cell migration","description":"This cluster shows shared themes of morphogenesis across diverse tissues (e.g., midbrain, cardiac atrium, pericardium, anterior midgut) and processes tied to cell movement and signaling (Rac signaling, podosome regulation, chemotaxis). The combination suggests a functional grouping in developmentally regulated tissue morphogenesis coupled with cell migration and barrier modulation.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0022011","count":2},{"id":"GO:0043114","count":2},{"id":"GO:0016601","count":2},{"id":"GO:0007375","count":2},{"id":"GO:0002408","count":2}]},{"hash":"1174167507588428837","title":"Neuronal development and cell adhesion regulation","description":"This cluster centers on terms like axonogenesis, synapse assembly, and regulation of integrin- or extracellular matrix\u2013mediated cell adhesion, pointing to a cohesive theme of neural development and adhesion signaling. Though some terms are more general or non-neuronal (e.g., biofilm or meiotic spindle regulation), the dominant pattern is neural differentiation and cell\u2013matrix interactions, supporting this label as representative.","confidence":"High","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000727","count":14},{"id":"GO:0001952","count":14},{"id":"GO:0006349","count":14},{"id":"GO:0021952","count":14},{"id":"GO:0090606","count":14}]},{"hash":"2066920697690465623","title":"Neural development and synaptic signaling","description":"This cluster is enriched for neural-related terms: excitatory postsynaptic potential, visual perception, long-term potentiation, and Schwann cell development, suggesting roles in neural signaling and development. The presence of kinase-related phosphorylation and some cell-cycle/apoptosis terms may reflect multifunctionality or broader signaling roles, but the neural terms appear most representative of the cluster\u2019s core function.","confidence":"Medium","size":14,"edges":32,"triangles":20,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010800","count":9},{"id":"GO:0060079","count":9},{"id":"GO:0007601","count":9},{"id":"GO:0000086","count":9},{"id":"GO:0007507","count":9}]},{"hash":"399634649871117794","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":26,"triangles":22,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006223","count":4},{"id":"GO:0046038","count":3},{"id":"GO:0006178","count":3},{"id":"GO:0048813","count":3},{"id":"GO:0021895","count":3}]},{"hash":"1706006266522095985","title":"Heart development and broad tissue differentiation","description":"The top GO terms cluster around developmental differentiation with emphasis on heart-related processes (endocardial cushion mesenchymal transition, heart valve formation, cardiac differentiation) and skeletal muscle/oiligodendrocyte development, plus broader differentiation signals (Notch involvement, transcription by RNA polymerase II, hormone-responsive pathways). This suggests a theme of developmental morphogenesis across multiple tissues, not limited to a single tissue or pathway, hence a label that highlights both heart morphogenesis and general tissue differentiation is appropriate.","confidence":"Medium","size":14,"edges":86,"triangles":310,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:2001016","count":12},{"id":"GO:0045668","count":9},{"id":"GO:0006366","count":9},{"id":"GO:0060766","count":9},{"id":"GO:0035481","count":8}]},{"hash":"145147499031920489","title":"Urogenital organogenesis and MET","description":"The top GO terms cluster around mesenchymal-to-epithelial transition (MET), ureteric bud formation, mesonephros and male gonad development, pointing to embryonic development of the kidney/urinary tract and reproductive organs, with MET as a central process. Some terms like norepinephrine biosynthesis and IL-5 production are less connected, but they do not override the core urogenital organogenesis theme. ","confidence":"Medium","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0060231","count":14},{"id":"GO:0072107","count":14},{"id":"GO:2000734","count":14},{"id":"GO:0032912","count":14},{"id":"GO:0042421","count":14}]},{"hash":"1809454058140288637","title":"Plant shoot meristem development and RNA processing","description":"This cluster combines terms tied to axillary shoot meristem initiation and regulation of secondary shoot formation with multiple RNA-processing and chromatin-regulation processes (ribosome biogenesis, splicing, ncRNA-mediated silencing, chromatin remodeling), suggesting a cohesive theme around transcriptional/post-transcriptional control impacting shoot development. Some terms (hemidesmosome assembly, amino acid starvation response) appear noisy, but the dominant signal points to plant shoot development linked to RNA biology.","confidence":"Medium","size":14,"edges":10,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0034198","count":3},{"id":"GO:2000032","count":3},{"id":"GO:0031581","count":3},{"id":"GO:0000028","count":3},{"id":"GO:0006407","count":3}]},{"hash":"1266415528045023666","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":16,"triangles":2,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":6},{"id":"GO:0006469","count":5},{"id":"GO:0036494","count":4},{"id":"GO:0090084","count":4},{"id":"GO:0006458","count":4}]},{"hash":"1728700184886725965","title":"DNA replication and cell cycle proteins","description":"Top GO terms include DNA replication and DNA replication initiation, as well as cell division, pointing to roles in genome duplication and cell cycle progression. While other terms (mitochondrion inheritance, proteasome assembly, Golgi retention) suggest broader housekeeping functions, the recurring replication/division signals support naming this cluster around DNA replication and cell cycle processes.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007605","count":3},{"id":"GO:0000001","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0045053","count":2}]},{"hash":"2268116874061410843","title":"Bacterial lipid, quinone, and cell-wall biosynthesis","description":"The GO terms in this cluster center on biosynthetic and activation processes for lipid-related molecules (fatty acids, menaquinone), cell-wall components like lipoteichoic acid, and secondary metabolite pathways (siderophore biosynthesis, NRPS-related activation). This combination points to a cohesive theme of bacterial lipid/quinone production and cell-envelope assembly, with associated secondary metabolism, rather than a single signaling or transport pathway.","confidence":"Medium","size":14,"edges":17,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009234","count":6},{"id":"GO:0010124","count":6},{"id":"GO:0070395","count":5},{"id":"GO:0019290","count":5},{"id":"GO:0008206","count":5}]},{"hash":"2179677869615341289","title":"Nutrient-responsive transcription and vesicle transport","description":"The top GO terms point to DNA-templated transcription and ER-to-Golgi vesicle\u2013mediated transport, with several entries about transcriptional regulation in response to nutrients (oleic acid, carbon source, leucine biosynthesis) and even aflatoxin biosynthesis, suggesting a fungal context where transcriptional control is linked to secretion and secondary metabolism. While some terms are obsolete, the recurring themes are transcriptional regulation linked to vesicle trafficking and nutrient signaling.","confidence":"Medium","size":14,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0061429","count":1},{"id":"GO:0035961","count":1},{"id":"GO:0061415","count":1}]},{"hash":"2136659865203925676","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0000154","count":2}]},{"hash":"716103438245535642","title":"Jasmonic acid and oxylipin biosynthesis","description":"The top terms are dominated by jasmonic acid biosynthesis, oxylipin biosynthesis, and fatty acid beta-oxidation, with supporting stress-related terms like response to ozone and response to toxic substances, all pointing to a plant jasmonate/oxylipin signaling module involved in defense and development (e.g., JA-regulated stamen development). Some terms (e.g., visual learning, angiogenesis) appear as low-frequency annotations but do not override the core plant-specific theme.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":12},{"id":"GO:0033543","count":10},{"id":"GO:0010193","count":10},{"id":"GO:0048443","count":10},{"id":"GO:0031408","count":10}]},{"hash":"1463984166507971483","title":"Nuclear transcription initiation and telomere localization","description":"The top terms point to nuclear processes involved in gene expression and chromosome maintenance: transcription initiation (DNA-templated transcription initiation, RNA polymerase II preinitiation complex assembly), chromatin modification (histone H3 acetylation), and chromosome- or telomere-localization. While some terms (e.g., cell wall organization, obsolete GO terms) may reflect annotation noise, the dominant theme centers on nuclear transcription regulation and chromosomal localization/maintenance.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":2},{"id":"GO:0007221","count":1},{"id":"GO:0051123","count":1},{"id":"GO:0043966","count":1},{"id":"GO:0006352","count":1}]},{"hash":"14509984945562504","title":"Neural and glial development signaling","description":"This cluster\u2019s top GO terms predominantly revolve around nervous system development, including oligodendrocyte progenitor proliferation, neuron migration, and forebrain astrocyte development, with supporting signaling activities (GTPase regulation, phosphorylation/dephosphorylation). These collectively point to proteins involved in neural and glial lineage development and associated signaling pathways.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0043553","count":1},{"id":"GO:2001241","count":1},{"id":"GO:0035305","count":1}]},{"hash":"1317467176052482685","title":"Mitotic spindle assembly and cytokinesis","description":"The proteins cluster around mitosis: GO terms for cell cycle and cell division, plus specific mitotic spindle processes such as centrosome separation, chromosome alignment, microtubule polarity, and minus-end directed sliding. This points to a cohesive function in mitotic spindle assembly and chromosome segregation, with some evidence of complex formation (protein heterooligomerization) that is typical of spindle protein complexes.","confidence":"High","size":14,"edges":10,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006626","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0051291","count":2}]},{"hash":"613563909642233583","title":"mRNA processing and translation","description":"The cluster centers on mRNA maturation and control of translation, with strong representation of mRNA polyadenylation and spliceosome-mediated splicing, plus cytoplasmic translation and translation reinitiation terms. Few signaling-related GO terms appear, but they are peripheral to the main theme of RNA processing and protein synthesis.","confidence":"High","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0075525","count":1},{"id":"GO:0071356","count":1}]},{"hash":"875304486243748078","title":"Zinc Ion Transport and Homeostasis","description":"This cluster is dominated by GO terms related to zinc import across the plasma membrane, intracellular zinc ion homeostasis, detoxification of zinc, and metal ion transport (including cadmium). These indicate a cohesive theme around zinc uptake, balance, and handling within the cell. Some terms like limb development and cold response appear as minor associations and are less central to the core function of these proteins.","confidence":"High","size":14,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006830","count":3},{"id":"GO:0060173","count":3},{"id":"GO:0034224","count":3},{"id":"GO:0044749","count":3},{"id":"GO:1903615","count":3}]},{"hash":"316004746629523318","title":"Sphingolipid Metabolism and Signaling","description":"This cluster is dominated by GO terms related to sphingolipid metabolism and signaling, including sphinganine-1-phosphate metabolic process, sphingosine metabolic process, and regulation of sphingolipid mediated signaling pathway. While other terms like detoxification and phosphatidylglycerol biosynthesis appear, the sphingolipid-related terms are the clearest common theme tying the proteins together. Given there are no observed edges or interactions, the label reflects shared functional annotations rather than network structure.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":2},{"id":"GO:0006668","count":2},{"id":"GO:0044330","count":2},{"id":"GO:1902068","count":2},{"id":"GO:0006670","count":2}]},{"hash":"1908494248925432822","title":"Ribosome biogenesis and translational control","description":"This cluster is dominated by GO terms related to the ribosome and translation, including translation, ribosome biogenesis, ribosome disassembly, translational termination, selenocysteine incorporation, translation fidelity, and regulation of cytoplasmic translation. The presence of mRNA decay linked to translational control further supports a theme around mRNA handling in the context of protein synthesis. The glial cell proliferation term may reflect cellular contexts where translation is highly active, but the core signal is ribosome function and translational regulation.","confidence":"High","size":14,"edges":3,"triangles":0,"max_degree":2,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0042254","count":3},{"id":"GO:0000288","count":3},{"id":"GO:1990145","count":3},{"id":"GO:0046677","count":3}]},{"hash":"2055567858267078852","title":"Ribosome Large Subunit Biogenesis","description":"The top GO terms are overwhelmingly centered on large subunit ribosome production: large subunit assembly, export from the nucleus, and maturation of LSU rRNA, plus preribosome assembly. While a few terms touch on autophagy, glycogen metabolism, and signaling, the dominant pattern points to a ribosome biogenesis module focused on the large subunit.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000027","count":1},{"id":"GO:0000055","count":1},{"id":"GO:0000463","count":1},{"id":"GO:0000466","count":1},{"id":"GO:1902626","count":1}]},{"hash":"1018780317945055417","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048025","count":3},{"id":"GO:0006406","count":3},{"id":"GO:0000381","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0051301","count":2}]},{"hash":"34392518144197128","title":"Lipid biosynthesis and remodeling","description":"This cluster is defined by a set of GO terms centered on lipid biosynthesis and membrane lipid remodeling (platelet activating factor biosynthesis, CDP-diacylglycerol biosynthesis, cardiolipin remodeling, triglyceride biosynthesis, ether lipid biosynthesis, and regulation of phosphatidylcholine biosynthesis). While a couple terms touch on development or immune signaling, the overarching pattern points to lipid metabolism and membrane lipid production. Confidence: Medium.","confidence":"","size":14,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006663","count":3},{"id":"GO:0016024","count":2},{"id":"GO:0035965","count":2},{"id":"GO:0019432","count":2},{"id":"GO:0070236","count":2}]},{"hash":"108208051116820375","title":"Developmental chromatin regulation","description":"The top GO terms point to chromatin-related processes (nucleosome assembly, heterochromatin regulation, RNA processing/export) alongside a range of developmental processes (EMT in heart development, left-right patterning, trophoblast differentiation, pancreatic endocrine development). This suggests a theme of genes modulating gene expression via chromatin and RNA processing within developmental contexts.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006334","count":2},{"id":"GO:0061188","count":2},{"id":"GO:0032298","count":2},{"id":"GO:0060707","count":2},{"id":"GO:0060972","count":2}]},{"hash":"1576278276382916239","title":"Nuclear import and RNA transport","description":"The Top Terms cluster around nuclear import processes (NLS-bearing protein import, ribosomal protein import, nuclear pore complex assembly, import into nucleus) and RNA trafficking (mRNA transport). This points to a cohesive theme of proteins involved in shuttling macromolecules across the nuclear envelope, with supporting signals of related regulatory processes (desumoylation, protein turnover) that can modulate these transport pathways. Some terms (meiotic cohesion, extrinsic apoptotic signaling) may reflect multifunctionality but do not override the core nuclear transport/RNA trafficking theme.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000060","count":4},{"id":"GO:0060188","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0051292","count":4},{"id":"GO:0006610","count":4}]},{"hash":"856695084987066944","title":"Mitochondrial Transport and Metabolic Processes","description":"This cluster centers on transport across the mitochondrial membrane and related metabolic pathways, including phosphate and Mn2+ transport, pyrimidine nucleotide import, thiamine pyrophosphate transport, and the malate\u2013aspartate shuttle, along with mitochondrial membrane dynamics and apoptosis-related changes, suggesting a cohesive mitochondria-focused functional theme.","confidence":"High","size":14,"edges":12,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":8},{"id":"GO:1990544","count":6},{"id":"GO:0006828","count":6},{"id":"GO:0090152","count":6},{"id":"GO:0008637","count":6}]},{"hash":"2159797705495957640","title":"Spindle assembly via gamma-tubulin complex","description":"The top GO terms cluster around microtubule nucleation and spindle formation, including microtubule nucleation by spindle pole body, interphase MTOC nucleation, mitotic spindle assembly, and gamma-tubulin complex localization, indicating a coherent role in spindle assembly and centrosomal tubulin nucleation. Some autophagy-related terms appear but do not define the main function; the dominant theme is spindle assembly machinery driven by gamma-tubulin.","confidence":"High","size":14,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051417","count":1},{"id":"GO:0051415","count":1},{"id":"GO:0090307","count":1},{"id":"GO:0033566","count":1},{"id":"GO:0006508","count":1}]},{"hash":"951595021608973700","title":"Oocyte meiosis and spindle assembly","description":"Top terms point to meiosis-related processes (spindle assembly in female meiosis I, oocyte maturation) and microtubule dynamics, with supporting roles for ubiquitin-proteasome\u2013mediated protein turnover. While some terms touch on development or immune regulation, the strongest signals are meiotic progression and spindle function in oocytes, supporting this label.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902564","count":9},{"id":"GO:0008285","count":3},{"id":"GO:0007057","count":3},{"id":"GO:0001556","count":3},{"id":"GO:0046785","count":3}]},{"hash":"1898265593945538769","title":"Ubiquitin-Proteasome\u2013Mediated Protein Degradation","description":"The cluster is characterized by terms centered on ubiquitination and proteasomal degradation (protein polyubiquitination, ubiquitin-dependent proteolytic processes, SCF-dependent degradation, and positive regulation of ubiquitination), suggesting a cohesive theme of proteostasis. Additional terms hint at regulatory and stress-related implications (cell cycle/DNA replication initiation, metal stress responses), which can be downstream consequences of ubiquitin-mediated turnover of regulatory proteins.","confidence":"High","size":14,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":8},{"id":"GO:0000083","count":8},{"id":"GO:0046685","count":8},{"id":"GO:0060386","count":8},{"id":"GO:0071276","count":8}]},{"hash":"1767784920583188208","title":"Ubiquitin-Mediated Proteolysis in Mitosis","description":"This cluster centers on ubiquitin-dependent proteolysis and cell-cycle regulation, with GO terms such as ubiquitin-dependent protein catabolic process and K11-linked ubiquitination, APC-dependent catabolic process, and mitotic cell cycle, indicating a theme of proteostasis controlling mitosis. The presence of unfolded protein response and cadmium ion response terms suggests broader protein quality control and stress-related connections, but the dominant signal is ubiquitin-mediated degradation coordinating cell division.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902564","count":4},{"id":"GO:0042787","count":4},{"id":"GO:0070979","count":3},{"id":"GO:0071276","count":3},{"id":"GO:1903378","count":3}]},{"hash":"286000245403047919","title":"Synaptic vesicle trafficking and dopamine signaling","description":"The cluster is enriched for post-Golgi vesicle transport and general protein transport, along with small GTPase\u2013mediated signaling and positive regulation of GTPase activity, which points to vesicle trafficking and synaptic machinery. Several terms tie to neuronal function and movement, including regulation of dopamine receptor signaling, voluntary movement, and terminal button organization, indicating a neuronal synaptic context where vesicle trafficking intersects with dopaminergic signaling and locomotion.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006892","count":1},{"id":"GO:0015031","count":1},{"id":"GO:0007264","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0090326","count":1}]},{"hash":"222354153786875594","title":"Biosynthesis and Transcription Regulation","description":"The Top Terms show a mix of biosynthetic processes (phenylpropanoid, anthocyanin-containing compounds, galactose, colanic acid) and transcription-related functions (DNA-templated transcription; nitrogen catabolite repression of transcription). This suggests the cluster groups proteins involved in both metabolite biosynthesis and transcriptional control, rather than a single specific enzyme pathway, so the label captures the shared theme of metabolism and gene regulation across diverse organisms. Some terms are listed as obsolete, so interpretation should be cautious, but the core theme remains.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0006351","count":3},{"id":"GO:1901006","count":2},{"id":"GO:0001081","count":2},{"id":"GO:0009699","count":2}]},{"hash":"1210196014844992706","title":"Mitochondrial respiration and Complex II assembly","description":"The top GO terms point to mitochondrial energy production: NADH to ubiquinone electron transport and assembly of respiratory chain complex II. There is a single ER tubular network term, which could reflect ER-mitochondria contacts, but the two mitochondrial terms dominate, suggesting the cluster groups proteins involved in oxidative phosphorylation and assembly of Complex II. Overall, the theme is mitochondrial respiration with an incidental ER-associated term.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071786","count":1},{"id":"GO:0034553","count":1},{"id":"GO:0006120","count":1}]},{"hash":"544205658647166860","title":"Neuronal signaling and synaptic exocytosis","description":"The proteins are enriched for GO terms centered on neuronal communication and synaptic activity, including dopamine response, excitatory postsynaptic potential, ephrin signaling, JNK and Wnt pathways, and calcium-dependent exocytosis. This points to a cohesive theme of synaptic signaling and activity-dependent exocytosis, despite a few outliers like mitotic cell cycle terms and mast cell degranulation that may reflect shared signaling machinery or annotation noise.","confidence":"Medium","size":13,"edges":4,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043304","count":6},{"id":"GO:0045956","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0033138","count":6},{"id":"GO:1903351","count":6}]},{"hash":"1792107562765553651","title":"Ribosome Biogenesis and Translation","description":"Based on the prominence of translation-related terms (GO:0006412), ribosome biogenesis (GO:0042254, GO:0042274), and tRNA modification (GO:0006400), the cluster appears to group proteins involved in ribosome assembly and protein synthesis, with supporting roles in RNA processing and cell cycle progression. Minor associations to stress responses exist but do not define the core function.","confidence":"High","size":13,"edges":68,"triangles":196,"max_degree":12,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0051301","count":6},{"id":"GO:0042254","count":6},{"id":"GO:0006400","count":5},{"id":"GO:0000288","count":4}]},{"hash":"1543466116498434142","title":"Cell cycle and centromere chromatin assembly","description":"Dominant GO terms point to cell division, DNA replication, CENP-A chromatin assembly, and microtubule severing, suggesting proteins involved in cell cycle regulation and centromere/mitotic processes; a few terms appear unrelated (ERAD, viral replication, vesicle transport), likely noise. ","confidence":"Medium","size":13,"edges":5,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0030433","count":3},{"id":"GO:0061641","count":3},{"id":"GO:0051013","count":3},{"id":"GO:0051260","count":3}]},{"hash":"65289925326221932","title":"Neurodevelopment and Synaptic Regulation","description":"The cluster centers on neural development and synaptic signaling: nervous system development, long-term potentiation, calcium-dependent exocytosis, and Rho signaling for cytoskeletal dynamics, plus transcriptional regulation via DNA-templated transcription and phosphorylation. While some other development terms (heart, skeletal) appear, the strongest common theme is neural development and synaptic regulation.","confidence":"Medium","size":13,"edges":8,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007507","count":5},{"id":"GO:0007399","count":4},{"id":"GO:0007124","count":4},{"id":"GO:0045956","count":4},{"id":"GO:0001501","count":4}]},{"hash":"1167670519257126966","title":"Galactose-Driven Carbohydrate Metabolism","description":"This cluster centers on galactose-associated carbohydrate metabolism and related glycosylation processes, with GO terms like carbohydrate phosphorylation, galactitol metabolic process, glycolytic process from galactose, and GDP-L-fucose salvage. There is also a regulatory term linked to galactose-driven transcription, supporting a galactose-focused theme. Some other terms (isoprenoid biosynthesis) appear, but they are less representative of the main pattern.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":2},{"id":"GO:0032760","count":2},{"id":"GO:0019402","count":1},{"id":"GO:0009086","count":1},{"id":"GO:0019288","count":1}]},{"hash":"991802899365020711","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":37,"triangles":50,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0036494","count":4},{"id":"GO:0090084","count":4},{"id":"GO:0006458","count":4},{"id":"GO:0034975","count":4},{"id":"GO:0070843","count":4}]},{"hash":"309708000660018110","title":"Mitochondrial protein import and inner-membrane insertion","description":"The Top Terms clearly point to mitochondrial targeting and insertion into the inner membrane (GO:0045039) and protein transport to mitochondrion (GO:0006626), with supportive signals from chaperone-mediated transport. Although some terms are obsolete or unrelated, the strongest cohesive theme is mitochondrial import/assembly, suggesting the cluster comprises proteins involved in mitochondrial membrane targeting and insertion.","confidence":"Medium","size":13,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045039","count":2},{"id":"GO:0006626","count":2},{"id":"GO:0072321","count":2},{"id":"GO:0034368","count":1},{"id":"GO:0046272","count":1}]},{"hash":"2204752780643709144","title":"Neuronal endosomal trafficking and vesicle recycling","description":"This cluster centers on endosomal transport (to lysosome/melanosome), endocytic recycling, and vesicle fusion, with additional hints of synaptic activity and neuronal development. The shared theme appears to be intracellular vesicle trafficking in neurons, tying endosome dynamics to recycling and synaptic function, even though some unrelated developmental terms appear. ","confidence":"Medium","size":13,"edges":34,"triangles":45,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0035646","count":2},{"id":"GO:0008333","count":2},{"id":"GO:0060079","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0007507","count":2}]},{"hash":"1888766104215505599","title":"Vesicle trafficking and autophagy regulation","description":"These proteins cluster around secretory and autophagic processes: regulation of COPII vesicle coating, Golgi-to-plasma membrane transport, and late endosome-to-lysosome trafficking, plus protein localization to phagophore assembly sites and calcium-dependent exocytosis. Hedgehog/Smoothened signaling and developmental terms appear secondary to this core trafficking/autophagy theme, suggesting a role in coordinating vesicle transport with autophagic pathways.","confidence":"Medium","size":13,"edges":10,"triangles":0,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060999","count":6},{"id":"GO:0001822","count":6},{"id":"GO:0007049","count":6},{"id":"GO:0034497","count":6},{"id":"GO:0003400","count":6}]},{"hash":"2256985409058631284","title":"Bacterial lipid metabolism and NRPS biosynthesis","description":"The top GO terms cluster around fatty acid metabolism across multiple chain lengths (long, medium, very long), fatty acid import, and lipoteichoic acid biosynthesis, indicating lipid envelope biosynthesis in bacteria. The presence of nonribosomal peptide biosynthesis terms (amino acid activation for NRPS) and siderophore biosynthesis suggests production of NRPS-derived secondary metabolites. Together, these terms point to a cluster of proteins involved in lipid-based envelope components and NRPS-derived metabolite pathways in bacteria.","confidence":"High","size":13,"edges":14,"triangles":1,"max_degree":4,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0070395","count":6},{"id":"GO:0036112","count":6},{"id":"GO:0019290","count":5},{"id":"GO:0008206","count":5},{"id":"GO:0019654","count":5}]},{"hash":"1432379461482316045","title":"Bacterial fatty acid and lipid biosynthesis","description":"The cluster shows strong enrichment for fatty acid biosynthetic processes (fatty acid biosynthetic process; long-chain and very long-chain fatty acid metabolism; long-chain fatty acid import) and lipoteichoic acid biosynthesis, indicating a core role in lipid production and cell-envelope lipid assembly in bacteria. Additional enrichment for siderophore biosynthesis and nonribosomal peptide activation suggests broader bacterial secondary metabolite capacity, but the common thread remains lipid biosynthesis and related cell-envelope components.","confidence":"High","size":13,"edges":55,"triangles":113,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0070395","count":9},{"id":"GO:0019290","count":8},{"id":"GO:0008206","count":8},{"id":"GO:0019654","count":8},{"id":"GO:0000038","count":8}]},{"hash":"206626487067936826","title":"DNA Repair and Oxidative Stress Response","description":"The top GO terms are dominated by DNA repair and genome maintenance (DNA recombination, base-excision repair) along with stress response categories (cellular response to hydrogen peroxide, response to xenobiotic stimulus). These together point to a function cluster centered on DNA damage repair and oxidative/detox stress responses, with a few unrelated terms present as noise. ","confidence":"Medium","size":13,"edges":19,"triangles":5,"max_degree":6,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":4},{"id":"GO:0042493","count":4},{"id":"GO:0007568","count":4},{"id":"GO:0006284","count":4},{"id":"GO:0070301","count":4}]},{"hash":"839512903183620860","title":"Unknown","description":"The terms span metabolism (gluconeogenesis; valine biosynthesis; glyoxylate and taurine catabolism) and some cell-cycle or RNA processing terms, with several entries labeled obsolete, suggesting no coherent single function tying all proteins together. Therefore, a specific label cannot be confidently assigned.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010971","count":2},{"id":"GO:0030010","count":2},{"id":"GO:0001302","count":2},{"id":"GO:0006094","count":2},{"id":"GO:0090305","count":1}]},{"hash":"128433522811386427","title":"Nucleobase Transporters","description":"The GO terms show repeated transport of nucleobases and related compounds across membranes: urate, adenine, hypoxanthine, guanine, xanthine, uracil, and general transmembrane/vitamin transport terms. This pattern strongly suggests a cluster of membrane transport proteins dedicated to importing or exporting nucleobases and related metabolites. The \"positive regulation of replicative senescence\" term appears infrequently and is not coherent with the core transport theme, likely noise. Overall, the dominant function theme is nucleobase transport.","confidence":"High","size":13,"edges":17,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0015747","count":4},{"id":"GO:0098710","count":2},{"id":"GO:1903825","count":2},{"id":"GO:0098702","count":2},{"id":"GO:0035344","count":2}]},{"hash":"1454607604675752629","title":"Fatty acid metabolism and biosynthesis","description":"The top GO terms are dominated by fatty-acyl-CoA catabolic and biosynthetic processes (medium-/long-chain), including palmitic acid and various fatty acid biosynthetic pathways, indicating a core theme of lipid metabolism. There is also a note of negative regulation of fatty acid biosynthesis, with a minor signal for enterobactin biosynthesis and transcriptional regulation terms, suggesting some peripheral regulatory or ancillary functions. Overall, the cluster seems to group proteins involved in fatty acid turnover and synthesis.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036114","count":2},{"id":"GO:0036116","count":2},{"id":"GO:1900535","count":2},{"id":"GO:0045717","count":2},{"id":"GO:0009239","count":2}]},{"hash":"227410455269347420","title":"Chromatin Ubiquitination and Cell Cycle Regulation","description":"The presence of chromosome segregation, cell division, histone ubiquitination, and specific ubiquitin-linkage terms (K29, K11) points to a core theme of chromatin modification controlling the cell cycle and transcription, including transcriptional regulation via degradation pathways. A couple of terms (immune signaling and synapse assembly) appear ancillary but do not outweigh the dominant chromatin- and cell-cycle-focused signals.","confidence":"Medium","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0007059","count":13},{"id":"GO:0071347","count":13},{"id":"GO:0033128","count":13},{"id":"GO:0070987","count":13},{"id":"GO:0035519","count":13}]},{"hash":"1834467292690426830","title":"Neural development and synaptic organization","description":"The terms cluster around brain development and neural function: midbrain morphogenesis, regulation of myelination, striated muscle differentiation (likely reflecting broader developmental processes), synaptic vesicle budding, and actin cytoskeleton organization all point to neuronal growth, connectivity, and glial interactions. A few immune-related terms (GM-CSF response, microglial migration) can be linked to microglia involvement in CNS development, supporting a CNS development/synaptic organization theme. Overall, a cohesive interpretation centers on neural development and synaptic/membrane trafficking activities, with modest support from glial/immunological context. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097011","count":2},{"id":"GO:1904140","count":1},{"id":"GO:0051146","count":1},{"id":"GO:0031641","count":1},{"id":"GO:0016185","count":1}]},{"hash":"2015126655613974010","title":"Epigenetic Regulation & Transcription","description":"Among the top GO terms, several point to chromatin modification and transcription control (histone H3-K9 and K27 methylation, DNA-templated transcription, RNA guanine-N7 methylation) and protein oligomerization, suggesting a theme of gene expression regulation at chromatin/RNA levels. Additional terms like microtubule movement and Golgi-ER transport indicate broader cellular roles, but the core signal supports epigenetic regulation and transcription. Therefore, this label captures the dominant functional theme of the cluster.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051567","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0061087","count":3},{"id":"GO:0007018","count":3},{"id":"GO:0036265","count":3}]},{"hash":"606618220435137211","title":"Actin dynamics and membrane organization","description":"The cluster combines strong signals for actin cytoskeleton remodeling (actin crosslink formation; actin cytoskeleton organization) with membrane-related processes (GPI anchor biosynthesis; caveola assembly) and signaling regulation (GTPase and Ras pathways), plus heart development context. This suggests proteins coordinating cytoskeletal changes at the membrane with signaling, relevant to cardiac tissue and vesicular/membrane dynamics.","confidence":"Medium","size":13,"edges":13,"triangles":1,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0051764","count":3},{"id":"GO:0006506","count":2},{"id":"GO:0045953","count":2}]},{"hash":"490505637041696211","title":"Transmembrane transporters","description":"The proteins are linked to diverse transmembrane transport processes (nitrite, sodium, arabinose, potassium, vitamin, xenobiotic transport) and vesicle-associated neurotransmitter loading, pointing to a cohesive function in membrane transport rather than a single metabolic or structural role.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":3},{"id":"GO:0035725","count":3},{"id":"GO:0015751","count":3},{"id":"GO:0006004","count":3},{"id":"GO:0006855","count":3}]},{"hash":"1039191041105931146","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045493","count":2},{"id":"GO:0005977","count":2},{"id":"GO:0007283","count":1},{"id":"GO:2000344","count":1},{"id":"GO:0016042","count":1}]},{"hash":"2126838657766788356","title":"Neuronal development and cell cycle regulation","description":"The cluster shows strong enrichment for cell division and cell cycle terms, with 12 and 11 counts, and also includes neural development terms (brain development, dendritic spine development) along with trafficking and signaling processes (ER-Golgi transport, GTPase regulation). This suggests proteins that coordinate neural development with cell cycle control and intracellular trafficking. ","confidence":"Medium","size":12,"edges":49,"triangles":111,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":12},{"id":"GO:0007049","count":11},{"id":"GO:0007420","count":8},{"id":"GO:0070208","count":8},{"id":"GO:0010255","count":8}]},{"hash":"1063323353708221611","title":"Sugar Catabolism and Carbohydrate Metabolism","description":"The cluster is dominated by GO terms for catabolic processing of various sugars (arabinose, xylose, glycerol, fucose, xylulose, glucuronate, D-xylose) and related carbohydrate phosphorylation, indicating a coherent theme of sugar breakdown pathways. A couple of outliers (cellular response to IL-13, quorum sensing) appear peripheral or noisy relative to the core sugar metabolism signals. Overall, the label captures the main function of the proteins in this cluster.","confidence":"High","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0046835","count":2},{"id":"GO:0019569","count":2},{"id":"GO:0019563","count":2},{"id":"GO:0042732","count":2}]},{"hash":"495883297682416467","title":"Neural and cardiac differentiation programs","description":"The top GO terms point to differentiation and development across neural lineages (oligodendrocyte development; amacrine cell differentiation; cerebral cortex GABAergic interneuron differentiation; inner ear auditory receptor cell differentiation) and heart-associated processes (Notch signaling in heart induction; endocardial cushion to mesenchymal transition in heart valve formation). While there are also terms for pancreas, osteoblasts, and reproductive tissues, the strongest theme is developmental differentiation spanning neural and cardiac lineages, justifying the label. ","confidence":"Medium","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035481","count":7},{"id":"GO:2000074","count":7},{"id":"GO:0014003","count":7},{"id":"GO:0045668","count":7},{"id":"GO:0003199","count":7}]},{"hash":"2230878752361443753","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":12},{"id":"GO:0048026","count":12},{"id":"GO:0006306","count":11},{"id":"GO:0070417","count":11},{"id":"GO:0071031","count":11}]},{"hash":"760220374187826544","title":"Cell Cycle Regulation and Chromosome Segregation","description":"This cluster is dominated by GO terms linked to cell division control, chromosome segregation, and the broader cell cycle, indicating a core theme around how cells manage division and genome partitioning. While a few terms touch on related processes like plasmid partitioning and metal ion responses, the strongest and most coherent signal is cell cycle regulation and chromosome segregation.","confidence":"Medium","size":12,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007059","count":1},{"id":"GO:0051782","count":1},{"id":"GO:0000750","count":1},{"id":"GO:0016226","count":1},{"id":"GO:0007049","count":1}]},{"hash":"388242328384634474","title":"Neuronal synapse development and protein trafficking","description":"The cluster shows enrichment for neuronal/synaptic functions (negative regulation of excitatory postsynaptic potential, positive regulation of dendritic spine development) together with intracellular transport and processing (protein localization to Golgi, endosome-to-melanosome transport, tubulin complex assembly, ubiquitination). This suggests a theme of synaptic regulation linked to trafficking and protein modification, rather than a single isolated pathway. Some terms like SOS response or DNA replication may be incidental background associations. ","confidence":"Medium","size":12,"edges":26,"triangles":20,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0090394","count":3},{"id":"GO:0000042","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0007021","count":3},{"id":"GO:0009432","count":2}]},{"hash":"421474632706988162","title":"Transmembrane transporters for diverse substrates","description":"This cluster is enriched for GO terms describing transport across membranes of a wide range of substrates\u2014vitamins, sugars, nitrite/nitrate, phosphate, potassium ions, and even neurotransmitter loading into synaptic vesicles\u2014indicating a common function as diverse membrane transport proteins.","confidence":"High","size":12,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":9},{"id":"GO:0042891","count":9},{"id":"GO:0015757","count":9},{"id":"GO:0015707","count":9},{"id":"GO:0042128","count":9}]},{"hash":"255170888490941718","title":"Drug Metabolism and Cellular Stress Response","description":"The top GO terms point to drug metabolism (doxorubicin/daunorubicin pathways) and cellular stress responses (oxidative stress markers like H2O2 and methylglyoxal), with supporting signals in JAK-STAT and retinoic acid pathways and broader metabolism (cholesterol turnover, vitamin C biosynthesis, water homeostasis). This suggests a coherent theme around processing xenobiotics and managing cellular stress via metabolic and signaling processes, so the name emphasizes both drug metabolism and stress signaling.","confidence":"Medium","size":12,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2000353","count":1},{"id":"GO:0019853","count":1},{"id":"GO:0044598","count":1},{"id":"GO:0046427","count":1},{"id":"GO:0097238","count":1}]},{"hash":"896072114957801853","title":"Mitotic progression and DNA replication","description":"This cluster is dominated by cell cycle-related GO terms: G1/S and G2/M transitions, re-entry into mitosis, and DNA replication, plus a term for spindle pole separation. Together they point to proteins coordinating cell cycle progression and DNA synthesis, with ancillary signals related to growth regulation. The strong alignment around mitosis and replication supports this as the core theme.","confidence":"High","size":12,"edges":5,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000082","count":3},{"id":"GO:0046626","count":3},{"id":"GO:0000320","count":3},{"id":"GO:0000086","count":3}]},{"hash":"1060936339099565927","title":"Actin Cytoskeleton Regulation and Kinase Signaling","description":"This cluster is enriched for GO terms tied to actin dynamics and signaling, notably positive regulation of GTPase activity and positive regulation of Arp2/3 complex\u2013mediated actin nucleation, which point to cytoskeletal remodeling driven by small GTPases. Additional terms on kinase activity and phosphorylation support a signaling axis that modulates these cytoskeletal processes, with associations to development. Together, these terms suggest a cohesive theme of actin cytoskeleton regulation linked to signaling pathways during development.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:2000601","count":3},{"id":"GO:0071456","count":3},{"id":"GO:0043588","count":3},{"id":"GO:0071902","count":3}]},{"hash":"1052329684589032930","title":"Immune and Growth-Factor Signaling","description":"The cluster centers on signaling pathways involved in immune cell differentiation and cytokine responses (interleukin-4 production, NK T cell differentiation, B cell maturation, IL-7 response) together with growth-factor signaling (insulin receptor, EGFR). It also includes regulation of Ras signaling and cytoskeletal/adhesion processes (lamellipodium assembly, cell spreading), suggesting a link between immune signaling, growth-factor cues, and cell migration, with a possible developmental component (heart development).","confidence":"High","size":12,"edges":5,"triangles":0,"max_degree":3,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0046580","count":7},{"id":"GO:0032633","count":7},{"id":"GO:0008286","count":7},{"id":"GO:0001865","count":7},{"id":"GO:0002344","count":7}]},{"hash":"790508389478152741","title":"Mitochondrial Metabolite and Ion Transport","description":"The GO terms cluster around transport of metabolites and ions across the mitochondrial membrane (ATP, manganese, alpha-ketoglutarate, thiamine pyrophosphate, pyrimidines) and related mitochondrial localization and apoptotic changes, including the malate-aspartate shuttle, suggesting a cohesive set of mitochondrial transport/metabolism proteins. Some terms are obsolete, but the overall theme remains mitochondrial transport-related function.","confidence":"High","size":12,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1990544","count":6},{"id":"GO:0006828","count":6},{"id":"GO:0090152","count":6},{"id":"GO:0008637","count":6},{"id":"GO:0060546","count":6}]},{"hash":"1606248362341241386","title":"Lipid Biosynthesis and Membrane Lipid Remodeling","description":"The top GO terms are dominated by lipid-related biosynthetic processes (CDP-diacylglycerol biosynthesis, cardiolipin remodeling, triglyceride biosynthesis, ether lipid biosynthesis, phosphatidylcholine biosynthesis, platelet activating factor biosynthesis, cutin biosynthesis). This points to a shared function in producing and remodeling membrane lipids, with a few outlier terms that are less directly related (e.g., cerebellum morphogenesis, glandular epithelial maturation). Overall, the lipid metabolism theme best explains the cluster.","confidence":"High","size":12,"edges":11,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0021587","count":5},{"id":"GO:0016024","count":4},{"id":"GO:0035965","count":4},{"id":"GO:0019432","count":4},{"id":"GO:0070236","count":4}]},{"hash":"397670322974407412","title":"Unknown","description":"The set of GO terms is highly diverse, spanning antibiotic response, DNA replication, nitric oxide\u2013related signaling and nitrosylation, lipid oxidation, muscle growth regulation, ergosterol biosynthesis, demethylation, and pyrroloquinoline quinone biosynthesis. There is no clear, cohesive biological theme tying these terms together, so a concise, representative label cannot be confidently assigned.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0006271","count":2},{"id":"GO:0098924","count":1},{"id":"GO:0018119","count":1},{"id":"GO:0019395","count":1}]},{"hash":"1888002243545588947","title":"Cytoskeletal dynamics and cell polarity in development","description":"Though the terms span development and cytoskeletal organization, a unifying theme is cytoskeletal remodeling linked to cell polarity and developmental differentiation. Actin filament depolymerization and actomyosin contractile ring localization point to cytoskeletal rearrangements during cell division and shape changes, while gamma-tubulin complex localization to the mitotic spindle pole body and terminal web assembly reflect cytoskeletal scaffolding in division and epithelial structures. Developmental contexts like somatic embryogenesis, microgametogenesis, and R7 cell differentiation suggest these remodeling and polarity processes are invoked across diverse organisms during differentiation. Overall, this cluster seems to capture cytoskeletal dynamics coupled with polarity and development rather than a single coherent signaling pathway.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010262","count":1},{"id":"GO:0055046","count":1},{"id":"GO:0045466","count":1},{"id":"GO:1902405","count":1},{"id":"GO:0061171","count":1}]},{"hash":"1329089043084033101","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0038202","count":2},{"id":"GO:0070262","count":2},{"id":"GO:0051301","count":2}]},{"hash":"2261620042157416159","title":"Stress-responsive transcription and cell cycle regulation","description":"The top terms cluster around transcriptional regulation (negative regulation of transcription by RNA Pol II, chromatin remodeling) and cell-cycle control (regulation of cell cycle, G0 to G1 transition), with stress-related responses (hypoxia, UV-C). Together these suggest transcriptional control mechanisms that modulate the cell cycle under stress. Some development terms appear but seem incidental, so the core theme remains stress- and cell-cycle\u2013related transcription.","confidence":"Medium","size":12,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0061408","count":2},{"id":"GO:0006977","count":1},{"id":"GO:0071157","count":1},{"id":"GO:0071456","count":1}]},{"hash":"301118228162241482","title":"Membrane Transport and Cytoskeleton Regulation","description":"The cluster's dominant GO terms cluster around intracellular trafficking between the ER, Golgi, and plasma membrane (ER-Golgi vesicle transport and Golgi-to-plasma membrane transport) and actin dynamics (barbed-end actin filament capping) with related GTPase signaling. This points to a cohesive theme of vesicle trafficking guided by the cytoskeleton, even though a few terms reflect broader developmental or apoptotic processes that may be incidental. Confidence: Medium","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0060041","count":2},{"id":"GO:0051016","count":2},{"id":"GO:0006446","count":2}]},{"hash":"499831965447891714","title":"Transmembrane Ion and Metabolite Transporters","description":"The top GO terms are dominated by transmembrane transport functions, including ion transport (potassium and sodium) and transport of metabolites such as citrate, succinate, malate, and arsenite. This points to a cohesive group of membrane transporter proteins rather than non-transport roles, despite one outlier term related to cell division.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"transmembrane transport","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:2000185","count":3},{"id":"GO:0055085","count":3},{"id":"GO:0015746","count":3},{"id":"GO:0098656","count":3}]},{"hash":"1073892149772241959","title":"Mitochondrial metabolite and ion transport","description":"The top GO terms cluster around transport across mitochondrial membranes and related metabolic exchange, including ATP transmembrane transport, manganese ion transport, alpha-ketoglutarate and thiamine pyrophosphate transport, and the malate-aspartate shuttle. Several terms touch on mitochondrial localization and apoptotic changes, suggesting a coherent theme of mitochondria-centered substrate transport and energy metabolism. Overall, the proteins likely function as mitochondrial transporters or regulators of mitochondrial metabolite flux.","confidence":"High","size":12,"edges":7,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1990544","count":9},{"id":"GO:0006828","count":9},{"id":"GO:0090152","count":9},{"id":"GO:0008637","count":9},{"id":"GO:0060546","count":9}]},{"hash":"1760594809212613472","title":"Ubiquitin-Mediated Regulation of Development and Signaling","description":"The cluster centers on ubiquitin-dependent protein catabolic processes, ubiquitin recycling, and deubiquitination, suggesting a core role for the ubiquitin-proteasome system in protein turnover. The accompanying terms also touch on development (skeletal muscle differentiation, CNS morphogenesis), transcription regulation, and stress-related signaling (RIPoptosome in necroptosis) with brain-related phenotypes (behavioral response to ethanol). This combination points to a theme where ubiquitin-mediated regulation modulates development and cellular signaling, with connections to proteostasis and cell death pathways.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006511","count":2},{"id":"GO:0035914","count":2},{"id":"GO:0034729","count":1},{"id":"GO:0048149","count":1},{"id":"GO:1901026","count":1}]},{"hash":"1111889057508206592","title":"Ubiquitin-mediated proteolysis and circadian regulation","description":"This cluster is dominated by GO terms for ubiquitin-dependent protein catabolic processes (SCF-dependent) and positive regulation of protein ubiquitination, pointing to proteostasis via the ubiquitin\u2013proteasome system. The presence of circadian rhythm regulation and cell-cycle-related initiation/damage checkpoint terms suggests a cohesive theme where protein turnover modulates cell-cycle and clock-related processes. While a few terms touch on neuronal stress responses, the central thread remains ubiquitin-mediated proteolysis linked to circadian and cell-cycle regulation.","confidence":"Medium","size":12,"edges":12,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":8},{"id":"GO:0042752","count":7},{"id":"GO:1902916","count":7},{"id":"GO:0000083","count":7},{"id":"GO:1903378","count":7}]},{"hash":"1919120127869513965","title":"Proteolysis and peptide processing","description":"This cluster is unified by multiple peptide-centered processing and proteolytic activities: general proteolysis and protein catabolic processes, protein autoprocessing, maturation of peptide hormones like angiotensin, and downstream effects on amyloid-beta metabolism and APP processing. Additionally, antigen processing via MHC II depends on proteolysis, and regulation of peptide-mediated signals (including drinking behavior linked to angiotensin) ties the theme to neuroimmune signaling. Overall, the common thread is protein/peptide processing and metabolism driving signaling and immune functions.","confidence":"High","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0002016","count":3},{"id":"GO:0042985","count":3},{"id":"GO:0016540","count":3},{"id":"GO:0050435","count":3},{"id":"GO:0002803","count":3}]},{"hash":"942483755183284476","title":"Plant meiosis and gametogenesis","description":"These terms cluster around meiotic chromosome events (synaptonemal complex assembly, meiotic recombination, double-strand break repair, telomere clustering, chiasma assembly) and plant reproductive development (pollen and embryo sac development, seed development), suggesting a cohesive role in meiosis followed by gametophyte formation in plants.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007130","count":1},{"id":"GO:0007131","count":1},{"id":"GO:0007141","count":1},{"id":"GO:1990918","count":1},{"id":"GO:0042139","count":1}]},{"hash":"73171421414420768","title":"Skeletal muscle development and sarcomere organization","description":"The cluster is dominated by GO terms related to skeletal muscle biology: skeletal muscle fiber development, skeletal muscle tissue development, and sarcomere organization, all present with multiple proteins. Other terms (positive regulation of GTPase activity, positive regulation of protein serine/threonine kinase activity, ubiquitin-dependent protein catabolic process) suggest muscle signaling and protein turnover, with additional links to hypoxia response and mRNA splicing, but the clear muscle-development/sarcomere theme supports a muscle-structure/function interpretation.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0051260","count":3},{"id":"GO:0042787","count":3},{"id":"GO:0048741","count":3},{"id":"GO:0007519","count":3}]},{"hash":"1778783300423618927","title":"Unknown","description":"The top GO terms cover very diverse processes\u2014from organelle dynamics and protein degradation regulation to stress responses, RNA splicing, translation initiation, and development\u2014showing no single coherent function or pathway that ties all members together. Therefore a specific, representative label cannot be reliably assigned.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016559","count":1},{"id":"GO:0010387","count":1},{"id":"GO:0045471","count":1},{"id":"GO:0000393","count":1},{"id":"GO:0070452","count":1}]},{"hash":"382055299259642772","title":"Rac GTPase signaling regulators","description":"The dominant GO terms point to Rac and small GTPase signaling regulation (negative regulation of Rac signal transduction, positive regulation of GTPase activity, and small GTPase-mediated signal transduction). A few other terms refer to various biosynthetic processes, likely incidental or representing multifunctional annotations, but they do not define the cluster's core function. Therefore, the cluster is best described as Rac GTPase signaling regulators.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035021","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0007264","count":2},{"id":"GO:0019428","count":1},{"id":"GO:0042244","count":1}]},{"hash":"62033064753035468","title":"Cell Cycle and DNA Replication","description":"This cluster is enriched with GO terms centered on DNA replication, cell cycle progression (including G1/S transition and cell division), and kinetochore localization, pointing to a core function in mitosis and genome duplication. Vesicle transport to the ER-Golgi pathway also aligns with general cellular processes supporting cell division. The few outlier terms related to neuronal development or drug response are less representative of the dominant theme.","confidence":"High","size":11,"edges":19,"triangles":14,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0042220","count":5},{"id":"GO:0007049","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0060079","count":4}]},{"hash":"771169703509862452","title":"Developmental gene regulation and differentiation","description":"This cluster is enriched for nuclear processes involved in gene expression (DNA replication, DNA-templated transcription, mRNA processing, imprinting regulation) and for developmental programs (cranial skeleton morphogenesis, CNS neuron axonogenesis, cardiac muscle differentiation, regulation of cell-matrix adhesion). A few outliers (e.g., biofilm formation, meiosis spindle regulation) exist, but the dominant theme is regulation of gene expression guiding development and cell differentiation.","confidence":"Medium","size":11,"edges":54,"triangles":156,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0048701","count":7},{"id":"GO:0006351","count":6},{"id":"GO:0006397","count":6},{"id":"GO:2000727","count":5}]},{"hash":"486455594542459420","title":"Ketone body and acetyl-CoA metabolism","description":"This cluster is dominated by GO terms tied to ketone body catabolic/biosynthetic processes and acetyl-CoA catabolic pathways, plus L-isoleucine catabolism feeding into those energy pathways. The brain, liver, and adipose development terms likely reflect tissue-context associations rather than a single developmental process. Overall, the common theme is energy metabolism centered on ketone bodies and acetyl-CoA, with amino-acid catabolism contributing substrates.","confidence":"Medium","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006550","count":6},{"id":"GO:0007420","count":6},{"id":"GO:0060612","count":6},{"id":"GO:0001889","count":6},{"id":"GO:0046952","count":6}]},{"hash":"2037088459269247332","title":"Mitochondrial Metabolite Transporters","description":"The GO terms point to a set of proteins involved in transmembrane transport of various mitochondrial metabolites (ATP, Mn2+, alpha-ketoglutarate, thymine pyrophosphate, pyrimidine nucleotides) and components of the malate-aspartate shuttle, suggesting a cohesive role as mitochondrial metabolite transporters; the presence of apoptotic mitochondrial changes and necroptosis regulation hints at involvement in mitochondrial stress responses and cell death pathways, strengthening the link between transport and apoptosis in this cluster.","confidence":"Medium","size":11,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1990544","count":2},{"id":"GO:0006828","count":2},{"id":"GO:0090152","count":2},{"id":"GO:0008637","count":2},{"id":"GO:0060546","count":2}]},{"hash":"1707452955506954359","title":"Viral Translation Initiation and Reinitiation","description":"Dominant terms center on translation initiation/reinitiation, preinitiation complex assembly, and IRES-dependent viral translation, with mRNA export also tying into gene expression. Other terms like proteasome assembly, transcription regulation, and stress responses are present but less central.","confidence":"Medium","size":11,"edges":39,"triangles":67,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0075525","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0006406","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0006446","count":2}]},{"hash":"926846682845720354","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0045471","count":2},{"id":"GO:0032355","count":2},{"id":"GO:0001516","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0006296","count":2}]},{"hash":"560577770645034036","title":"Aromatic compound and amino acid catabolism","description":"Top terms are dominated by catabolic processes for aromatic substrates and amino acids (e.g., phenylalanine, tyrosine, 3-phenylpropionate, 4-hydroxyphenylacetate) and by fatty acid beta-oxidation, suggesting a cluster of enzymes involved in degradation and energy-yielding metabolism of aromatics and related substrates. A few terms like menaquinone biosynthesis and an obsolete oxidation-reduction process are peripheral and do not negate the main aromatic/amino acid catabolic signal. Overall, the cluster corresponds to aromatic compound and amino acid catabolism.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0019380","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0009234","count":2},{"id":"GO:0071555","count":2}]},{"hash":"1218375256284649952","title":"Epithelial Polarity and Migration in Organogenesis","description":"The cluster shows enrichment for epithelial cell polarity establishment, actin filament bundle assembly, and cell migration, with organogenesis-related terms such as pancreas and prostate development and morphogenetic movements like gastrulation and convergent extension, indicating a shared role in epithelial organization and cell movement during organ formation.","confidence":"High","size":11,"edges":11,"triangles":1,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0090162","count":2},{"id":"GO:0051017","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0060770","count":1}]},{"hash":"2268466960316607068","title":"Ribosome biogenesis and cell cycle","description":"The top GO terms indicate strong emphasis on ribosome production and function (ribosome biogenesis, cytoplasmic translation, ribosomal subunit export from the nucleus, tRNA modification) together with cell division processes (cell division, cell cycle, cell septum assembly). This points to a cohesive group of proteins coordinating ribosome assembly and translation with progression through the cell cycle. Some stress-response regulation terms appear but do not override the dominant ribosome/translation and division theme.","confidence":"Medium","size":11,"edges":13,"triangles":0,"max_degree":5,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0000055","count":5},{"id":"GO:0007049","count":4},{"id":"GO:1901001","count":4},{"id":"GO:0006400","count":4}]},{"hash":"437777814910590216","title":"Lipid metabolism and ER organization","description":"The cluster shows several GO terms centered on lipid biology and ER-associated processes: galactolipid biosynthesis, fatty acid catabolism, triglyceride biosynthesis, lipid droplet organization, and endoplasmic reticulum organization. These point to lipid remodeling and membrane biogenesis as the core function of the group. Some terms related to nucleus organization and transcription regulation are present but less representative of the main theme, suggesting possible secondary roles or annotation overlap. Overall, the label reflects the lipid metabolism and ER/lipid droplet dynamics.","confidence":"Medium","size":11,"edges":37,"triangles":55,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0045944","count":2},{"id":"GO:0006997","count":2},{"id":"GO:0019375","count":2},{"id":"GO:0034389","count":2},{"id":"GO:0007029","count":2}]},{"hash":"894481073979259319","title":"Ubiquitin-Mediated Circadian Clock Regulation","description":"Most enriched terms point to ubiquitin-dependent proteolysis (ubiquitin-dependent protein catabolic process; SCF-dependent proteasomal ubiquitin-dependent protein catabolic process; positive regulation of protein polyubiquitination) and regulation of circadian rhythm, which together imply circadian clock control by proteasomal degradation. Additional terms touch on DNA replication/cell cycle and neuronal stress responses, which may be secondary connections or pleiotropic effects within the same ubiquitin system.","confidence":"Medium","size":11,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:0031146","count":5},{"id":"GO:0042752","count":4},{"id":"GO:1902916","count":4},{"id":"GO:0000083","count":4}]},{"hash":"193304837489066801","title":"TLR and T cell signaling with raft localization","description":"Based on enriched GO terms, this cluster centers on immune signaling, including positive regulation of toll-like receptor 3 signaling, T cell receptor signaling, and interleukin-2 production, indicating coordinated innate and adaptive immune responses. The term protein localization to membrane raft aligns with signaling platforms at the cell surface, supported by positive regulation of GTPase activity that can drive cytoskeletal and trafficking changes. Some terms like extracellular matrix disassembly and mitochondrial-related processes are less central, but do not outweigh the immune signaling theme.","confidence":"Medium","size":11,"edges":14,"triangles":5,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0022617","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0070584","count":2},{"id":"GO:1903044","count":2},{"id":"GO:0045861","count":2}]},{"hash":"658339456202343893","title":"DNA replication and genome maintenance","description":"The proteins in this cluster show a cohesive signal for DNA replication and repair processes: initiation and elongation of DNA synthesis, RNA-templated DNA biosynthesis, translesion synthesis, UV-damage repair, and telomere maintenance via recombination. While a couple of terms hint at unrelated RNA processing/import concepts, the dominant GO terms point to genome replication and integrity maintenance.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":1},{"id":"GO:0042276","count":1},{"id":"GO:0006279","count":1},{"id":"GO:0000722","count":1},{"id":"GO:0000060","count":1}]},{"hash":"1864349628144675581","title":"Pol III Transcription Regulation","description":"This cluster is dominated by GO terms tied to RNA polymerase III transcription, including TFIIIB complex assembly and negative regulation of Pol III transcription, with a related tRNA locus-associated regulatory term. Other terms (myelination, virus detection, lipid metabolism, ER stress) are present but appear as ancillary annotations; the core signal points to Pol III transcription control.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042552","count":2},{"id":"GO:0061587","count":1},{"id":"GO:0070217","count":1},{"id":"GO:0016480","count":1},{"id":"GO:1902237","count":1}]},{"hash":"2132739801295605003","title":"Actin Cytoskeleton Assembly and Remodeling","description":"The cluster\u2019s GO terms overwhelmingly point to actin dynamics, including positive/negative regulation of stress fiber assembly, mitotic contractile ring actin bundle formation, and actin cortical patch organization, indicating a cohesive set of proteins involved in actin cytoskeleton assembly and remodeling, with a few peripheral terms related to trafficking or signaling.","confidence":"High","size":11,"edges":53,"triangles":147,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0042147","count":2},{"id":"GO:2000678","count":2},{"id":"GO:0035193","count":1},{"id":"GO:0032220","count":1},{"id":"GO:1900028","count":1}]},{"hash":"1633536277741241331","title":"Ribosome Biogenesis and Translation","description":"The highest-frequency terms cluster around ribosome biogenesis and protein synthesis (ribosome biogenesis, small/large subunit biogenesis, cytoplasmic translation, tRNA modification, and ribosomal subunit export). Cell-cycle and cell-division terms align with growth linked to ribosome production. Some stress-response terms are present but not central to the cluster\u2019s primary function.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0042274","count":3},{"id":"GO:0007049","count":3},{"id":"GO:0000747","count":3},{"id":"GO:1901001","count":3}]},{"hash":"1946234444738841354","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":2},{"id":"GO:0006412","count":1},{"id":"GO:0075525","count":1},{"id":"GO:0006396","count":1},{"id":"GO:0006376","count":1}]},{"hash":"625497549594967288","title":"Oxidative phosphorylation","description":"The cluster is dominated by terms tied to proton transmembrane transport, mitochondrial electron transport, and aerobic respiration, suggesting a core theme of energy production via oxidative phosphorylation; other terms like PQQ biosynthesis and viral/symbiont processes appear as outliers or annotation noise but do not override the respiration signal.","confidence":"Medium","size":11,"edges":17,"triangles":7,"max_degree":10,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:1902600","count":6},{"id":"GO:0006122","count":6},{"id":"GO:0009060","count":6},{"id":"GO:0051289","count":5},{"id":"GO:0018189","count":5}]},{"hash":"1294262357115228584","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":2},{"id":"GO:0050853","count":2},{"id":"GO:0046626","count":2},{"id":"GO:0045737","count":2},{"id":"GO:0016554","count":1}]},{"hash":"1258485994956742483","title":"Cytoskeletal remodeling and calcium signaling","description":"This cluster is dominated by terms tied to actin filament assembly and cytoskeletal dynamics (GO:0051017; GO:0030476), cell migration (GO:0090131), and calcium-responsive processes (GO:0051592) including muscle adaptation (GO:0043503) and growth (GO:0009825). While there are some outliers (ascospore wall assembly, substantia nigra development, platelet aggregation) the overarching theme appears to be cytoskeletal remodeling modulated by calcium signaling, influencing development and cellular growth. ","confidence":"Medium","size":10,"edges":40,"triangles":87,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0032508","count":6},{"id":"GO:0090131","count":6},{"id":"GO:0009825","count":6},{"id":"GO:0043503","count":6},{"id":"GO:0051592","count":6}]},{"hash":"889003323692881534","title":"Mitochondrial copper homeostasis and COX assembly","description":"The cluster is dominated by terms tied to copper ion transport and intracellular copper homeostasis, plus a specific link to respiratory chain complex IV (cytochrome c oxidase) assembly. Copper is a key cofactor for COX, so these annotations suggest a shared function in delivering copper for COX assembly and maintaining mitochondrial redox balance (supported by the \u201cremoval of superoxide radicals\u201d term). The presence of a translation term may reflect mitochondrial translation or general annotation noise, and an outlier term about oocyte construction; overall the strongest theme is mitochondrial copper handling and COX assembly.","confidence":"High","size":10,"edges":43,"triangles":105,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0045454","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0019430","count":2},{"id":"GO:0008535","count":2}]},{"hash":"951476012766013193","title":"Oxidative stress response and redox homeostasis","description":"The most frequent GO terms point to redox biology: cellular response to hydrogen peroxide, cellular oxidant detoxification, and cell redox homeostasis, all indicating roles in managing oxidative stress and maintaining redox balance. Some other terms (methylamine metabolism, UTP biosynthesis, regulation of pinocytosis) appear less connected and may reflect multifunctionality or annotation noise, but overall the redox theme dominates.","confidence":"High","size":10,"edges":44,"triangles":112,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0070301","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0030416","count":2},{"id":"GO:2000255","count":2}]},{"hash":"1430241587069902832","title":"Mitotic spindle and microtubule dynamics","description":"Based on the GO terms, the cluster is enriched for microtubule-related processes (cytoplasmic microtubule organization, microtubule nucleation), spindle assembly (mitotic spindle midzone assembly, spindle pole body duplication), and cell cycle/cytokinesis, indicating proteins involved in mitosis and microtubule dynamics. A few terms related to mechanosensation and IL-4 response are present but less central to the core theme. ","confidence":"High","size":10,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071353","count":3},{"id":"GO:2000767","count":2},{"id":"GO:1905792","count":2},{"id":"GO:0051256","count":2},{"id":"GO:0031122","count":2}]},{"hash":"1975775818752881367","title":"Chromatin Regulation and Transcription Control","description":"The GO terms cluster around chromatin dynamics (rDNA heterochromatin formation; chromatin silencing at telomeres), transcriptional activity (DNA-templated transcription), and broader regulation of gene expression and signaling during development (negative regulation of osteoblast differentiation; androgen receptor signaling). This combination points to proteins involved in modulating chromatin state and nuclear transcription, rather than a single metabolic or signaling pathway.","confidence":"Medium","size":10,"edges":29,"triangles":48,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000183","count":5},{"id":"GO:0045668","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0045128","count":4},{"id":"GO:0060766","count":4}]},{"hash":"190475949541526267","title":"Central Carbon Metabolism (Glycolysis and TCA)","description":"Most frequent terms cluster around core energy production pathways: glycolysis and the TCA cycle, with related steps for acetyl-CoA formation and catabolism of carbon sources (amino acids, glycerol). This points to a cohesive theme of central carbon metabolism and energy generation, despite a few outlier terms likely reflecting broader annotations. Confidence in this label is High.","confidence":"","size":10,"edges":18,"triangles":12,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0006096","count":4},{"id":"GO:0006099","count":4},{"id":"GO:0010510","count":3},{"id":"GO:0061732","count":3}]},{"hash":"1099071405974570011","title":"Neurotransmitter Metabolism and Redox Detoxification","description":"The top GO terms point to oxidative detoxification and redox homeostasis alongside neurotransmitter-related processes (dopamine and serotonin metabolism/catabolism), with ancillary signals like LPS response and development. This suggests a cluster centered on redox-balanced neurotransmitter turnover, particularly dopamine pathways, making this a concise, specific label that captures the main function without overgeneralizing.","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":4},{"id":"GO:0045454","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0042135","count":3},{"id":"GO:0042420","count":3}]},{"hash":"1202747576877777805","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0071374","count":3},{"id":"GO:1901621","count":3},{"id":"GO:0001707","count":3},{"id":"GO:0006260","count":3}]},{"hash":"966407008288848526","title":"Calcium signaling in EMT and tissue remodeling","description":"The top GO terms cluster around calcium signaling (detection of calcium ion; ryanodine receptor\u2013mediated Ca2+ release; calcineurin-NFAT signaling) and processes linked to tissue remodeling and differentiation, such as epithelial\u2013mesenchymal transition, connective tissue remodeling, and cardiac hypertrophy. This suggests a motif of calcium-dependent signaling guiding EMT and remodeling across epithelial and cardiac contexts, with related differentiation processes in lung and neural development. Some terms are developmentally broad or outlier, but the core theme is Ca2+-mediated signaling in remodeling and differentiation.","confidence":"Medium","size":10,"edges":17,"triangles":9,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0051343","count":2},{"id":"GO:0060316","count":2},{"id":"GO:0001837","count":2},{"id":"GO:1903244","count":2},{"id":"GO:1903799","count":2}]},{"hash":"1316026460760278206","title":"GTPase-Driven Cytoskeletal Remodeling and Trafficking","description":"This cluster centers on GTPase-regulated actin dynamics (positive regulation of GTPase activity, barbed-end capping, depolymerization) and COPII vesicle cargo loading, indicating coordinated cytoskeletal remodeling and early secretory trafficking driven by GTPase signaling. Additional terms referencing TGF-beta signaling and cell-cycle regulation suggest integration of growth signals with the cytoskeleton and trafficking program.","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0071560","count":2},{"id":"GO:0050731","count":2},{"id":"GO:0051016","count":2},{"id":"GO:0090110","count":2}]},{"hash":"440104901978030668","title":"Chromosome segregation and spindle checkpoint proteins","description":"The top GO terms cluster around sister chromatid cohesion, biorientation, and establishing protein localization to chromosomes, along with mitotic spindle orientation checkpoint signaling and septin ring organization, all highlighting chromosome segregation and mitotic/spindle machinery. While a few terms (like P granule assembly and neurotrophin signaling) are less central, the dominant theme is chromosome maintenance and cell division processes.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051754","count":5},{"id":"GO:1903863","count":3},{"id":"GO:0051388","count":3},{"id":"GO:0090005","count":3},{"id":"GO:0031134","count":3}]},{"hash":"952723862113707114","title":"Unknown","description":"The top terms span unrelated processes (iron-sulfur assembly, chromatid cohesion/separation, apoptosis signaling, mRNA transport, nuclear import, kinase regulation, ciliogenesis, TORC1). No single shared function ties the cluster, so a coherent label cannot be inferred.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016226","count":2},{"id":"GO:0051754","count":2},{"id":"GO:2001241","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0000060","count":2}]},{"hash":"1967322299208930272","title":"mRNA processing and translational control","description":"This cluster centers on RNA maturation and export (splicing, poly(A)+ mRNA export) and on regulation of translation (initiation, reinitiation, and miRNA-mediated silencing). A couple of terms (e.g., DNA repair) appear less connected and may reflect annotation noise, but the dominant signal ties to RNA processing and control of gene expression at the translational level.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:1990414","count":2},{"id":"GO:0075525","count":1},{"id":"GO:0006376","count":1},{"id":"GO:0002188","count":1}]},{"hash":"882216130438656909","title":"DNA Damage Response and Ubiquitination","description":"This cluster centers on cellular stress responses tied to DNA damage sensing and programmed cell death, reinforced by ubiquitin-mediated regulation (K11-linked ubiquitination and ligase activity) and signals between mitochondria and the nucleus. While terms like brain development and cardiac muscle cell apoptosis appear, the dominant theme links DNA damage checkpoints with controlled protein turnover and apoptotic regulation, justifying a DNA damage/ubiquitination label.","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0072432","count":2},{"id":"GO:0030042","count":2},{"id":"GO:0010659","count":2},{"id":"GO:0006349","count":2},{"id":"GO:1904668","count":2}]},{"hash":"1625522252271989023","title":"DNA Damage Response and Ubiquitin Signaling","description":"The top GO terms point to DNA damage checkpoint signaling (G1), mitochondrial-nucleus communication, and regulation of apoptotic DNA fragmentation, along with ubiquitin-mediated processes (K11-linked ubiquitination and ligase activity). Other terms touch on cytoskeletal dynamics and development, plus translation reinitiation, suggesting a broader stress-response and protein-turnover theme rather than a single precise function. This supports a label around DNA damage response, apoptosis regulation, and ubiquitin signaling as the cohesive theme, albeit with some terms reflecting additional developmental or cellular processes.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072432","count":1},{"id":"GO:0030042","count":1},{"id":"GO:0010659","count":1},{"id":"GO:0006349","count":1},{"id":"GO:1904668","count":1}]},{"hash":"327029057841636543","title":"Carbohydrate and Energy Metabolism","description":"This cluster is dominated by central carbon metabolism terms: glycolytic process, tricarboxylic acid cycle, gluconeogenesis, and 2-oxoglutarate metabolism, indicating a core role in energy production and carbon flux. Additional GO terms point to lipid biosynthesis (malonyl-CoA) and amino acid catabolism (leucine), which feed into energy pathways. The presence of a nucleotide metabolism term and a stress-related term (cellular response to sucrose starvation) suggests coordinated metabolic and energy-status signaling. Taken together, these proteins likely participate in metabolic pathways that generate and balance cellular energy from carbohydrates and amino acids. ","confidence":"High","size":10,"edges":41,"triangles":92,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":8},{"id":"GO:0006103","count":6},{"id":"GO:0006096","count":6},{"id":"GO:0000002","count":5},{"id":"GO:0006094","count":5}]},{"hash":"55934271601009892","title":"Sebaceous gland lipid metabolism","description":"The cluster shows GO terms focused on sebaceous/tarsal gland differentiation and multiple lipid biosynthesis processes (monounsaturated fatty acid biosynthesis, sphingosine biosynthesis, cholesterol esterification), suggesting a theme of skin-gland lipid production and barrier formation. While some terms are unrelated noise, the strongest signals point to sebaceous gland function and lipid metabolism.","confidence":"Medium","size":10,"edges":9,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0001949","count":1},{"id":"GO:1903699","count":1},{"id":"GO:0010205","count":1},{"id":"GO:0033561","count":1},{"id":"GO:0006675","count":1}]},{"hash":"1797514716396625113","title":"Neuronal development and synaptic regulation","description":"These proteins show a bias toward neural development and synaptic function, with terms like long-term synaptic potentiation and CNS projection neuron axonogenesis, plus regulation of cell-matrix adhesion that can influence neuronal connectivity. The presence of broader developmental terms (mesoderm formation, cardiac differentiation) alongside some non-neural terms suggests a cluster enriched for neural development signals but not exclusively limited to neurons.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060291","count":5},{"id":"GO:0001707","count":4},{"id":"GO:2000727","count":3},{"id":"GO:0001952","count":3},{"id":"GO:0006349","count":3}]},{"hash":"651948515563211715","title":"Fungal cytokinesis and cell wall remodeling","description":"This cluster centers on division-related processes: division septum site selection, actomyosin contractile ring contraction, and cell wall organization, pointing to cytokinesis and septum formation typical of fungi/yeast. Additional terms touch on vacuole fusion and autophagy regulation but do not override the core theme of cell division and wall remodeling.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034217","count":1},{"id":"GO:0071555","count":1},{"id":"GO:0000920","count":1},{"id":"GO:0000918","count":1},{"id":"GO:0000916","count":1}]},{"hash":"1289901754581530737","title":"Olfactory and neuronal development","description":"The enrichment highlights nose development, olfactory pit development, and neuron differentiation, with retinoic acid receptor signaling underpinning developmental patterning in sensory and neural lineages. While other terms touch on unrelated processes (UPR, DNA replication, osmolyte metabolism), the strongest cohesive theme is sensory-neural developmental programs.","confidence":"Medium","size":9,"edges":10,"triangles":5,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006986","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0060487","count":4},{"id":"GO:0030182","count":4},{"id":"GO:0048384","count":4}]},{"hash":"1342310044980145692","title":"Metabolic and stress-response signaling","description":"The terms cluster around cellular signaling in response to energy/nutrient cues (insulin/glucose/ATP/cAMP) and stress (hypoxia, epinephrine), with downstream transcriptional regulation and programmed cell death, plus a developmental hint from seed maturation. This suggests a theme of energy/metabolism-linked stress signaling rather than a single specialized process, giving a cohesive, though broad, functional label.","confidence":"Medium","size":9,"edges":31,"triangles":53,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032869","count":4},{"id":"GO:0001666","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0033198","count":3},{"id":"GO:0012501","count":3}]},{"hash":"2021191403459886993","title":"Folate-Mediated One-Carbon Metabolism","description":"This cluster is enriched for GO terms centered on folate metabolism and one-carbon transfer: tetrahydrofolate biosynthesis, one-carbon metabolic process, dTMP and glycine biosynthesis, and methotrexate response; these indicate involvement in the folate cycle and nucleotide biosynthesis pathways (thymidylate and amino acid biosynthesis). A few terms about redox regulation and axon regeneration appear, but they are likely secondary to the core folate/one-carbon metabolism theme.","confidence":"High","size":9,"edges":32,"triangles":62,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0046654","count":2},{"id":"GO:0031427","count":2},{"id":"GO:0032259","count":2},{"id":"GO:0006545","count":2},{"id":"GO:2000121","count":2}]},{"hash":"848772199175777824","title":"TGF-\u03b2 and NF-\u03baB signaling regulation","description":"Based on the GO terms, the cluster centers on regulation of signaling pathways, especially TGF-\u03b2/SMAD signaling (positive/negative regulation of TGF-\u03b2 receptor signaling, cellular response to TGF-\u03b2, SMAD-related assembly) and non-canonical NF-\u03baB signaling, with supporting evidence from peptidyl-threonine dephosphorylation. While a few terms appear unrelated (e.g., vacuole fusion, photosystem adjustments, germ-line masculinization), the dominant theme is modulation of signaling cascades, justifying a focused label on transcriptional and signaling regulation.","confidence":"Medium","size":9,"edges":33,"triangles":64,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":5},{"id":"GO:0061191","count":4},{"id":"GO:0030512","count":4},{"id":"GO:0000173","count":4},{"id":"GO:0071560","count":4}]},{"hash":"2026009453394797321","title":"Biosynthesis and Chromatin Regulation","description":"The cluster includes multiple biosynthetic processes (thiamine biosynthesis, L-glutamate biosynthesis, hormone biosynthesis) together with epigenetic regulation signals (positive regulation of chromatin binding, negative regulation of histone methylation). This suggests proteins involved in both metabolic biosynthesis and modulation of gene expression via chromatin, giving a label that captures both themes rather than a single narrow function. Some terms are obsolete, but the overall pattern points to intertwined metabolism and chromatin regulation.","confidence":"Medium","size":9,"edges":34,"triangles":71,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0009228","count":7},{"id":"GO:0043046","count":7},{"id":"GO:0055114","count":7},{"id":"GO:0051572","count":6},{"id":"GO:2000179","count":6}]},{"hash":"1459718401376846690","title":"Adhesion and Cytoskeleton-Driven Cell Migration","description":"The dominant terms point to desmosome assembly, actin cytoskeleton regulation by cell-cell adhesion, and cortical microtubule localization, all of which connect adhesion to cytoskeletal dynamics driving cell migration. Additional neural development terms (cranial ganglion development, dorsal identity) fit within this framework as migration and tissue organization during development rely on adhesion\u2013cytoskeleton interplay. Overall, a coherent theme centers on adhesion-modulated cytoskeleton remodeling facilitating cell movement and tissue patterning.","confidence":"Medium","size":9,"edges":25,"triangles":36,"max_degree":8,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0015991","count":6},{"id":"GO:0006355","count":4},{"id":"GO:0090138","count":4},{"id":"GO:0030997","count":4},{"id":"GO:0072699","count":4}]},{"hash":"1389738118866224467","title":"Fungal cell wall synthesis and mating","description":"The standout terms are fungal-specific: beta-glucan biosynthesis for the cell wall and karyogamy involved in cellular fusion, suggesting a fungal-focused theme in this cluster. Other terms are more general cellular processes, but the fungal signals are distinct enough to justify a fungal cell wall/mating label, with some residual non-fungal annotations. ","confidence":"Medium","size":9,"edges":10,"triangles":5,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0031204","count":5},{"id":"GO:1903751","count":5},{"id":"GO:0000742","count":5},{"id":"GO:0006880","count":5}]},{"hash":"1900674671867090370","title":"Fungal mating and cell wall biosynthesis","description":"The cluster is anchored by fungal-specific processes: karyogamy involved in conjugation with cellular fusion and fungal-type cell wall beta-glucan biosynthetic process, which point to mating/conjugation and cell wall construction in fungi. Other terms like DNA replication and iron-sulfur cluster assembly suggest general cellular maintenance, but the explicit fungal terms provide a coherent fungal-focused theme for this cluster.","confidence":"Medium","size":9,"edges":32,"triangles":60,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0031204","count":3},{"id":"GO:1903751","count":3},{"id":"GO:0000742","count":3},{"id":"GO:0006880","count":3}]},{"hash":"1299821123370542475","title":"Unknown","description":"The Top Terms are highly diverse, including chromosome segregation, photoreception, chemotaxis, ethylene signaling, protein folding, DNA replication, xenobiotic/cocaine response, and protein autophosphorylation. There is no single coherent theme linking these functions, so a concise, meaningful label cannot be assigned.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein folding","top_go_terms":[{"id":"GO:0007059","count":4},{"id":"GO:0009584","count":4},{"id":"GO:0006935","count":4},{"id":"GO:0010105","count":4},{"id":"GO:0006457","count":4}]},{"hash":"1242297142692605029","title":"Endocytosis and vesicle recycling in muscle cells","description":"The main enriched GO terms cluster around pinocytosis and endocytic recycling, including regulation of myoblast fusion and voltage-gated calcium channel activity in muscle contexts, suggesting a focus on vesicle trafficking in muscle cell function. Additional terms for Golgi organization, ribosome biogenesis, and cell cycle likely reflect general cellular maintenance rather than defining the cluster\u2019s core function. Confidence reflects this partial alignment with a coherent endocytic/membrane trafficking theme in muscle.","confidence":"Medium","size":9,"edges":2,"triangles":0,"max_degree":1,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006907","count":4},{"id":"GO:0086036","count":4},{"id":"GO:0032456","count":4},{"id":"GO:1901741","count":4},{"id":"GO:1901387","count":4}]},{"hash":"1301448926082532700","title":"Flavonoid biosynthesis and glycosylation","description":"Most terms describe enzymatic steps in producing and modifying flavonoids and anthocyanins (kaempferol/quercetin/cyanidin glycosides, anthocyanin-containing compounds) and related glycosylation/detoxification processes, with a broader link to lignin/phenylpropanoid metabolism. This cohesive theme supports labeling the cluster as flavonoid biosynthesis and glycosylation.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071412","count":3},{"id":"GO:0052696","count":3},{"id":"GO:0033330","count":3},{"id":"GO:0052697","count":3},{"id":"GO:0033303","count":3}]},{"hash":"672675740033228376","title":"Cardiac muscle regulation and ion transport","description":"These terms converge on cardiomyocyte function: regulation of cardiac hypertrophy and contraction, T-tubule organization essential for excitation-contraction coupling, and ion transport/membrane potential maintenance (K+, copper transport, electrochemical gradient). The overall theme is heart muscle regulation and ion homeostasis, justifying this label.","confidence":"High","size":9,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:1903243","count":6},{"id":"GO:0033292","count":6},{"id":"GO:0098736","count":6},{"id":"GO:0010107","count":6},{"id":"GO:0006825","count":6}]},{"hash":"234203691832970370","title":"Translation machinery and RNA Pol III transcription","description":"The cluster centers on ribosome-related processes (translation, initiation, ribosome biogenesis, ribosome disassembly) and on transcription by RNA polymerase III (promoter initiation, tRNA transcription, and Pol III transcription regulation), suggesting a cohesive theme around the assembly and control of the translation apparatus and its RNA components. The combination of core translation terms with Pol III\u2013driven transcription terms supports a linked function in ribosome/translation machinery and its transcriptional regulation.","confidence":"High","size":9,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006384","count":1}]},{"hash":"2032107201211573532","title":"Mitochondrial Transport and Metabolic Shuttles","description":"Top terms center on transport across the mitochondrial membrane and exchange of metabolites (e.g., alpha-ketoglutarate, malate-aspartate shuttle, thiamine pyrophosphate, pyrimidine nucleotides), with additional signals for mitochondrial membrane remodeling and apoptosis regulation. This suggests a cohesive role in coordinating mitochondrial transport, metabolism, and related cell death pathways.","confidence":"High","size":9,"edges":19,"triangles":8,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1990544","count":6},{"id":"GO:0006828","count":6},{"id":"GO:0090152","count":6},{"id":"GO:0008637","count":6},{"id":"GO:0060546","count":6}]},{"hash":"239053401262518322","title":"Plant hormone signaling and defense responses","description":"The terms point to plant-specific signaling and responses, including hormone-related pathways (gibberellin, ethylene/ACC) and defense cues (salicylic acid, chitin, antifungal response), alongside development and differentiation processes (atrichoblast, sclerenchyma). This suggests proteins coordinating growth with immune responses and tissue development in plants.","confidence":"High","size":9,"edges":9,"triangles":3,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0009751","count":1},{"id":"GO:0080169","count":1},{"id":"GO:1905034","count":1},{"id":"GO:0009938","count":1},{"id":"GO:0010055","count":1}]},{"hash":"573886406159292455","title":"Cardiac muscle stress signaling and apoptosis","description":"This cluster is anchored by terms related to cardiac muscle function, notably ventricular cardiac muscle cell action potential, and cardiac muscle cell apoptotic processes, along with an intrinsic apoptotic signaling pathway in response to ER stress. Additional GO terms point to stress-responsive signaling (cAMP, DNA damage checkpoint) and cytoskeletal remodeling (actin depolymerization), suggesting a broader cellular stress response that prominently includes cardiac muscle signaling and apoptosis. While there are outliers related to development, the strongest and most cohesive theme centers on cardiac muscle stress signaling and programmed cell death.","confidence":"Medium","size":9,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0070059","count":2},{"id":"GO:0043588","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0086005","count":2},{"id":"GO:0071320","count":2}]},{"hash":"860776858075389255","title":"Epigenetic Transcription Regulation","description":"The dominant GO terms point to histone modifications (H3K9/K27 marks, histone acetylation) and regulation of transcription by RNA polymerase II, indicating epigenetic control of gene expression; a few developmental or organogenesis terms appear as outliers, but the core signal centers on epigenetic transcription regulation.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036123","count":1},{"id":"GO:0036091","count":1},{"id":"GO:0045038","count":1},{"id":"GO:0098532","count":1},{"id":"GO:0048752","count":1}]},{"hash":"4010663971817664","title":"Translation Machinery Linked to DNA Damage Response","description":"Dominated by translation-related terms (translation, ribosome biogenesis, regulation of translation) with some links to DNA damage response and radiation response, suggesting these proteins are mainly ribosomal/translation factors that also participate in stress response signaling (p53-mediated pathways).","confidence":"Medium","size":9,"edges":33,"triangles":66,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0042254","count":2},{"id":"GO:1902164","count":2},{"id":"GO:0006977","count":2},{"id":"GO:0071480","count":2}]},{"hash":"1065393012063718258","title":"Transcription Regulation & Chromatin Modification","description":"The cluster\u2019s top GO terms cluster around transcription control and chromatin state\u2014DNA-templated transcription, positive regulation of transcription elongation by RNA polymerase II, and histone modifications (deacetylation, acetylation, and H3K4 methylation). These point to a shared function in regulating gene expression via chromatin remodeling and transcription machinery, with some related translation initiation and DNA repair/hypoxia terms likely reflecting broader nuclear regulatory roles. Confidence: Medium","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006349","count":3},{"id":"GO:0016575","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0043984","count":3},{"id":"GO:0032968","count":3}]},{"hash":"738098101466548877","title":"Neuronal signaling and sensory perception","description":"The cluster is dominated by terms linked to brain function and neuronal activity: synaptic plasticity (long-term depression), mechanosensory detection (pain and touch), membrane hyperpolarization, and potassium ion export, plus globus pallidus development. While a couple of terms pertain to general cellular processes (ribosome biogenesis, DNA repair), the convergence on brain-specific signaling and sensory pathways suggests a neuronal signaling/sensory perception theme. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042273","count":2},{"id":"GO:0045910","count":1},{"id":"GO:0006298","count":1},{"id":"GO:0071435","count":1},{"id":"GO:0021759","count":1}]},{"hash":"1784487465175165682","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016554","count":3},{"id":"GO:0031426","count":3},{"id":"GO:1905639","count":3},{"id":"GO:0031425","count":3},{"id":"GO:0001682","count":3}]},{"hash":"1874927267632053941","title":"Mitotic Cell Cycle and Nuclear Organization","description":"This cluster\u2019s top GO terms cluster around nucleus organization, mitotic chromosome condensation and alignment, and the broader cell cycle, pointing to proteins involved in mitotic chromosome dynamics and cell-cycle progression. Other terms about ubiquitin-mediated and -independent degradation via MVB pathways and Golgi retention suggest regulatory turnover linked to mitosis, but the dominant theme remains mitosis/cell-cycle control.","confidence":"High","size":9,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006997","count":2},{"id":"GO:0007076","count":1},{"id":"GO:1902188","count":1},{"id":"GO:0090611","count":1},{"id":"GO:0000920","count":1}]},{"hash":"1741651012445243650","title":"Developmental Signaling and Apoptosis","description":"This cluster mixes terms tied to development (heart development), neuronal signaling and survival (neurotrophin signaling, neuron apoptotic process), transcription, and signal transduction (TGF-beta response, GTPase regulation), suggesting a broadly developmental and cell fate\u2013related theme rather than a single specific function.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000920","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0071560","count":2}]},{"hash":"2099092036534098973","title":"Glycan and glycolipid biosynthesis","description":"This cluster's top GO terms point to carbohydrate-related biosynthesis, including glycogen, glycolipid, and GPI-anchor biosynthesis, plus bacillithiol biosynthesis, with some sugar-response terms. The shared theme is assembly/modification of glycan- and lipid-containing molecules, suggesting a coherent carbohydrate biosynthesis cluster.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0005978","count":3},{"id":"GO:0001780","count":2},{"id":"GO:0009744","count":2},{"id":"GO:0009247","count":2},{"id":"GO:0071793","count":2}]},{"hash":"499633002895012353","title":"Vacuolar amino acid transport","description":"The top GO terms are all about transmembrane transport of amino acids into or out of the vacuole (serine, lysine, glutamate, arginine, proline, asparagine, etc.), with one term for lithium ion transport, suggesting a set of vacuolar membrane transporters focused on amino acid flux; root cap development is a less central annotation but does not override the clear transport theme.","confidence":"High","size":9,"edges":12,"triangles":3,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0090516","count":6},{"id":"GO:0089707","count":6},{"id":"GO:0090452","count":6},{"id":"GO:0090515","count":6},{"id":"GO:0090517","count":6}]},{"hash":"431850247763866993","title":"RNAP II Transcription Regulation","description":"The top GO terms are centered on DNA-templated transcription and positive regulation of transcription from RNA polymerase II promoters, across various metabolic and environmental contexts (nitrogen/carbon source cues, pyrimidine biosynthesis), indicating the proteins function mainly as transcriptional regulators rather than metabolic enzymes. Some unrelated terms (e.g., copper stress, cardiac fate) may reflect annotation noise, but the dominant pattern points to transcriptional regulation by RNAP II as the cluster\u2019s unifying theme.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0035959","count":1},{"id":"GO:0001080","count":1},{"id":"GO:2001158","count":1},{"id":"GO:1901717","count":1}]},{"hash":"268958579430709597","title":"Developmental and Neural Signaling","description":"Reasoning: The cluster is enriched for developmental processes (angiogenesis, heart development, multicellular organism development) as well as neural signaling and plasticity (excitatory postsynaptic potential, long-term potentiation, visual perception). This combination suggests proteins involved in embryonic development with roles in neural differentiation and synaptic signaling; the presence of mitotic cell cycle terms may reflect shared regulatory modules or pleiotropy.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0010800","count":3},{"id":"GO:0060079","count":3},{"id":"GO:0007601","count":3}]},{"hash":"632819610511299367","title":"Head and sensory organ development","description":"The top GO terms point to development and patterning of head sensory structures\u2014nose and olfactory pit, embryonic eye development\u2014and associated vasculature, suggesting a cohesive theme of head sensory organ formation. Some unrelated metabolic terms appear but do not override the dominant developmental signal, supporting this label as representative of the cluster\u2019s function.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0048384","count":7},{"id":"GO:0019285","count":7},{"id":"GO:0051591","count":7},{"id":"GO:0060166","count":7},{"id":"GO:0043584","count":7}]},{"hash":"1120508155035896930","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":19,"triangles":19,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0000740","count":2},{"id":"GO:0036494","count":2},{"id":"GO:0006924","count":2},{"id":"GO:0090084","count":2}]},{"hash":"646305355188982833","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0046020","count":3},{"id":"GO:0001892","count":2},{"id":"GO:0048096","count":2},{"id":"GO:0007492","count":2},{"id":"GO:0003007","count":2}]},{"hash":"2231608083784162782","title":"RNA processing and methylation","description":"These proteins group around RNA maturation and RNA modification activities: mRNA polyadenylation and pre-mRNA cleavage, snoRNA splicing, and tRNA methylation. Additional entries reference peptide methylation, reflecting broader post-translational modification roles. While there are a couple of unrelated terms (antibiotic biosynthesis, xenobiotic response), the dominant signals point to RNA processing and modification as the cluster's shared theme.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0043029","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0098789","count":2},{"id":"GO:0034247","count":2}]},{"hash":"1945839508356645575","title":"Cytoskeleton and Membrane Organization","description":"The strongest shared themes among the GO terms are actin cytoskeleton organization and caveola assembly, indicating roles in cytoskeletal dynamics and membrane organization. Other terms span immune signaling and translation that are less clearly connected, so this label remains a cautious, general characterization of the cluster's functions.","confidence":"Low","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001878","count":1},{"id":"GO:0045953","count":1},{"id":"GO:0090162","count":1},{"id":"GO:0016191","count":1},{"id":"GO:0031139","count":1}]},{"hash":"2008329160272756655","title":"Ribosome Biogenesis and RNA Pseudouridylation","description":"This cluster is dominated by translation-related terms and RNA modification activities, especially pseudouridine synthesis on rRNA, tRNA, and snRNA, along with ribosome biogenesis and maturation of SSU rRNA. The convergence on assembling ribosomes and modifying RNAs needed for accurate translation explains the cluster\u2019s theme, with a plausible link to the antibiotic response through ribosome-targeted mechanisms.","confidence":"High","size":8,"edges":22,"triangles":35,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0031120","count":2},{"id":"GO:0031118","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0046677","count":2}]},{"hash":"5633807712877449","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006295","count":2},{"id":"GO:0035753","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0045893","count":1},{"id":"GO:0007283","count":1}]},{"hash":"1677731009140447865","title":"Cross-species developmental morphogenesis","description":"The top GO terms cluster around development and morphogenesis across diverse tissues and lineages (heart valve, flower, primordial streak, endochondral ossification, glomerulus), with an additional note on transcriptional/epigenetic regulation (trichostatin A response). While the specific processes span plants and animals, the common theme is morphogenesis and organ formation during development, rather than a single pathway or function.","confidence":"Medium","size":8,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0003185","count":1},{"id":"GO:0010582","count":1},{"id":"GO:0009908","count":1},{"id":"GO:0001197","count":1},{"id":"GO:0090009","count":1}]},{"hash":"213889232235708235","title":"RNA Processing and Translational Regulation","description":"This cluster centers on RNA metabolism and regulation of gene expression, with splicing and mRNA export terms alongside ncRNA- and miRNA-mediated silencing and translation initiation/reinitiation terms, indicating coordinated RNA processing and translation control.","confidence":"High","size":8,"edges":15,"triangles":8,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":4},{"id":"GO:0048026","count":4},{"id":"GO:0006376","count":4},{"id":"GO:0075525","count":3},{"id":"GO:0002188","count":3}]},{"hash":"143278050851141586","title":"ER folding and vacuolar acidification","description":"This cluster includes GO terms for protein folding in the endoplasmic reticulum and processes related to vacuolar/lysosomal function (vacuolar acidification, V-type ATPase assembly) as well as endosome transport, suggesting a partial theme around ER protein quality control and vesicular/lysosomal trafficking. Other terms (nucleosome assembly, histone acetylation regulation, microtubule polymerization) appear present but less cohesive with the core vesicle/ER theme, making the overall linkage modest.","confidence":"Low","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034975","count":2},{"id":"GO:0045022","count":1},{"id":"GO:1901546","count":1},{"id":"GO:0070072","count":1},{"id":"GO:0007035","count":1}]},{"hash":"110084719316370349","title":"Spliceosome-dependent mRNA processing and translation regulation","description":"Dominant terms are about mRNA splicing via the spliceosome, including regulation of alternative splicing and splice-site recognition, which points to core spliceosome components or splicing regulators. The presence of translation reinitiation, miRNA-mediated silencing, and mRNA export terms suggests these proteins also participate in broader post-transcriptional regulation, linking splicing to downstream translation control. ","confidence":"High","size":8,"edges":12,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":3},{"id":"GO:0048025","count":3},{"id":"GO:0000381","count":3},{"id":"GO:0075525","count":2},{"id":"GO:0006376","count":2}]},{"hash":"2280102266585143992","title":"Ubiquitin-Dependent Signaling and Apoptosis","description":"This cluster is dominated by terms tied to ubiquitination (protein autoubiquitination; K6- and K48-linked ubiquitination) and apoptosis regulation, with TNF-mediated signaling and links to receptor turnover (Wnt receptor catabolic process) suggesting a broader role in ubiquitin-driven signaling and cell survival. Some terms appear unrelated (dosage compensation; intracellular transport of viral material), likely annotation noise, but the central theme remains ubiquitin-mediated control of signaling and apoptosis.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901253","count":3},{"id":"GO:0033209","count":3},{"id":"GO:1900095","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0038018","count":3}]},{"hash":"513004844568726837","title":"Regulated Translation Initiation and Stress Response","description":"The cluster emphasizes regulation of translation initiation (GO:0006446, GO:0002183) alongside various stress-related responses (cellular response to nitric oxide, ethylene stimulus) and mitochondrial fission, suggesting a theme of coordinating protein synthesis with cellular stress and dynamics. There is also an occasional signal related to oligodendrocyte development, but the dominant signals are translation control and stress response.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006446","count":3},{"id":"GO:0071732","count":2},{"id":"GO:0014003","count":2},{"id":"GO:0002183","count":2},{"id":"GO:1903833","count":2}]},{"hash":"149079826206152028","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":8,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0071321","count":2},{"id":"GO:0007608","count":2},{"id":"GO:0010754","count":2},{"id":"GO:0009086","count":1}]},{"hash":"1564835823866067156","title":"SnoRNP assembly and ribosome biogenesis","description":"These proteins show strong signals for RNA processing and RNP assembly, especially snoRNP- and snoRNA-guided pseudouridylation, box H/ACA snoRNP assembly, snRNA pseudouridine synthesis, and ribosome biogenesis, plus telomerase RNA handling in Cajal bodies. A few other terms (xylan catabolic process, iron response) are minor by comparison, reinforcing the RNA-processing theme.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0045493","count":2},{"id":"GO:0031120","count":1},{"id":"GO:1905323","count":1},{"id":"GO:0000493","count":1}]},{"hash":"2017193122460123917","title":"Cell cycle and cytokinesis regulators","description":"The Top Terms include cell cycle (GO:0007049) and regulation of cytokinesis (GO:0032465), with an additional term for regulation of protein localization to the nucleus (GO:1900180), pointing to proteins involved in controlling cell division and related nuclear processes. Other terms (e.g., protein folding, PPIase activity) are minor or orthogonal, but do not override the central theme of cell cycle and cytokinesis regulation.","confidence":"High","size":8,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0060274","count":1},{"id":"GO:0080182","count":1},{"id":"GO:0007049","count":1},{"id":"GO:0043525","count":1},{"id":"GO:0000413","count":1}]},{"hash":"1675503250404673683","title":"Developmental signaling and transcription","description":"Top terms point to growth and development signaling (multicellular organism development; insulin receptor signaling pathway) and gene expression control (DNA-templated transcription). A few items are obsolete or broad (rRNA maturation, imprinting, ERAD), which may reflect annotations that are less informative. Overall, the cluster seems to connect developmental signaling with transcriptional regulation, justifying this label.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0043966","count":2},{"id":"GO:0008286","count":2},{"id":"GO:0035948","count":2},{"id":"GO:0006349","count":2}]},{"hash":"1541135120517826205","title":"Unknown","description":"The terms are scattered across very different processes (TNF signaling, autoubiquitination, iron homeostasis, septin ring assembly, Wnt receptor catabolism, plant stomatal morphogenesis, dosage compensation), with no shared pathway or function linking the proteins, and the network shows no edges. Therefore no coherent label can be assigned beyond Unknown.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010513","count":1},{"id":"GO:1901253","count":1},{"id":"GO:0033209","count":1},{"id":"GO:1900095","count":1},{"id":"GO:0051865","count":1}]},{"hash":"599281234232661924","title":"Golgi-dependent protein trafficking and glycosylation","description":"These proteins cluster around the secretory pathway, with GO terms emphasizing Golgi-to-plasma membrane transport, retrograde Golgi-ER transport, Golgi ribbon formation, and N- and O-linked glycosylation. The inclusion of exocytosis regulation and leukocyte adhesion-related processes reinforces a theme of Golgi-mediated vesicle trafficking and glycoprotein maturation in immune contexts. Confidence: High.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045956","count":1},{"id":"GO:0015031","count":1},{"id":"GO:0050715","count":1},{"id":"GO:0045806","count":1},{"id":"GO:0050901","count":1}]},{"hash":"162156555599953932","title":"Fungal sterol and lipid biosynthesis","description":"The top GO terms are dominated by lipid metabolism and sterol biosynthesis in fungi, including regulation of ergosterol biosynthetic process, unsaturated fatty acid biosynthetic process, and sphingolipid (MIPC) metabolism, which together point to a cluster of proteins involved in fungal lipid and sterol biosynthesis. Some terms (e.g., CNS myelin maintenance, sebaceous gland differentiation) appear unrelated and may reflect annotation noise, while nitrate/nitric oxide terms are peripheral. Overall, the core theme is fungal lipid metabolism with supporting sterol regulation.","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0032286","count":3},{"id":"GO:0001949","count":3},{"id":"GO:0000001","count":3},{"id":"GO:0042128","count":3}]},{"hash":"168879032456426286","title":"Golgi Vesicle Trafficking and SNARE Assembly","description":"The GO terms highlight Golgi ribbon formation, vesicle fusion with the Golgi, ER-to-Golgi and intra-Golgi transport, and SNARE complex assembly, indicating a cohesive function in vesicle trafficking and membrane fusion at Golgi-related compartments. The inclusion of synaptic vesicle docking and exocytic receptor insertion suggests that this trafficking machinery also supports neurotransmitter release and postsynaptic membrane remodeling. Overall, the cluster appears driven by SNARE-mediated vesicle trafficking through Golgi and related secretory pathways; a minor term (cornified envelope assembly) is less connected but does not dominate.","confidence":"High","size":8,"edges":19,"triangles":20,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0090161","count":7},{"id":"GO:0048280","count":7},{"id":"GO:0006888","count":7},{"id":"GO:0006891","count":7},{"id":"GO:0035493","count":6}]},{"hash":"24611772553078708","title":"Protein modification and folding regulation","description":"The cluster centers on processes that modulate protein maturation and turnover, including heterooligomerization, negative regulation of protein modification, ubiquitination (K11-linked), and peptidyl-prolyl isomerization, with a stress-related signal (cellular response to hydrogen peroxide) also present. Some terms (plant hormone signaling and sex development) appear species- or context-specific and introduce noise, but the dominant pattern links regulation of protein processing, modification, and folding. ","confidence":"Low","size":8,"edges":4,"triangles":0,"max_degree":4,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0051291","count":4},{"id":"GO:0031400","count":3},{"id":"GO:0035955","count":3},{"id":"GO:0070301","count":3},{"id":"GO:0009938","count":3}]},{"hash":"856100325836969721","title":"Carbohydrate Catabolism","description":"Most top GO terms describe catabolic processes for various sugars (arabinose, xylose, glucose-related pathways, glycerol, fucose, glucuronate) and related phosphorylation steps, indicating a cluster centered on carbohydrate metabolism. The presence of quorum sensing hints at potential microbial community regulation of metabolism, while terms like regulation of mRNA stability and cellular response to interleukin-13 are less central to the core theme. Overall, the proteins are best viewed as participants in sugar degradation/utilization pathways.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":3},{"id":"GO:0043488","count":2},{"id":"GO:0019569","count":2},{"id":"GO:0019563","count":2},{"id":"GO:0042732","count":2}]},{"hash":"1860447734483097437","title":"Membrane trafficking and Notch-related proteolysis","description":"The Top Terms center on intracellular transport between ER, Golgi, and endosomes, i.e., protein transport and vesicle trafficking, plus proteolysis of membrane proteins (ectodomain and ICD). The notable inclusion of Notch signaling and pharynx development hints at developmental membrane signaling tied to proteolytic processing. A concise label that ties trafficking with membrane proteolysis, especially in the context of Notch, fits best.","confidence":"Medium","size":8,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":1},{"id":"GO:0015031","count":1},{"id":"GO:0042147","count":1},{"id":"GO:0035786","count":1},{"id":"GO:0015986","count":1}]},{"hash":"1957012550349677541","title":"Embryonic development and patterning (retinoic acid signaling)","description":"The top GO terms center on retinoic acid receptor signaling and various organogenesis processes (nose/olfactory development, eye development, blood vessel development) as well as proximal/distal pattern formation, suggesting a cohesive theme of embryonic morphogenesis guided by RA signaling. Some terms appear unrelated (metabolic/bio-synthesis processes) and may reflect noise, but the developmental cluster signal remains dominant.","confidence":"Medium","size":7,"edges":8,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0048384","count":2},{"id":"GO:0019285","count":2},{"id":"GO:0051591","count":2},{"id":"GO:0060166","count":2},{"id":"GO:0043584","count":2}]},{"hash":"582546494637975999","title":"Ribosome biogenesis and translation","description":"The cluster is dominated by GO terms related to ribosomal small subunit assembly and translation, suggesting a core theme of protein synthesis. Although there are additional signals for protein modification (deglycosylation), DNA repair, and some stress/neuronal signaling, these are less represented, making ribosome biogenesis and translation the most representative and specific common function for this group.","confidence":"Medium","size":7,"edges":6,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006517","count":2},{"id":"GO:0000028","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0097238","count":1}]},{"hash":"936763115165200567","title":"Viral replication and virion assembly","description":"The top GO terms cluster around steps of the viral life cycle\u2014host-mediated activation of viral genome replication, virion assembly, membrane fusion for entry, uncoating, and viral release\u2014with supporting terms for protein folding and processing that aid viral protein maturation. While a couple of terms like sepal formation may be unrelated, the dominant pattern points to proteins involved in viral replication, assembly, and release.","confidence":"High","size":7,"edges":3,"triangles":0,"max_degree":2,"top_function":"protein folding","top_go_terms":[{"id":"GO:0050714","count":5},{"id":"GO:0044829","count":5},{"id":"GO:0000413","count":5},{"id":"GO:0019068","count":5},{"id":"GO:0006457","count":5}]},{"hash":"843235581123437133","title":"RNA Pol II Transcription and Chromatin Regulation","description":"This cluster is enriched for transcription by RNA polymerase II and regulators of DNA replication initiation, plus histone methylation-related terms, pointing to a core theme of transcriptional control and chromatin state. Some terms (e.g., vascular wound healing, cobalamin biosynthesis) seem peripheral or artifact but do not override the main signal of transcriptional/chromatin regulation.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":2},{"id":"GO:0035470","count":2},{"id":"GO:0090055","count":2},{"id":"GO:0090419","count":2},{"id":"GO:1903468","count":2}]},{"hash":"2003973960825433798","title":"RNA splicing and translation regulation cluster","description":"The terms cluster around RNA processing (splicing, export, polyadenylation) and control of translation (initiation/reinitiation, miRNA/ncRNA-mediated silencing), suggesting proteins that coordinate RNA maturation with translation. This points to a functional group specialized in RNA processing and translational control.","confidence":"Medium","size":7,"edges":19,"triangles":26,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":7},{"id":"GO:0048026","count":7},{"id":"GO:0075525","count":5},{"id":"GO:0006376","count":5},{"id":"GO:0002188","count":5}]},{"hash":"2274941174846591259","title":"NER and UV protection","description":"The proteins are largely associated with nucleotide-excision repair (NER), including transcription-coupled NER, DNA incision and unwinding steps, and overall NER activity, plus UV protection. While a few terms touch on development or signaling, the strongest signal is DNA-damage repair and UV response, pointing to a repair/defense role rather than developmental programming.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000717","count":5},{"id":"GO:0048568","count":5},{"id":"GO:0009650","count":5},{"id":"GO:0035315","count":5},{"id":"GO:0001666","count":5}]},{"hash":"2004978691377994106","title":"Flavonoid and lignin biosynthesis","description":"The top GO terms point to synthesis of flavonoids (anthocyanins, kaempferol/quercetin glucosides, cyanidin glucoside) and also include lignin metabolism, suggesting a shared theme of plant phenylpropanoid-derived secondary metabolite biosynthesis.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009718","count":3},{"id":"GO:0071412","count":2},{"id":"GO:0052696","count":2},{"id":"GO:0033330","count":2},{"id":"GO:0052697","count":2}]},{"hash":"1660530484137210390","title":"Transmembrane transport of small molecules","description":"This cluster is enriched for GO terms describing transport across the plasma membrane for diverse small molecules (vitamins, sugars, ions, nitrite, organic anions, selenite, etc.). The shared theme is membrane transport rather than a single substrate or pathway, implying these proteins are transporters or transporter-associated. The variety of substrates supports a general label for small-molecule transmembrane transport rather than a substrate-specific class.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":2},{"id":"GO:1904728","count":2},{"id":"GO:0042891","count":2},{"id":"GO:0043252","count":2},{"id":"GO:0097080","count":2}]},{"hash":"1017876926619018223","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034476","count":1},{"id":"GO:0071033","count":1},{"id":"GO:1901917","count":1},{"id":"GO:0071039","count":1},{"id":"GO:0071035","count":1}]},{"hash":"2115458743065054505","title":"Ubiquitin-Dependent Degradation & T Cell Signaling","description":"This cluster is dominated by GO terms for ubiquitin-dependent proteolysis (ERAD pathway, polyubiquitination) and protein turnover, with overlapping immune signaling terms (T cell proliferation, TNF signaling). The common thread appears to be ubiquitin-mediated proteostasis connected to T cell\u2013related signaling pathways, suggesting a group of ubiquitination/ERAD-related proteins that also influence immune signaling.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0030433","count":6},{"id":"GO:0042787","count":6},{"id":"GO:0097039","count":4},{"id":"GO:0042098","count":4},{"id":"GO:0033209","count":4}]},{"hash":"2125239812797892367","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0005975","count":2},{"id":"GO:0048666","count":2},{"id":"GO:0032094","count":2},{"id":"GO:0006207","count":2},{"id":"GO:0042594","count":2}]},{"hash":"1116382413841380969","title":"Developmental Signaling and Tissue Differentiation","description":"The GO terms show development-related processes across multiple tissues (heart, cerebral cortex, visual system, fat cells) and signaling regulation (GPCR desensitization, peptidyl-threonine phosphorylation). This points to a theme of developmental programs coupled with modulation of signaling pathways, rather than a single tissue-specific function, indicating a broad but coherent developmental and signaling-related cluster.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048240","count":3},{"id":"GO:0007601","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0021987","count":3},{"id":"GO:0010614","count":3}]},{"hash":"210248248384493169","title":"Activated sugar-nucleotide biosynthesis","description":"The GO terms point mainly to the synthesis of activated sugar donors (UDP-xylose, UDP-arabinose, UDP-galactose, dTDP-rhamnose) and related sugar metabolism, with supporting references to SAM biosynthesis and other biosynthetic pathways. This suggests the proteins cluster around production of activated sugars and their immediate metabolic context, despite some broader/metabolic outliers.","confidence":"High","size":7,"edges":7,"triangles":2,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0006556","count":4},{"id":"GO:0017000","count":3},{"id":"GO:0033320","count":3},{"id":"GO:0033358","count":3}]},{"hash":"1326097967911765060","title":"Mitotic spindle assembly and microtubule dynamics","description":"This cluster is dominated by GO terms tied to mitosis and spindle/microtubule functions (e.g., cytokinesis, metaphase chromosome alignment, centrosome separation, microtubule polarity, plus/minus-end sliding, spindle midzone assembly, and spindle pole separation). These themes collectively point to microtubule-based spindle organization and chromosome segregation. A couple terms (karyogamy, ureteric bud invasion) are less related but do not override the main pattern.","confidence":"High","size":7,"edges":15,"triangles":14,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000911","count":7},{"id":"GO:0007080","count":7},{"id":"GO:0007100","count":7},{"id":"GO:0030951","count":7},{"id":"GO:0031534","count":7}]},{"hash":"496022004817190453","title":"Mitochondrial energy metabolism and stress response","description":"These GO terms point to mitochondria-centered functions: energy production (ATP synthesis, respiratory chain complex IV assembly), and related quality-control and stress pathways (mitophagy regulation, apoptotic signaling with phosphatidylserine exposure, and lipid/cholesterol homeostasis). The translation term may reflect mitochondrial protein synthesis, while the lipopolysaccharide response suggests mitochondria-associated inflammatory signaling. Overall, the cluster appears to represent mitochondrial energy metabolism intertwined with stress and apoptosis pathways.","confidence":"High","size":7,"edges":16,"triangles":16,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0001300","count":1},{"id":"GO:0060368","count":1},{"id":"GO:1903147","count":1},{"id":"GO:0071222","count":1}]},{"hash":"2072536706225225869","title":"Unknown","description":"The GO terms span diverse areas (renin-angiotensin regulation, amyloid-beta metabolism, digestion, antigen processing, and general proteolysis) with no clear shared function or pathway tying the proteins together, so a cohesive label is not evident.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002016","count":1},{"id":"GO:0042985","count":1},{"id":"GO:0002018","count":1},{"id":"GO:0050435","count":1},{"id":"GO:0002803","count":1}]},{"hash":"1191973998294525091","title":"Phytochrome-Driven Light Signaling and Flowering","description":"The top GO terms cluster around red/far-red light perception and phototransduction, plus positive regulation of flower development, pointing to phytochrome-mediated light signaling controlling flowering in plants; JA signaling suggests defense cross-talk, but the core theme remains light-regulated flowering. ","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010218","count":1},{"id":"GO:0009585","count":1},{"id":"GO:0010114","count":1},{"id":"GO:0009867","count":1},{"id":"GO:0071158","count":1}]},{"hash":"2162292983144389243","title":"Translational control and mRNA processing","description":"The proteins appear linked to translation initiation and reinitiation (formation of the preinitiation complex, eIF4F assembly), as well as mRNA processing/export and miRNA-mediated translational silencing, indicating a cohesive role in coordinating translation with mRNA maturation and stability. This suggests the cluster represents general translational control coupled with mRNA metabolism rather than a single specific step.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0075525","count":2},{"id":"GO:0006376","count":2},{"id":"GO:0002188","count":2},{"id":"GO:1905663","count":2}]},{"hash":"159106251980870363","title":"Neural development and cell-adhesion regulation","description":"The cluster shows enrichment for terms connecting neural connectivity and cell-surface interactions: axonogenesis and synapse assembly point to neural development, while regulation of cell-matrix adhesion and integrin-mediated adhesion indicate control of cell adhesion interfaces. Additional phosphorylation regulation supports signaling modulation. Some outliers exist (e.g., biofilm formation, meiotic kinetochore regulation), but the dominant theme fits developmental signaling guiding adhesion and neural connectivity.","confidence":"Medium","size":7,"edges":7,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000727","count":4},{"id":"GO:0001952","count":4},{"id":"GO:0006349","count":4},{"id":"GO:0021952","count":4},{"id":"GO:0090606","count":4}]},{"hash":"2142988615906507322","title":"Chromatin remodeling and transcription regulation","description":"Selected GO terms point to chromatin state control and transcriptional regulation, including regulation of DNA-templated transcription, chromatin remodeling, and histone methylation (H3K4 and H3K79). These features define epigenetic regulation of gene expression. A few spliceosome-related terms and ubiquitin-dependent protein catabolic process appear but are less dominant, suggesting some multifunctionality or co-purified processes; however the core theme remains chromatin-based transcription control.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0034729","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0051568","count":2},{"id":"GO:0006338","count":1}]},{"hash":"1620833724748786834","title":"T cell immune signaling and ER protein retention","description":"The top GO terms cluster around T cell\u2013related immune functions (cytokine production, apoptotic processes) and ER-associated protein handling (protein retention in the ER lumen, protein transport), with a supporting innate immune signaling term. This suggests a theme of T cell\u2013mediated immune signaling coupled to ER protein processing, while a few non-immune terms may reflect noise. ","confidence":"High","size":7,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0002369","count":2},{"id":"GO:0006621","count":2},{"id":"GO:0070231","count":2},{"id":"GO:0010204","count":2},{"id":"GO:0015031","count":2}]},{"hash":"1097586974069653021","title":"Actin dynamics and COPII vesicle trafficking","description":"Top GO terms point to cytoskeletal remodeling and secretory pathway activity, with actin depolymerization and Arp2/3-mediated nucleation suggesting dynamic actin rearrangements, and COPII-coated vesicle budding indicating ER-to-Golgi transport. Additional terms for cell division, transcription, and ER-stress\u2013triggered apoptosis imply broader roles in proliferation and stress responses. Overall, the cluster seems best described by actin dynamics linked to vesicle trafficking.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0030042","count":3},{"id":"GO:0006349","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0031145","count":3}]},{"hash":"1747794817084992315","title":"ER trafficking and calcium-regulated apoptosis","description":"This cluster centers on endoplasmic reticulum\u2013related processes:ER-to-Golgi transport, ER exit site localization, and retrograde transport from ER to cytosol, plus regulation of ER and mitochondrial calcium. The presence of intrinsic apoptotic signaling suggests a link between ER stress, calcium handling, and apoptosis, justifying a label focused on ER trafficking with calcium-regulated apoptosis.","confidence":"High","size":7,"edges":11,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0001649","count":1},{"id":"GO:1903071","count":1},{"id":"GO:0032471","count":1},{"id":"GO:0035584","count":1},{"id":"GO:1904154","count":1}]},{"hash":"1354462017784170210","title":"Glycosylated cell wall protein biosynthesis","description":"This cluster centers on glycosylation pathways (N- and O-linked), glycoprotein maturation, and cell-wall\u2013associated proteins such as mannoproteins and arabinogalactan proteins. The GO terms point to synthesis/modification of glycosylated cell wall proteins involved in adhesion and cell-wall integrity across plant and fungal contexts, with some plant-specific processes (mucilage and AGP metabolism) also present. Overall, a cohesive theme of glycosylated cell wall protein production and processing.","confidence":"High","size":7,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0043710","count":1},{"id":"GO:0000032","count":1},{"id":"GO:0006487","count":1},{"id":"GO:0006493","count":1},{"id":"GO:0044845","count":1}]},{"hash":"1133312603811114852","title":"Lymphocyte Activation and Apoptosis Regulation","description":"The Top Terms point to immune cell processes: T and B cell activation/differentiation, IL-4 production, and apoptosis (AICD and execution phase), indicating a cluster centered on lymphocyte activation and regulated cell death. While there are related metabolic signaling terms (insulin/IGF pathways and fatty acid oxidation) and JNK modulation, they seem to support rather than define the core immune theme.","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006924","count":2},{"id":"GO:0032633","count":2},{"id":"GO:0046329","count":2},{"id":"GO:2001275","count":2},{"id":"GO:0008286","count":2}]},{"hash":"266395502391943559","title":"Skeletal muscle signaling and calcium regulation","description":"Based on the top GO terms, this cluster centers on skeletal muscle functions such as regulation of muscle relaxation, satellite cell activation for skeletal muscle regeneration, and calcium release from the sarcoplasmic reticulum, suggesting roles in calcium-dependent muscle signaling and maintenance/regeneration. Additional terms related to phosphorylation, ubiquitination, and cytoskeletal/neuronal signaling hint at broader regulatory interactions that accompany muscle physiology. Overall, the theme points to calcium-mediated signaling in skeletal muscle and its regenerative processes rather than a single isolated pathway.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1901077","count":6},{"id":"GO:0010595","count":6},{"id":"GO:1902896","count":6},{"id":"GO:0014808","count":6},{"id":"GO:0007205","count":6}]},{"hash":"1076296395418307602","title":"Unknown","description":"The top terms span many unrelated processes (transcription termination, apoptosis signaling, cytokinesis localization, isoprenoid biosynthesis, T cell homeostasis, lipid A biosynthesis, excitatory synaptic activity, and mitochondrial DNA repair), with no clear common function or pathway linking them. This suggests no cohesive theme for a single label.","confidence":"","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030846","count":6},{"id":"GO:2001241","count":6},{"id":"GO:1901901","count":6},{"id":"GO:1900486","count":6},{"id":"GO:0043029","count":6}]},{"hash":"1807534475207717303","title":"Developmental Differentiation Signaling","description":"This cluster centers on development-related processes, including embryonic cranial skeleton morphogenesis, neural axonogenesis, and cardiac muscle differentiation, along with related regulation of cell-matrix adhesion and signaling via phosphorylation. While a DNA replication term is present, the predominant signals point to developmental growth and cell differentiation and their regulation, suggesting a cohesive theme of developmental processes rather than a single specific function.","confidence":"Medium","size":6,"edges":11,"triangles":8,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0048701","count":6},{"id":"GO:2000727","count":3},{"id":"GO:0001952","count":3},{"id":"GO:0006349","count":3}]},{"hash":"722005105873144423","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":11,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0070365","count":1},{"id":"GO:0044210","count":1},{"id":"GO:0006207","count":1},{"id":"GO:0045471","count":1},{"id":"GO:0032868","count":1}]},{"hash":"2235103533667671770","title":"Cell Cycle and Telomere Regulation","description":"The prominent terms center on cell cycle, cell division, and telomere-related processes (including localization to telomeres and telomerase activity regulation), suggesting a core theme of cell cycle progression and telomere maintenance. A few immune signaling terms (e.g., IL-6 production, B cell cytokine production) and other items appear as less central or incidental, likely reflecting annotation noise or multi-function proteins. Overall, the dominant signal is cell cycle/telomere dynamics.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0033198","count":6},{"id":"GO:0002368","count":6},{"id":"GO:0007049","count":6},{"id":"GO:0051973","count":6},{"id":"GO:2000778","count":6}]},{"hash":"754821805335050685","title":"Chromatin remodeling and DNA repair","description":"The GO terms cluster around chromatin state regulation (pericentric heterochromatin formation, histone H3-K9 acetylation regulation, H2B ubiquitination), transcription-related processes (RNA polymerase II termination, RNA-protein covalent cross-linking, post-transcriptional gene silencing), and genome maintenance (double-strand break repair via SDSA, meiotic gene conversion). This suggests a cohesive theme of chromatin dynamics coupled to DNA repair and transcription control, possibly in meiotic or stress-related contexts. Confidence: High.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001666","count":3},{"id":"GO:0070417","count":2},{"id":"GO:0031508","count":2},{"id":"GO:2000616","count":2},{"id":"GO:0016441","count":2}]},{"hash":"806865615486320656","title":"RNA Processing and Spliceosome Assembly","description":"The dominant GO terms center on RNA maturation and processing, including mRNA splicing via the spliceosome, snRNP assembly, and processing of tRNA and rRNA, with supporting processes like nuclear import and P-body assembly. This pattern indicates a cluster enriched for RNA processing machinery and spliceosome components rather than unrelated functions.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":6},{"id":"GO:0008033","count":5},{"id":"GO:0008334","count":5},{"id":"GO:0030490","count":5},{"id":"GO:0000387","count":5}]},{"hash":"568103319669443112","title":"Viral replication and virion assembly","description":"The top GO terms cluster around stages of the viral life cycle: virion assembly, viral release from host cell, fusion of viral membranes with host, and RNA-templated DNA biosynthesis, with host-mediated activation of viral genome replication and chaperone-related protein folding suggesting support for viral protein production. While a couple of terms appear unrelated (e.g., sepal formation), the dominant signal points to virus replication and assembly processes. Confidence: Medium","confidence":"","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"protein folding","top_go_terms":[{"id":"GO:1901407","count":5},{"id":"GO:0050714","count":4},{"id":"GO:0044829","count":4},{"id":"GO:0000413","count":4},{"id":"GO:0019068","count":4}]},{"hash":"1938649054073595718","title":"RNA splicing and transcription regulation","description":"These proteins cluster around RNA-level gene expression control: regulatory ncRNA-mediated gene silencing, mRNA splicing via the spliceosome and its positive regulation, and transcription initiation/termination by RNA Pol II, with additional post-transcriptional silencing signals. While a few terms relate to DNA recombination or chromatin (e.g., histone acetylation) or stress responses (cold), the dominant theme ties to RNA processing and transcriptional regulation, justifying the label. ","confidence":"Medium","size":6,"edges":13,"triangles":13,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0006367","count":2},{"id":"GO:0070417","count":1}]},{"hash":"813581930724967182","title":"Unknown","description":"The GO terms span several unrelated biosynthetic and metabolic processes (sphinganine, protoporphyrinogen IX, aspartate, oxaloacetate, lysine pathways, alanine catabolism), plus a defense signaling term and transcription, with no clear shared function. The minimal connectivity (one edge, max degree 1) and presence of obsolete terms suggest no cohesive cluster function, so a specific label isn\u2019t supported.","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009862","count":2},{"id":"GO:0046511","count":2},{"id":"GO:0006782","count":2},{"id":"GO:0097053","count":2},{"id":"GO:0006532","count":2}]},{"hash":"364675792663796788","title":"Ubiquitin-dependent protein degradation","description":"The top GO terms cluster around ubiquitination and proteolytic pathways (e.g., ubiquitin-dependent protein catabolic process, autoubiquitination, ERAD), indicating a cohesive function in ubiquitin-mediated proteolysis.","confidence":"High","size":6,"edges":6,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0051865","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0009190","count":2},{"id":"GO:0090055","count":2}]},{"hash":"34891653874595162","title":"Nucleotide-sugar Biosynthesis","description":"This cluster\u2019s top GO terms center on the biosynthesis of nucleotide-activated sugars, including UDP-xylose, UDP-arabinose, UDP-galactose, dTDP-rhamnose, and ADP-glycero-manno-heptose, along with galactose metabolic processes. Although a few terms are obsolete, the prevailing theme is carbohydrate-activation/nucleotide-sugar production and related galactose metabolism, suggesting a coherent role in glycan precursor biosynthesis. Confidence: High","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0033320","count":1},{"id":"GO:0033358","count":1},{"id":"GO:0033499","count":1},{"id":"GO:0097171","count":1}]},{"hash":"2177035952095894775","title":"Plant defense signaling and metabolism","description":"The terms include systemic acquired resistance via salicylic acid signaling, alongside diverse biosynthetic and metabolic processes (amino acids, porphyrin, sphinganine) and DNA-templated transcription, suggesting a module that links plant defense signaling with core metabolism. However, the connections are not tightly cohesive across all terms, so the label is best described as a defense/metabolism cluster with moderate confidence.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0009862","count":1},{"id":"GO:0046511","count":1},{"id":"GO:0006782","count":1},{"id":"GO:0097053","count":1}]},{"hash":"930759230368373344","title":"Plastid ribosome biogenesis and translation","description":"The top terms center on translation and preribosome/large subunit maturation, indicating a ribosome biogenesis and protein synthesis theme. The photosynthesis-related term suggests plastid/chloroplast localization, aligning ribosome biogenesis and translation with chloroplast context. Some iron-sulfur cluster assembly terms may reflect Fe-S\u2013dependent maturation steps that connect to ribosome-related processes, and the antibiotic/cycloheximide responses reinforce a connection to translation regulation/inhibition. Taken together, the cluster most plausibly represents plastid ribosome biogenesis and translation.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0016226","count":1},{"id":"GO:0097428","count":1},{"id":"GO:0090070","count":1},{"id":"GO:1902626","count":1}]},{"hash":"1110253699422858281","title":"Small-molecule biosynthesis and catabolism","description":"Based on the GO terms, the proteins are linked to multiple metabolic pathways involving amino acid derivatives and related compounds (beta-alanine, ornithine/lysine pathways, putrescine, GABA, porphyrinogen/heme/chlorophyll biosynthesis, ectoine), suggesting a general theme of small-molecule metabolism rather than a single, cohesive pathway. The lone stress-response term (response to flooding) appears incidental. Thus, a broad label of small-molecule biosynthesis and catabolism best fits the cluster.","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019483","count":1},{"id":"GO:0006593","count":1},{"id":"GO:0009447","count":1},{"id":"GO:0009450","count":1},{"id":"GO:0009413","count":1}]},{"hash":"2139476201605653185","title":"Nucleocytoplasmic mRNA and ribosome export","description":"The top GO terms cluster around export from the nucleus: mRNA export and ribosomal subunit export (GO:0006406, GO:0000055, GO:0000056) and general mRNA transport (GO:0051028), with supporting Ran signaling (GO:0031291). This strongly points to a function in nucleocytoplasmic transport of RNA and ribosomal components rather than cytoplasmic processes.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":4},{"id":"GO:0000055","count":4},{"id":"GO:0000122","count":3},{"id":"GO:0042176","count":2},{"id":"GO:0031291","count":2}]},{"hash":"933128042783684750","title":"Cytoplasmic Translation and Ribosome Biogenesis","description":"The top GO terms are dominated by translation, cytoplasmic translation, and ribosome biogenesis (including ribosomal large subunit biogenesis) with SRP-dependent targeting to membranes, all pointing to the core machinery and assembly of the protein-synthesis apparatus in the cytoplasm. A TOR signaling and translational fidelity term further support a role in regulation of translation, indicating this cluster centers on translation and ribosome biogenesis rather than unrelated processes; the apoptosis and T cell proliferation terms are likely ancillary or context-related. Therefore, this label captures the primary function of the cluster.","confidence":"High","size":6,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0042254","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0006614","count":1}]},{"hash":"1317506797389699950","title":"Unknown","description":"The GO terms span transcription, imprinting regulation, cell cycle, development, stress responses, cytoskeleton dynamics, immune defense, and more, with no obvious single function tying the six proteins together. There are no edges among them, suggesting no cohesive pathway or process to label this cluster beyond Unknown.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006349","count":3},{"id":"GO:0001403","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0070059","count":3}]},{"hash":"740105734272591207","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0006378","count":3},{"id":"GO:0001731","count":3}]},{"hash":"362254867715765434","title":"Unknown","description":"The top GO terms are highly diverse, including histone acetylation, telomere maintenance, transcription of snRNA, various plant developmental and stress responses, viral processes, and neural development concepts. With no clear shared function or pathway across the six proteins and zero edges, there isn\u2019t a coherent biological theme to name a specific cluster; thus Unknown is the appropriate label.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043969","count":1},{"id":"GO:0061820","count":1},{"id":"GO:0018076","count":1},{"id":"GO:0009301","count":1},{"id":"GO:1905615","count":1}]},{"hash":"776860578823217177","title":"Root hair cell wall biosynthesis","description":"The proteins here are tied to plant-specific processes, notably root hair development and cell wall construction. Terms like root hair cell development, cell wall organization, and RG-II biosynthetic process point to a cohesive theme of building and modifying the plant cell wall during root hair formation. Some other terms are obsolete or broad, but the dominant signal supports a plant cell wall biosynthesis role during root hair growth.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071931","count":1},{"id":"GO:0080147","count":1},{"id":"GO:0010306","count":1},{"id":"GO:0071555","count":1},{"id":"GO:0051096","count":1}]},{"hash":"444463199055522649","title":"Mitochondrial Translation and tRNA Charging","description":"The Top Terms cluster around mitochondrial tRNA aminoacylation (lysyl-, asparaginyl-, aspartyl-, lysyl-tRNA charging) and translation (GO:0006412). This points to a cohesive set of proteins involved in mitochondrial protein synthesis, despite some obsolete or broad terms present. The strongest signal is mitochondrial translation machinery, which justifies naming the cluster after this function; some non-specific terms may reflect annotation noise. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0072581","count":1},{"id":"GO:0070145","count":1},{"id":"GO:0070146","count":1},{"id":"GO:0071915","count":1}]},{"hash":"291108472326980186","title":"Developmental differentiation and cytoskeletal dynamics","description":"This cluster includes terms for spermatogenesis, neurogenesis, wing disc development, and sperm individualization, all clearly linked to development and differentiation. The presence of actin filament bundle assembly and spindle orientation points to cytoskeletal remodeling during development, while transcription and autophagy reflect broader cellular remodeling processes that accompany differentiation. Together, they suggest proteins involved in developmental regulation with cytoskeletal and cellular remodeling, rather than a single narrow function.","confidence":"Medium","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007283","count":1},{"id":"GO:1904801","count":1},{"id":"GO:0022008","count":1},{"id":"GO:0007291","count":1},{"id":"GO:0051017","count":1}]},{"hash":"1561929053485470189","title":"Regulated vesicle trafficking and secretion","description":"The cluster centers on vesicle transport and secretory processes: endosome to melanosome transport, regulation of COPII vesicle coating, protein localization to phagophore assembly site, and regulation of mast cell degranulation. While there are some development-related terms, the dominant pattern is controlled trafficking and secretion pathways that coordinate cargo delivery and signaling.","confidence":"Medium","size":6,"edges":13,"triangles":13,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060999","count":6},{"id":"GO:0060684","count":6},{"id":"GO:0035646","count":6},{"id":"GO:0001822","count":6},{"id":"GO:0010629","count":6}]},{"hash":"422229944539239002","title":"Signaling and Translation Regulation","description":"Based on the top GO terms, the proteins cluster around regulatory processes: positive regulation of GTPase activity (signaling), regulation of translational initiation, phosphorylation (a common regulatory modification), and modulation of ubiquitin ligase activity. Although some terms are obsolete or less directly connected, the prevailing themes point to control of signaling networks, protein synthesis, and protein turnover rather than a single concrete pathway. The lack of direct interactions in this cluster suggests these proteins may participate in multiple regulatory processes across different contexts.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0019284","count":2},{"id":"GO:0019509","count":2},{"id":"GO:0016310","count":2}]},{"hash":"1289182782361840601","title":"RNA and protein methyltransferases","description":"The top GO terms are dominated by methylation activities, including N-terminal peptidyl-glycine methylation, rRNA methylation, and peptidyl-lysine methylations, suggesting the proteins function primarily as methyltransferases acting on RNA and proteins; other biosynthetic terms are present but less central. ","confidence":"High","size":6,"edges":7,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0018013","count":2},{"id":"GO:0031167","count":2},{"id":"GO:0018027","count":2},{"id":"GO:0015937","count":2},{"id":"GO:0000183","count":1}]},{"hash":"530469891372897264","title":"Unknown","description":"The top GO terms span transcription termination, apoptotic signaling, cytokinesis localization, isoprenoid biosynthesis, T cell homeostasis, lipid A biosynthesis, neuronal signaling, and mitochondrial DNA repair, a broad and disparate mix with no single unifying function. This suggests there isn\u2019t a cohesive theme tying the proteins together, so an Unknown label is appropriate.","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030846","count":5},{"id":"GO:2001241","count":5},{"id":"GO:1901901","count":5},{"id":"GO:1900486","count":5},{"id":"GO:0043029","count":5}]},{"hash":"2084358753674959643","title":"DNA replication and repair","description":"The cluster is dominated by GO terms tied to genome maintenance, including DNA replication, DNA biosynthetic process, and double-strand break repair involved in meiotic recombination, as well as translesion synthesis. These collectively suggest a core function in maintaining replication fidelity and DNA integrity. Some terms (ER-Golgi transport, mitochondrial complex assembly) appear peripheral to this core theme, contributing less to the primary label. Confidence: Medium.","confidence":"","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0006888","count":3},{"id":"GO:0071897","count":3},{"id":"GO:0051260","count":3},{"id":"GO:1990918","count":2}]},{"hash":"615861101339182482","title":"RNA Splicing and Translation Regulation","description":"This cluster centers on mRNA processing and control of translation: splicing via the spliceosome and splice-site recognition, mRNA export and stability under stress, translation reinitiation and preinitiation complex formation, and miRNA-mediated translation inhibition. The combination of spliceosome-related terms with translation initiation/reinitiation and mRNA export suggests a cohesive group coordinating post-transcriptional gene expression.","confidence":"Medium","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010610","count":3},{"id":"GO:0045292","count":3},{"id":"GO:0075525","count":2},{"id":"GO:0006376","count":2},{"id":"GO:0002188","count":2}]},{"hash":"252215592016296242","title":"Unknown","description":"The top GO terms are scattered across signaling pathways (TGF-beta/SMAD, NF-kappaB), general processes (DNA replication), chaperone-assisted refolding, vesicle fusion regulation, and even photosystem adjustments, with several terms marked obsolete. There is no single cohesive function that clearly ties these proteins together, so a precise, representative label cannot be assigned.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070389","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0061191","count":2},{"id":"GO:0030512","count":2},{"id":"GO:0000173","count":2}]},{"hash":"328869622409863179","title":"Cardiac contractility regulation and T-tubule organization","description":"The cluster is dominated by GO terms linked to heart muscle function\u2014negative regulation of cardiac hypertrophy under stress, regulation of the force of heart contraction, and striated muscle contraction\u2014along with structural and electrophysiological components like T-tubule organization, potassium ion transport, and maintenance of transmembrane electrochemical gradients. These collectively point to a module governing excitation-contraction coupling and cardiac electrophysiology; a few terms (e.g., stilbene catabolic process) appear less relevant but do not override the central cardiac theme.","confidence":"High","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1903243","count":3},{"id":"GO:0033292","count":3},{"id":"GO:0098736","count":3},{"id":"GO:0010107","count":3},{"id":"GO:0010751","count":3}]},{"hash":"1912304209095651474","title":"Unknown","description":"The GO terms cover a wide range of distinct processes (epigenetic regulation, ribosome assembly, spindle pole body duplication, GPCR internalization, TLR signaling, calcium transporter activity, action potential, DNA binding regulation, and deubiquitination), with no clear single function or pathway tying the proteins together. This diversity makes it hard to assign a meaningful, specific label beyond Unknown.","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051572","count":5},{"id":"GO:0030474","count":5},{"id":"GO:1904021","count":5},{"id":"GO:0034126","count":5},{"id":"GO:0000028","count":5}]},{"hash":"1469190888572878340","title":"Nucleotide and small-molecule catabolism","description":"The Top Terms are dominated by a set of catabolic processes for nucleotides and other small molecules (nicotinamide, nicotinate salvage, uracil, guanosine, polyphosphate, creatinine, ppGpp, nitrogen utilization). This points to a cluster of proteins involved in breaking down diverse metabolites to harvest energy or recycle components, a common bacterial metabolic module. While some terms are loosely connected, the unifying theme is general catabolism of nucleotides and related small molecules.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006769","count":1},{"id":"GO:0002047","count":1},{"id":"GO:0019358","count":1},{"id":"GO:0006212","count":1},{"id":"GO:0006602","count":1}]},{"hash":"749953036360431088","title":"Amino acid metabolism","description":"The cluster\u2019s top GO terms are dominated by amino acid metabolic processes (alanine catabolic, valine biosynthetic, methionine cycle, serine biosynthesis) and related dicarboxylic acid metabolism, suggesting a shared function in amino acid metabolism, despite a few obsolete or unrelated terms.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0042853","count":2},{"id":"GO:0009099","count":1},{"id":"GO:0043648","count":1},{"id":"GO:0042745","count":1}]},{"hash":"1536783307623798600","title":"Lipid and steroid metabolism","description":"Top GO terms cluster around lipid processing (fatty acid omega-oxidation, lipid hydroxylation) and steroid biosynthesis (aldosterone, calcitriol, ecdysone), plus xenobiotic metabolism (insecticide and coumarin). The hepatocyte differentiation and copper ion response terms support a liver-related metabolic theme, suggesting a cohesive cluster of lipid/steroid metabolism and detoxification.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010430","count":3},{"id":"GO:0036378","count":3},{"id":"GO:0002017","count":3},{"id":"GO:0070365","count":3},{"id":"GO:0017143","count":3}]},{"hash":"124756020232176014","title":"Mitotic spindle assembly and cytokinesis","description":"Top GO terms center on mitotic spindle assembly and function, including metaphase chromosome alignment, centrosome/pole separation, spindle midzone formation, and microtubule sliding, plus cytokinesis (cell plate formation). These collectively point to proteins involved in spindle organization and cell division.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000911","count":5},{"id":"GO:0007080","count":5},{"id":"GO:0007100","count":5},{"id":"GO:0030951","count":5},{"id":"GO:0031534","count":5}]},{"hash":"1847903797627525711","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000740","count":1},{"id":"GO:0036494","count":1},{"id":"GO:0090084","count":1},{"id":"GO:0006458","count":1},{"id":"GO:0034975","count":1}]},{"hash":"2078146303248259626","title":"Diverse Solute Transporters","description":"Based on the GO terms, this cluster centers on transmembrane transport activities across a range of substrates (nitrate/nitrite, galactose/arabinose, phosphate, potassium, 4-hydroxyphenylacetate, vitamins) and even neurotransmitter loading into synaptic vesicles. This pattern strongly suggests a group of membrane transporter proteins handling diverse solutes. The lack of network edges does not undermine the functional theme. ","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":5},{"id":"GO:0035461","count":4},{"id":"GO:0042891","count":4},{"id":"GO:0015757","count":4},{"id":"GO:0015707","count":4}]},{"hash":"1606375698591597699","title":"Amino acid biosynthesis and central carbon metabolism","description":"The top GO terms cluster around amino acid biosynthesis (L-leucine, glutamate, lysine) and central carbon metabolism (TCA cycle, glyoxylate cycle, 2-oxoglutarate metabolism), with some signals of lipid biosynthesis regulation. This points to a cohesive metabolic module focused on amino acid production and carbon flux rather than signaling or migration, hence a metabolism-centric label.","confidence":"Medium","size":5,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009098","count":3},{"id":"GO:0006099","count":3},{"id":"GO:0019878","count":3},{"id":"GO:0006537","count":3},{"id":"GO:0071071","count":2}]},{"hash":"1513978421080054190","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010571","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0007098","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0048701","count":2}]},{"hash":"2283401413848778304","title":"Developmental cell cycle regulation","description":"This cluster's top GO terms emphasize developmental processes (seminiferous tubule development, brain and cardiac muscle development) alongside core cell-cycle activity (mitotic cell cycle, DNA damage checkpoint signaling), plus regulators of GTPase activity, actin dynamics, and ubiquitin ligase activity. The overall pattern suggests coordination of development with cell-cycle control rather than a single, narrowly defined pathway, so the label Developmental cell cycle regulation is appropriate.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0072520","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0072432","count":2},{"id":"GO:0030042","count":2}]},{"hash":"1133455404802690226","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000472","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0034476","count":1},{"id":"GO:0071033","count":1},{"id":"GO:0000973","count":1}]},{"hash":"1758140592260726391","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0000467","count":1},{"id":"GO:0006261","count":1}]},{"hash":"178978854220785652","title":"Ubiquitin-Dependent Protein Degradation","description":"The top GO terms cluster around ubiquitin-mediated processes (protein autoubiquitination, ubiquitin-dependent protein catabolic process, and ubiquitin-dependent ERAD) and a cellular cadmium response, suggesting a proteostasis/quality-control theme under metal stress. Other terms like ribosomal assembly and spindle pole body duplication are present but less central. Thus, labeling this cluster as ubiquitin-dependent protein degradation best captures the main function represented.","confidence":"High","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071276","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0042787","count":2},{"id":"GO:0051572","count":2}]},{"hash":"1312531367246231998","title":"Fungal cell wall biosynthesis and polysaccharide production","description":"This cluster is dominated by GO terms related to fungal-type cell wall biogenesis, cell wall organization, and biosynthesis of cell wall components (mannoproteins and polysaccharides), plus pathways for UDP-N-acetylglucosamine. These collectively point to synthesis and assembly of the fungal cell wall and its glycans, with related polysaccharide production being the common theme.","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0000032","count":2},{"id":"GO:0045228","count":2},{"id":"GO:0006048","count":2},{"id":"GO:0019877","count":2}]},{"hash":"2201755239877076381","title":"Ribosome biogenesis and rRNA processing","description":"These proteins are strongly associated with ribosome production and function: multiple terms for ribosome biogenesis and ribosome assembly (GO:0042254, GO:0042255, GO:0000028) and maturation of rRNA (GO:0000462, GO:0000463, GO:0000466), plus active translation (GO:0006412). A lone term related to autophagy of mitochondrion is incidental and does not define the cluster\u2019s core function.","confidence":"High","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:1903146","count":1},{"id":"GO:1903955","count":1},{"id":"GO:0000463","count":1},{"id":"GO:0000466","count":1}]},{"hash":"164269170302549408","title":"Transmembrane Transporters (ions and metabolites)","description":"Top terms are dominated by transmembrane transport of multiple substrates (nitrite, sodium, potassium, arabinose, fucose, vitamins, xenobiotics) and related metabolic contexts, including neurotransmitter packaging; this points to a cluster of membrane transporter proteins with broad substrate specificity.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":4},{"id":"GO:0015707","count":3},{"id":"GO:0035725","count":3},{"id":"GO:0015751","count":3},{"id":"GO:0006004","count":3}]},{"hash":"210670912425924458","title":"Mitotic spindle regulation and chromatid segregation","description":"The top GO terms cluster around mitotic processes: positive regulation of spindle microtubule\u2013kinetochore attachment, mitotic cell cycle, positive regulation of microtubule polymerization, and mitotic sister chromatid biorientation, which together suggest involvement in spindle assembly and chromosome segregation during cell division. A few terms about histone modification or chloroplast import appear incidental, but the dominant theme is mitotic machinery.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051987","count":1},{"id":"GO:0000278","count":1},{"id":"GO:0031116","count":1},{"id":"GO:1990758","count":1},{"id":"GO:0006508","count":1}]},{"hash":"399843671441959086","title":"Ubiquitin-regulated cell cycle and DNA damage response","description":"This cluster is dominated by terms tied to cell division and chromosome segregation (cell cycle, division) and by ubiquitin-related regulation (K29- and K11-linked ubiquitination), as well as DNA damage tolerance (error-free translesion synthesis) and transcriptional control via factor degradation. While one term touches on synapse assembly and a couple entries are obsolete, the core pattern points to ubiquitin-mediated regulation of mitosis and DNA damage response. ","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0007059","count":5},{"id":"GO:0071347","count":5},{"id":"GO:0033128","count":5},{"id":"GO:0070987","count":5},{"id":"GO:0035519","count":5}]},{"hash":"1330142941497485288","title":"Unknown","description":"The top terms include skin/nerve-related processes (sebaceous gland differentiation, CNS myelin maintenance) alongside fungal lipid metabolism (MIPC, ergosterol, unsaturated fatty acid biosynthesis), nitrate/nitric oxide metabolism, and general mitochondrial inheritance. The terms span disparate biology with no clear, cohesive function tying all proteins together, so a specific label cannot be confidently assigned.","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001949","count":5},{"id":"GO:0006675","count":5},{"id":"GO:0032286","count":5},{"id":"GO:0042128","count":5},{"id":"GO:0000001","count":5}]},{"hash":"2219392739319754124","title":"Unknown","description":"The terms are scattered across RNA surveillance, cell-cycle regulation, iron-sulfur cluster assembly, and various biosynthetic/metabolic processes with little overlap, giving no clear single function for the cluster.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000184","count":2},{"id":"GO:0051782","count":1},{"id":"GO:0016226","count":1},{"id":"GO:0007049","count":1},{"id":"GO:0009103","count":1}]},{"hash":"303588274674202086","title":"Multitissue development regulators","description":"The top GO terms cluster around regulation of differentiation and development across a variety of tissues (bone, heart, neural/retinal cells, inner ear, pancreas) and include signaling pathway regulation and hormone responses. This suggests the proteins act as broad developmental regulators rather than a single tissue-specific function, tying together cell fate and morphogenesis across multiple organ systems.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045668","count":4},{"id":"GO:0060766","count":4},{"id":"GO:0035481","count":3},{"id":"GO:2000074","count":3},{"id":"GO:0014003","count":3}]},{"hash":"2105388980502954171","title":"DNA Damage Response and Genome Maintenance","description":"The proteins cluster around DNA repair processes (error-free translesion synthesis, DNA recombination), cell division, and oxidative stress response, suggesting a common theme of maintaining genome integrity under stress. There are also hints of broader RNA metabolism (mRNA export, RNA-protein cross-linking) that can tie into stress-related regulation, with some peroxisomal import signals possibly reflecting related metabolic stress connections. Overall, the core theme appears to be genome maintenance and cellular stress response, though some annotations are peripheral. ","confidence":"Medium","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0016558","count":4},{"id":"GO:0034599","count":4},{"id":"GO:0070987","count":3},{"id":"GO:0006310","count":3}]},{"hash":"1796807470817762434","title":"Nuclear DNA Replication and Chromatin Regulation","description":"The top GO terms cluster around core nuclear processes: DNA replication and DNA recombination indicate maintenance and propagation of the genome, while several chromatin-related terms point to regulation of DNA accessibility and transcription (histone modification, RNA Pol II termination, and RNA-protein interactions). The presence of an embryonic development term likely reflects broader roles of chromatin dynamics in development, but the dominant signal remains nuclear DNA processing and chromatin state control, justifying the label. ","confidence":"Medium","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0048701","count":4},{"id":"GO:0070417","count":2},{"id":"GO:2000616","count":2},{"id":"GO:0006310","count":2}]},{"hash":"2119981763380116078","title":"Innate Immune Activation and Antigen Presentation","description":"GO terms point to innate immune activation (innate immune response-activating signaling pathway; non-canonical NF-kappaB signaling), dendritic cell chemotaxis, and antigen processing/presentation (peptide antigen assembly with MHC class I). Additional terms on vesicle endocytosis and cell-cycle regulation reflect immune cell trafficking and regulation. Overall, these items suggest a cohesive theme around immune signaling and antigen presentation.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2000510","count":1},{"id":"GO:0048387","count":1},{"id":"GO:0071157","count":1},{"id":"GO:0007339","count":1},{"id":"GO:0048488","count":1}]},{"hash":"516106363045769530","title":"TNF/NF-\u03baB immune signaling and antigen presentation","description":"The dominant GO terms cluster around TNF-mediated and non-canonical NF-kappaB signaling, involvement in proteasome-related processes (proteasome core assembly, deubiquitination), and MHC class I antigen processing/presentation, all pointing to an immune signaling module with antigen processing. Other terms like Wnt regulation, salt stress, and G2/M control are present but appear less central to the core theme. ","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0033209","count":4},{"id":"GO:0038061","count":4},{"id":"GO:0016032","count":4},{"id":"GO:0010972","count":4},{"id":"GO:0090090","count":4}]},{"hash":"798770927552329339","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030007","count":2},{"id":"GO:1990573","count":2},{"id":"GO:0036494","count":2},{"id":"GO:0090084","count":2},{"id":"GO:0006458","count":2}]},{"hash":"2204952202183409525","title":"Ribosome Biogenesis and RNA Processing","description":"This cluster is dominated by GO terms related to ribosome assembly and RNA processing (GO:0042254, GO:0042274, GO:0000462, GO:0006396). While a few outliers exist (embryo sac development, autophagy activation, proteasome assembly, viral protein processing), the overarching pattern centers on ribosome biogenesis and rRNA maturation, suggesting these proteins function together in ribosome construction and RNA maturation processes.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":1},{"id":"GO:0042274","count":1},{"id":"GO:0043248","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0009553","count":1}]},{"hash":"428152795933418431","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0006919","count":2},{"id":"GO:0000147","count":2},{"id":"GO:0036494","count":1},{"id":"GO:0090084","count":1}]},{"hash":"1657525611946167303","title":"Ribosome Biogenesis and Translation","description":"The GO terms show strong representation for translational processes (initiation, translation, termination) together with rRNA maturation (SSU/LSU) and RNA surveillance/no-go decay pathways. This points to a cohesive theme around ribosome assembly/maintenance and translation quality control, despite the small, sparsely connected protein set. Confidence in this label is High.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006413","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006415","count":2},{"id":"GO:0070481","count":1},{"id":"GO:0070966","count":1}]},{"hash":"2054478758256852672","title":"Developmental Trafficking Processes","description":"The top GO terms point to tissue development, especially neuron migration and skin/keratinocyte development, plus related processes like substantia nigra development and keratinization. There is also a theme of intracellular trafficking and localization (protein targeting, nuclear export, Golgi reassembly) and a note on synaptic plasticity regulation, which together suggest a cluster of proteins involved in developmental programs with emphasis on proper trafficking and organelle organization. An outlier term relates to DNA damage response, but the core signal appears to be development coupled with trafficking mechanisms.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006977","count":4},{"id":"GO:0046827","count":4},{"id":"GO:0006605","count":4},{"id":"GO:0001764","count":4},{"id":"GO:0021762","count":4}]},{"hash":"1584822597874150413","title":"Ubiquitin-mediated circadian and cell-cycle regulation","description":"The top GO terms point to circadian rhythm regulation and multiple ubiquitination-related processes (positive regulation of protein polyubiquitination; ubiquitin-dependent protein catabolic process; protein ubiquitination), alongside cell-cycle and DNA replication initiation/regulation terms. This suggests a cohesive theme where ubiquitin signaling modulates circadian timing and cell-cycle progression, with some neuronal context implied by oxidative stress\u2013related and synapse-associated terms. Confidence: High","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042752","count":4},{"id":"GO:1902916","count":4},{"id":"GO:0000083","count":4},{"id":"GO:1903378","count":4},{"id":"GO:0030174","count":4}]},{"hash":"2084509339209469139","title":"Signaling Regulation and Endocytosis","description":"The terms co-occur around regulation of Rho signaling, GPCR internalization and clathrin-mediated endocytosis, plus ubiquitination and transcription processes, suggesting a cluster tied to membrane signaling and trafficking regulation.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035025","count":2},{"id":"GO:0031398","count":1},{"id":"GO:0032092","count":1},{"id":"GO:0045953","count":1},{"id":"GO:0090240","count":1}]},{"hash":"726335724352646006","title":"Ubiquitin-mediated protein modification","description":"Based on the GO terms, the cluster is dominated by ubiquitin-related processes: protein deubiquitination, autoubiquitination, and K6-linked deubiquitination, indicating a focus on ubiquitin conjugation/deconjugation and protein turnover. Some translation-related terms are present, which may reflect general cellular housekeeping or ribosome-associated QC, but the ubiquitin-centric theme appears to be the primary signal linking these proteins.","confidence":"Medium","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1903071","count":3},{"id":"GO:0071276","count":2},{"id":"GO:0060340","count":2},{"id":"GO:0030474","count":2},{"id":"GO:1904021","count":2}]},{"hash":"1274605392130134249","title":"Ubiquitin-Dependent Signaling and Apoptosis Control","description":"The GO terms cluster around ubiquitination (K6- and K48-linked ubiquitination, autoubiquitination) and regulation of apoptosis (including TNF signaling), with supporting hints from receptor turnover (Wnt catabolic process) and antiviral transport regulation. This suggests a cohesive theme of ubiquitin-mediated control of signaling pathways and cell fate decisions.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1901253","count":1},{"id":"GO:0033209","count":1},{"id":"GO:1900095","count":1},{"id":"GO:0051865","count":1},{"id":"GO:0038018","count":1}]},{"hash":"1356217499901999861","title":"Glycoprotein Biosynthesis and Pollen Tube Guidance","description":"The cluster features dolichol-linked oligosaccharide biosynthesis and GPI anchor biosynthesis, pointing to glycoprotein production and membrane anchoring; the pollen tube guidance term anchors this to a plant reproductive context, suggesting glycosylation-related proteins influence pollen tube growth. The malate transport term is less central, and the obsolete term can be ignored, but the overall theme links glycoprotein biosynthesis to pollen tube function.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0044148","count":1},{"id":"GO:0015743","count":1},{"id":"GO:0006488","count":1},{"id":"GO:0010183","count":1},{"id":"GO:0006506","count":1}]},{"hash":"1101872248052568669","title":"Unknown","description":"No top GO terms provided; only one interaction and four proteins, so there is no clear shared function to define a cluster theme.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[]},{"hash":"874549185878946232","title":"Immune Regulation and Androgen Signaling","description":"The cluster mixes immune-related regulation (negative regulation of neutrophil activation; cellular response to type I interferon) and ubiquitination with hormone-related processes (steroid hormone receptor complex assembly; prostate gland development; male sex differentiation). This suggests a theme where immune signaling intersects with androgen receptor\u2013mediated pathways, though the connection is not tightly cohesive, yielding a moderate confidence.","confidence":"Medium","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1902564","count":3},{"id":"GO:0071357","count":2},{"id":"GO:0070979","count":2},{"id":"GO:0030850","count":2},{"id":"GO:0046661","count":2}]},{"hash":"35987560233730499","title":"Ubiquitin-Mediated ERAD","description":"Reasoning: The top GO terms cluster around ubiquitination and deubiquitination (protein autoubiquitination, ubiquitin-dependent ERAD, protein deubiquitination) and ER quality control processes (ERAD-related terms, ER stress-related regulation). This suggests the proteins function together in the ubiquitin cycle and ER-associated degradation rather than a single other pathway. Some terms about translation or ribosome assembly may reflect broader protein homeostasis context or annotation noise, but the dominant theme remains ubiquitin-dependent ERAD.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0030474","count":2},{"id":"GO:1904021","count":2},{"id":"GO:0000028","count":2}]},{"hash":"2175581625830117592","title":"Ribosome biogenesis and translation machinery","description":"This cluster\u2019s top GO terms cluster around ribosome biogenesis, ribosomal large subunit assembly, cytoplasmic translation, and SRP-dependent cotranslational protein targeting to membranes, all pointing to ribosome function and protein synthesis. A few single terms related to immune signaling and cytoskeleton are incidental and less representative. Overall, the dominant theme is ribosome-related processes, justifying the label.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0032147","count":2},{"id":"GO:0000027","count":1},{"id":"GO:0071353","count":1},{"id":"GO:0006614","count":1}]},{"hash":"1599427355138043897","title":"Telomere maintenance and cell cycle regulation","description":"The top GO terms cluster around telomere-associated processes (positive regulation of telomerase activity, establishment of protein localization to telomere) and core cell cycle/division functions, suggesting a shared theme of telomere maintenance linked to cell cycle control. Some terms related to immune signaling or virion assembly seem incidental, but the strongest link appears to be telomere regulation coupled with cell cycle processes.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0033198","count":3},{"id":"GO:0002368","count":3},{"id":"GO:0007049","count":3},{"id":"GO:0051973","count":3},{"id":"GO:2000778","count":3}]},{"hash":"2010540243834193430","title":"Unknown","description":"The GO terms are highly diverse, including synaptic assembly at neuromuscular junction, eye morphogenesis, transcriptional regulation, stress responses, and locomotor rhythm, with no clear common function or pathway linking all members, and there are no interactions among the proteins in this cluster. ","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051124","count":1},{"id":"GO:0016330","count":1},{"id":"GO:0060195","count":1},{"id":"GO:0045128","count":1},{"id":"GO:1990440","count":1}]},{"hash":"1230305463111767658","title":"Oxidative metabolism and detoxification","description":"Top GO terms converge on redox chemistry and detoxification: fatty acid omega-oxidation, ethanol/aldehyde metabolism, formaldehyde catabolism, and S-nitrosylation of cysteine residues. A couple of stress-response terms (lipopolysaccharide and antineoplastic agent response) hint at broader redox defense. Overall, the cluster likely represents oxidative metabolism and detoxification functions.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0018119","count":2},{"id":"GO:0010430","count":2},{"id":"GO:0046294","count":2},{"id":"GO:0006116","count":2}]},{"hash":"5987394865435591","title":"RNA Processing and RNP Assembly","description":"This cluster is dominated by RNA handling activities: tRNA processing, maturation of SSU-rRNA, histone mRNA metabolism, spliceosomal snRNP assembly, and import into the nucleus, with P-body assembly also indicating RNA fate management. These terms point to a cohesive theme of RNA maturation and ribonucleoprotein assembly, with a few outliers (stress-response and chromatin-related terms) that are less central to the core function.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":3},{"id":"GO:0008334","count":3},{"id":"GO:0030490","count":3},{"id":"GO:0000387","count":3},{"id":"GO:0009414","count":3}]},{"hash":"924619573429816662","title":"Unknown","description":"The top GO terms are highly diverse, spanning DNA repair (DNA recombination, error-free translesion synthesis), basic RNA processing (mRNA export, RNA-protein covalent interactions), metabolism (ATP and FAD-related), photosynthesis-related biosynthesis (bacteriochlorophyll), and even virion attachment. There isn\u2019t a single coherent biological theme linking these proteins, suggesting the cluster does not correspond to a specific, unified function.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070987","count":1},{"id":"GO:0006310","count":1},{"id":"GO:0030494","count":1},{"id":"GO:0051301","count":1},{"id":"GO:1903007","count":1}]},{"hash":"2158483510628060530","title":"Muscle calcium handling and regeneration signaling","description":"The GO terms cluster around regulation of muscle relaxation, calcium release from the sarcoplasmic reticulum, satellite cell activation for skeletal muscle regeneration, and associated signaling events, pointing to skeletal muscle physiology and calcium-dependent signaling. While a few terms are less directly related or obsolete, the dominant theme is muscle function and regeneration.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1901077","count":1},{"id":"GO:1902896","count":1},{"id":"GO:0014808","count":1},{"id":"GO:0007205","count":1},{"id":"GO:0014718","count":1}]},{"hash":"2236459497424465249","title":"Translation initiation and mRNA processing","description":"This cluster is dominated by GO terms related to translation initiation, preinitiation complex formation, eIF4F complex assembly, and translation reinitiation, along with mRNA processing steps such as splicing recognition, export, and stability regulation. The repeated emphasis on initiation/reinitiation and post-transcriptional mRNA handling suggests a cohesive theme of coordinating mRNA maturation with translation control, despite a few obsolete terms. ","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0075525","count":2},{"id":"GO:0006376","count":2},{"id":"GO:0002188","count":2},{"id":"GO:1905663","count":2},{"id":"GO:0035278","count":2}]},{"hash":"121487231146210352","title":"Innate Immune Signaling and Cell Adhesion","description":"The GO terms highlight immune signaling (TLR3 pathway activation, IL-2 production) and components related to cell interactions and membrane organization (membrane rafts, cadherin-related adhesion). These together suggest a process focused on innate/adaptive immune signaling and cell adhesion rather than a single biochemical activity, with other terms being secondary or broad. ","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070584","count":1},{"id":"GO:1903044","count":1},{"id":"GO:0045861","count":1},{"id":"GO:0034141","count":1},{"id":"GO:1901585","count":1}]},{"hash":"975046729461280378","title":"Fungal nutrient-responsive transcription","description":"The GO terms emphasize transcription from RNA Pol II promoter regulated by metabolic cues (oleic acid, nonfermentable carbon source) and links to sterol/ergosterol metabolism and secondary metabolism (aflatoxin). This points to a cluster of proteins involved in regulating transcription in response to nutrient and lipid signals in fungi, rather than a single metabolic pathway.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0061429","count":1},{"id":"GO:0035961","count":1},{"id":"GO:0061415","count":1},{"id":"GO:1904741","count":1},{"id":"GO:2001278","count":1}]},{"hash":"1995701706006208815","title":"Biosynthesis-related processes","description":"The catalog of GO terms includes multiple biosynthetic pathways (tRNA methylation, glycolipid biosynthesis, GPI-anchor synthesis, phosphatidylinositol metabolism, bacillithiol biosynthesis, kanamycin biosynthesis) and related glycosylation steps, suggesting the proteins participate in diverse biosynthetic/modification tasks rather than a single, narrow function. Some \"response to\" terms may reflect regulatory responses, but the shared thread is biosynthesis and modification of macromolecules and lipids.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030488","count":2},{"id":"GO:0009744","count":1},{"id":"GO:0009247","count":1},{"id":"GO:0046488","count":1},{"id":"GO:0009405","count":1}]},{"hash":"255943577914142888","title":"Regulation of signaling and transcription","description":"The top GO terms cluster around regulatory processes: both positive/negative regulation of GPCR internalization and MyD88-dependent TLR signaling, negative regulation of DNA binding and transcription factor activity, and protein deubiquitination with links to chromatin modification (histone H3-K4 methylation). This suggests a set of proteins involved in modulating signaling pathways and transcriptional/chromatin states. Some terms (spindle pole body duplication, ribosomal subunit assembly) are more related to cell cycle/biogenesis, indicating the cluster may reflect broader regulatory roles rather than a single pathway.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051572","count":3},{"id":"GO:0030474","count":3},{"id":"GO:1904021","count":3},{"id":"GO:0034126","count":3},{"id":"GO:0000028","count":3}]},{"hash":"351902865535764093","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070417","count":2},{"id":"GO:0071031","count":2},{"id":"GO:0071051","count":2},{"id":"GO:0035640","count":2},{"id":"GO:0034475","count":2}]},{"hash":"872142949410235894","title":"Long-chain fatty acid metabolism and import","description":"These proteins repeatedly map to long-chain and very long-chain fatty acid metabolic processes, and to import across the plasma membrane or into the cell, suggesting a core role in lipid metabolism and transport. Additional lipid-related terms like lipoteichoic acid biosynthesis support a lipid-centric function in a bacterial context, though the exact specifics may vary. ","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070395","count":1},{"id":"GO:0019290","count":1},{"id":"GO:0008206","count":1},{"id":"GO:0019654","count":1},{"id":"GO:0000038","count":1}]},{"hash":"1171214754937383625","title":"Fungal stress response and cell wall biosynthesis","description":"This cluster shows signals of fungal-specific processes (fungal-type cell wall beta-glucan biosynthetic process and karyogamy) alongside stress-related responses (cellular response to unfolded protein, response to heat, and regulation of apoptotic signaling in oxidative conditions). The combination suggests a theme centered on fungal stress handling and cell-wall biosynthesis, despite some general housekeeping terms present. Confidence: Medium","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031204","count":1},{"id":"GO:1903751","count":1},{"id":"GO:0000742","count":1},{"id":"GO:0006880","count":1},{"id":"GO:0090084","count":1}]},{"hash":"1761294377822334190","title":"Unknown","description":"The GO terms are very heterogeneous, including mitochondrial complex III and inner membrane assembly, Golgi retention, ER-associated degradation, DNA repair/translesion synthesis, bacterial competence, viral replication, centrioles, and chromatin assembly. There isn\u2019t a single cohesive function linking all three proteins, so there\u2019s no clear, representative theme for a specific label.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0090261","count":3},{"id":"GO:0034551","count":3},{"id":"GO:0071712","count":3},{"id":"GO:0070987","count":3},{"id":"GO:0030420","count":3}]},{"hash":"856779044490491572","title":"Developmental Morphogenesis and Signaling","description":"Top GO terms cluster around development and morphogenesis (mesenchymal to epithelial transition, ureteric bud formation, pancreatic cell development, dendrite/dendritic spine morphogenesis). While some terms like corticosterone response and red light signaling are more general or incidental, the dominant pattern is developmental signaling and tissue morphogenesis, justifying this label.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1901536","count":3},{"id":"GO:0060231","count":2},{"id":"GO:2000074","count":2},{"id":"GO:0072107","count":2},{"id":"GO:0048813","count":2}]},{"hash":"1765228960695744372","title":"Ribosome Biogenesis and Translation","description":"The cluster is best described by terms focused on ribosome assembly, biogenesis, and translation (e.g., large subunit assembly/biogenesis and translation). These core GO terms repeatedly point to ribosomal production and protein synthesis, with accompanying hints about protein stability and targeting that may reflect regulation of ribosome components and translation factors. The combination suggests a cohesive group of proteins involved in ribosome assembly and the translation process, with some regulatory links to protein turnover.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2000059","count":1},{"id":"GO:0000027","count":1},{"id":"GO:1904667","count":1},{"id":"GO:0032092","count":1},{"id":"GO:0050821","count":1}]},{"hash":"399404117822905483","title":"RNA Splicing and mRNA Capping","description":"The proteins are enriched for RNA processing functions, especially mRNA capping and spliceosome-related splicing activities (7-methylguanosine cap, RNA splicing, regulation of alternative splicing, and spliceosomal complex dynamics). While a few terms touch on distant processes like nucleolar localization or telomere regulation, the dominant signal is RNA maturation via splicing and cap formation, suggesting they function as spliceosome-associated RNA processing factors.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006370","count":2},{"id":"GO:0000390","count":1},{"id":"GO:0000381","count":1},{"id":"GO:0008380","count":1},{"id":"GO:0051096","count":1}]},{"hash":"1304570110644647250","title":"Unknown","description":"The top GO terms are a wide mix of unrelated processes (ribosomal subunit export from the nucleus, ubiquitination, autophagy, cell cycle, fatty acid biosynthesis, olfactory nerve structure, etc.), with no edges linking the proteins and only singleton annotations. This lacks a coherent functional theme, so a specific, representative label cannot be assigned beyond Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000203","count":1},{"id":"GO:2000650","count":1},{"id":"GO:1901165","count":1},{"id":"GO:0045723","count":1},{"id":"GO:0021629","count":1}]},{"hash":"2085529631738131571","title":"Unknown","description":"This cluster has no GO terms or functional annotations to tie the three proteins together, and no edges or shared interactions are reported, making it impossible to infer a common function. ReCIPE-added members do not provide a clear functional signal here.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1479057607341569223","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000740","count":1},{"id":"GO:0036494","count":1},{"id":"GO:0090084","count":1},{"id":"GO:0006458","count":1},{"id":"GO:0034975","count":1}]},{"hash":"1114241640926281688","title":"ER Targeting and Membrane Lipid Biosynthesis","description":"Top GO terms indicate a core theme of ER-associated processes: post-translational targeting of proteins to the endoplasmic reticulum membrane and tail-anchored membrane protein insertion, together with lipid biosynthesis steps such as CDP-diacylglycerol biosynthesis, cardiolipin remodeling, and triglyceride synthesis. While a few terms are less connected, the dominant signals point to ER targeting and membrane lipid metabolism, justifying the label.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016192","count":1},{"id":"GO:0051220","count":1},{"id":"GO:1904378","count":1},{"id":"GO:0071816","count":1},{"id":"GO:0048767","count":1}]},{"hash":"2201365391654273699","title":"Cofactor biosynthesis and RNA modification pathways","description":"The terms cluster around diverse biosynthetic and maturation steps, including lipoylation and synthesis of cofactors like menaquinone and PQQ, as well as RNA-related modifications (tRNA/rRNA methylation and queuosine biosynthesis), indicating a broad theme of biosynthetic/modification processes rather than a single specific function.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009249","count":1},{"id":"GO:0008616","count":1},{"id":"GO:0018339","count":1},{"id":"GO:0070475","count":1},{"id":"GO:0009234","count":1}]},{"hash":"1452916147441125723","title":"Translation and ribosome biogenesis","description":"The top GO terms cluster around translation and ribosome-related processes (maturation of LSU rRNA, translation, translation reinitiation, and related reinitiation concepts), indicating a core theme of protein synthesis and ribosome assembly. Additional terms for proteasome assembly and ubiquitin-dependent protein catabolic processes suggest connection to protein quality control associated with translation. A few terms on stem cell differentiation and cell-cycle regulation are peripheral and less central to this theme. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0075525","count":1},{"id":"GO:1902416","count":1},{"id":"GO:0048863","count":1}]},{"hash":"112271453823298023","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007422","count":1},{"id":"GO:0021885","count":1},{"id":"GO:0032220","count":1},{"id":"GO:1902771","count":1},{"id":"GO:0021952","count":1}]},{"hash":"1388538804170619199","title":"RNA Methylation and Ribosome Export","description":"This cluster centers on methylation-related processes (peptidyl-arginine methylation, tRNA methylation, tRNA wobble uridine modification, histone methylation) and ribosome subunit export, suggesting a theme around RNA modification and ribosome biogenesis. The remaining terms are a mix of broader biosynthetic and stress-response annotations that may reflect broader protein functions or annotation noise, but the core connection is RNA modification and ribosome-related activity.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000056","count":2},{"id":"GO:0019919","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0030488","count":2},{"id":"GO:0010189","count":2}]},{"hash":"1410579468109496679","title":"Unknown","description":"The GO terms present are highly diverse, spanning tRNA modification, vitamin biosynthesis, mitochondrial autophagy and Cvt pathway targeting, protein lipidation and ufmylation, plus developmental and transcription regulatory terms, with no clear shared function tying the proteins together. This lack of a cohesive biological theme suggests the cluster does not reflect a single representative process, so a specific label cannot be confidently assigned.","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0002143","count":1},{"id":"GO:0009229","count":1},{"id":"GO:0000422","count":1},{"id":"GO:0006501","count":1},{"id":"GO:0032258","count":1}]},{"hash":"1161715282001432519","title":"Chromosome segregation and histone ubiquitination","description":"The top terms strongly point to cell division and chromosome segregation (GO:0007059, GO:0051301) and to chromatin regulation via histone ubiquitination (GO:0035519, GO:0070979, GO:0071894), suggesting a functional cluster centered on chromatin modifications during the cell cycle. Some terms are related to other processes (IL-1 response, transcription factor catabolism, translesion synthesis), but the dominant pattern ties histone modification with chromosome dynamics.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0007059","count":3},{"id":"GO:0071347","count":3},{"id":"GO:0033128","count":3},{"id":"GO:0070987","count":3},{"id":"GO:0035519","count":3}]},{"hash":"1020583174817086422","title":"Histone H3 Methylation Regulation","description":"Top terms indicate histone modifications (H3-K27 and H3-K4 methylation) and their negative regulation, pointing to epigenetic regulation of gene expression as the shared function of this protein set. The single centrosome cycle term is less informative for the core theme and may reflect a secondary association. Despite some obsolescence in GO annotations, the dominant signal is histone methylation control.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098532","count":1},{"id":"GO:0080182","count":1},{"id":"GO:0007098","count":1},{"id":"GO:0061086","count":1},{"id":"GO:1901674","count":1}]},{"hash":"1205027306819280558","title":"Fungal cell wall glycoproteins and glycosylation","description":"The cluster centers on cell wall mannoprotein biosynthesis and protein glycosylation (N- and O-linked, glycan processing), with an adhesion/biofilm association, consistent with fungal cell-wall glycoproteins.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043710","count":2},{"id":"GO:0000032","count":2},{"id":"GO:0006487","count":2},{"id":"GO:0006493","count":2},{"id":"GO:0044845","count":2}]}]