[{"hash":"1834124873444007834","title":"ER stress and protein quality control","description":"The top GO terms cluster around unfolded protein response, ER stress adaptation, regulation of translation initiation under ER stress, and ubiquitination, all pointing to a proteostasis-focused theme. While a few terms relate to cell division, metabolism, or immune defense, the strongest shared thread is maintaining protein homeostasis under stress, including quality control and degradation pathways relevant to photoreceptor protein trafficking. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050689","count":2},{"id":"GO:0090526","count":2},{"id":"GO:0007091","count":2},{"id":"GO:0051348","count":2},{"id":"GO:0070979","count":2}]},{"hash":"1613879389719716848","title":"GTPase-driven endocytosis and epithelial polarity","description":"This cluster\u2019s top GO terms center on endocytosis, small GTPase\u2013mediated signaling, and establishment of epithelial cell polarity, with components like podosome assembly and cytoskeletal regulation tying these processes together. The shared theme appears to be coordinated regulation of vesicle trafficking, actin dynamics, and cell polarity via small GTPases, supporting epithelial organization and related remodeling. Some terms related to transcriptional preinitiation complex assembly and nuclear quality control may reflect broader regulatory roles in these proteins, but the primary signal points to cytoskeleton\u2013endocytosis\u2013polarity coordination.","confidence":"Medium","size":29,"edges":10,"triangles":4,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006469","count":6},{"id":"GO:0006897","count":5},{"id":"GO:0007264","count":5},{"id":"GO:0090162","count":5},{"id":"GO:0071803","count":5}]},{"hash":"727786588265840149","title":"Transmembrane Transporters (ions and metabolites)","description":"This cluster is characterized by strong representation of GO terms describing transmembrane transport of a variety of ions and small molecules (nitrate, nitrite, sodium, potassium, phosphate, arabinose, xenobiotics) along with a term related to loading neurotransmitters into synaptic vesicles. This pattern points to a set of membrane transport proteins that mediate movement of diverse substrates across cellular membranes, rather than a single specific substrate pathway. Therefore, a concise label reflecting broad transporter activity is appropriate.","confidence":"High","size":29,"edges":8,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0015706","count":18},{"id":"GO:0042128","count":18},{"id":"GO:0006855","count":18},{"id":"GO:0015751","count":18},{"id":"GO:0035725","count":18}]},{"hash":"1404943743784477666","title":"Innate Immune Signaling and Actin Remodeling","description":"Top terms are dominated by Toll-like receptor signaling and innate immune responses (TLR1 signaling, MyD88-dependent TLR signaling, innate immune response, defense against virus), with actin filament severing suggesting cytoskeletal remodeling accompanying activation. While there are hints of dopaminergic signaling and energy-sensing pathways, the prevailing theme centers on innate immune signaling and cytoskeletal dynamics.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051014","count":7},{"id":"GO:0034130","count":7},{"id":"GO:0002755","count":7},{"id":"GO:0045087","count":6},{"id":"GO:0051607","count":6}]},{"hash":"334787323024855235","title":"Mitotic Division and Golgi-ER Trafficking","description":"The cluster shows strong signals for cell division and mitotic processes (cell division, mitotic spindle assembly, mitotic cell cycle) together with vesicle trafficking between the Golgi and ER (retrograde Golgi-to-ER transport, COPII-coated vesicle budding, Golgi-to-plasma membrane transport), suggesting a cohesive module linking mitosis with the secretory pathway and membrane remodeling during growth. This justifies a label that captures both themes.","confidence":"High","size":29,"edges":20,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008283","count":8},{"id":"GO:0006890","count":7},{"id":"GO:0000747","count":7},{"id":"GO:0051301","count":7},{"id":"GO:0090307","count":7}]},{"hash":"1939174149913465752","title":"Nuclear transcription and ribosome biogenesis","description":"The cluster centers on nuclear processes involved in RNA synthesis and ribosome production: ribosomal large subunit biogenesis and export from the nucleus, and transcription by RNA polymerases II and III. This suggests a cohesive theme of coordinating transcriptional machinery with ribosome assembly within the nucleus. Supporting terms related to maintaining protein localization in the nucleus and histone-related functions bolster a chromatin/nuclear regulation angle, while a few terms (interferon-beta regulation, fat cell differentiation, pseudohyphal growth) are less directly tied to this core theme.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000055","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0042797","count":2},{"id":"GO:0032728","count":2},{"id":"GO:0045598","count":1}]},{"hash":"189208395593990302","title":"Unknown","description":"The top GO terms cover a wide and disparate set of functions (cellulose and chlorophyll catabolism, xenobiotic response, transcription, various biosynthetic processes, detoxification, and protein tetramerization) with no single cohesive theme, so there isn\u2019t a clear, representative label for this cluster.","confidence":"","size":28,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030245","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0042493","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0017000","count":3}]},{"hash":"441742671974266257","title":"Cell Proliferation and Vesicle Trafficking","description":"The top GO terms cluster around cell division and mitotic spindle assembly, plus cell population proliferation and multicellular growth, suggesting a core focus on cell growth and division. Supporting this are ribosome biogenesis (protein synthesis) terms and mixed signals for intracellular trafficking between the Golgi and ER, which are common in actively proliferating or differentiating cells. The presence of developmental terms (brain development, macrophage differentiation) fits a broader growth/differentiation context, reinforcing a theme of proliferation with active biosynthesis and secretory pathways. Overall, this cluster seems best described as connected to cell proliferation with accompanying protein production and vesicle trafficking.","confidence":"Medium","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0090307","count":4},{"id":"GO:0032889","count":4},{"id":"GO:0030225","count":3},{"id":"GO:0042254","count":3}]},{"hash":"1165723640060114543","title":"Bacterial LPS and O-antigen biosynthesis","description":"The top GO terms are dominated by lipopolysaccharide and O-antigen biosynthesis, along with galactose metabolic and catabolic processes, indicating a cluster of proteins involved in bacterial cell-surface polysaccharide production and carbohydrate metabolism. Poly-hydroxybutyrate biosynthesis also points to general bacterial biosynthetic capacity, while other terms like antibiotic-related processes and transcription reflect broader cellular states but are less central. Overall, the common theme is biosynthesis of cell-envelope components and related carbohydrate pathways. ","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":16},{"id":"GO:0042619","count":12},{"id":"GO:0009103","count":11},{"id":"GO:0006541","count":8},{"id":"GO:0009243","count":8}]},{"hash":"155907057034177226","title":"Unknown","description":"The top GO terms reflect highly diverse processes: neural and skeletal muscle development, axon guidance, immune signaling, vesicle transport, transcription, sterol import, and transcriptional regulation. The lack of a unifying biological process across the cluster (no edges, suggesting dispersion) makes it hard to assign a specific, representative label. The set appears to be a heterogeneous collection involving development, signaling, and trafficking rather than a single cohesive module.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045071","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0050853","count":3},{"id":"GO:0007519","count":3}]},{"hash":"77846128859869702","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":53,"triangles":53,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006284","count":6},{"id":"GO:0006260","count":5},{"id":"GO:0035753","count":4},{"id":"GO:0005978","count":4},{"id":"GO:0006289","count":4}]},{"hash":"490652380240737556","title":"RNA Pol II\u2013Mediated Transcription Regulation","description":"This cluster is driven by GO terms centered on DNA-templated transcription and, in particular, positive regulation of transcription from RNA polymerase II promoters, indicating a primary role in transcriptional control. Some other terms (e.g., biosynthetic or metabolic processes) appear as secondary annotations or artifacts, but the prevailing signal is RNA Pol II\u2013driven transcription regulation.","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:0035948","count":7},{"id":"GO:0035961","count":5},{"id":"GO:1904741","count":5},{"id":"GO:0061429","count":5}]},{"hash":"484409736012204065","title":"DNA Replication and Cell Cycle Regulation","description":"This cluster is dominated by terms tied to DNA replication and transcription, along with cell-cycle processes, division, and kinetochore localization, plus regulation of CDK activity. Redox-related terms appear but are secondary to the core theme of replication and cell-cycle control, suggesting proteins that coordinate DNA synthesis with mitotic progression. Confidence: High","confidence":"","size":27,"edges":88,"triangles":84,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0055114","count":7},{"id":"GO:0045454","count":7},{"id":"GO:0035335","count":7},{"id":"GO:0006351","count":6}]},{"hash":"1479119554263966289","title":"Unknown","description":"The set shows no single coherent function: terms span DNA-templated transcription, differentiation of multiple tissues (lung epithelium, neurons, mesonephros), protein catabolic processes and unfolded protein response, and unrelated pathways like lipid A biosynthesis and xylan catabolism. This broad, mixed annotation suggests either heterogeneous functions or noise, so a unified label is not supported. ","confidence":"","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0060487","count":3},{"id":"GO:0030182","count":3},{"id":"GO:0009245","count":3},{"id":"GO:0006986","count":3}]},{"hash":"1064844257875461003","title":"Transcriptional regulation of metabolism","description":"This cluster\u2019s top terms are dominated by \u201cpositive regulation of transcription from RNA polymerase II promoter\u201d in response to various stimuli (oleic acid, starvation) along with multiple metabolic biosynthetic processes (ergosterol/sterol, pyrimidine, leucine, proline, aflatoxin). This pattern suggests proteins that regulate metabolic gene expression in response to nutrients or environmental cues, i.e., transcriptional regulators coordinating metabolism. ","confidence":"High","size":27,"edges":13,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035948","count":8},{"id":"GO:0035961","count":8},{"id":"GO:1904741","count":8},{"id":"GO:0061429","count":8},{"id":"GO:0043457","count":8}]},{"hash":"1702992639975508842","title":"Developmental transcriptional regulators","description":"The cluster centers on transcriptional control (DNA-templated transcription, regulation of transcription) with supporting RNA processing and degradation terms (miRNA catabolic process, obsolete pre-mRNA cleavage for polyadenylation), and includes development-related terms (haltere morphogenesis, floral meristem identity maintenance, motor neuron axon guidance). Together these suggest a theme of gene expression regulation guiding developmental programs across species.","confidence":"Medium","size":27,"edges":36,"triangles":9,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071374","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0010076","count":2},{"id":"GO:0048735","count":2},{"id":"GO:0006355","count":2}]},{"hash":"597894724265474732","title":"DNA-templated transcription and genome maintenance","description":"The top GO terms show a concentration of nuclear-related functions: DNA-templated transcription, meiotic joint molecule formation, and telomere maintenance via recombination, which point to a core theme of gene expression and chromosome maintenance. The presence of several metabolite catabolic terms is low in representation and likely reflects annotation noise or multifunctionality rather than a cohesive metabolic core. The absence of network edges further suggests a loosely connected set annotated with diverse functions, but the dominant nuclear terms support a transcription/genome maintenance theme.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0000733","count":2},{"id":"GO:0000709","count":2},{"id":"GO:0000722","count":2},{"id":"GO:0006099","count":1}]},{"hash":"1587839805809154508","title":"Developmental chromatin assembly and transcription","description":"The cluster\u2019s top GO terms cluster around chromatin-related processes (DNA-templated transcription, replication-dependent chromatin assembly, CENP-A chromatin assembly, histone H3 acetylation) and developmental functions (brain development, osteoblast differentiation, multicellular growth, single fertilization). This combination suggests a module of proteins coordinating chromatin structure and gene expression during development, with some links to germline/fertilization processes, justifying a label focused on developmental chromatin regulation.","confidence":"High","size":27,"edges":4,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050830","count":4},{"id":"GO:0007420","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0043966","count":3},{"id":"GO:0035264","count":3}]},{"hash":"498978605851808470","title":"Bacterial biosynthetic pathways and ion transport","description":"The top GO terms point to bacterial-specific biosynthesis (lipopolysaccharide, biotin, menaquinone) and ion/p proton transport, with supporting notes on vacuolar processes and metal homeostasis. Together these indicate a cluster of proteins involved in core metabolism and membrane-associated transport in bacteria, rather than a single narrow function. Confidence: Medium","confidence":"","size":27,"edges":150,"triangles":320,"max_degree":21,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006814","count":3},{"id":"GO:0009103","count":3},{"id":"GO:0009102","count":3},{"id":"GO:0009234","count":3},{"id":"GO:0006351","count":3}]},{"hash":"1339727468087174278","title":"Mitotic machinery and Golgi-ER trafficking","description":"This cluster mixes cell division and cytoskeletal processes (cell division, CENP-A chromatin assembly, microtubule severing) with components of the secretory pathway (ER-to-Golgi transport, Golgi retention, intralumenal vesicle formation, ubiquitin-dependent ERAD). The shared signals point to proteins involved in mitotic chromosome dynamics alongside vesicle trafficking and Golgi/ER organization, suggesting a dual role connecting division with intracellular transport.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0045053","count":2},{"id":"GO:0070676","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0051013","count":2}]},{"hash":"794052369645539733","title":"ER-Golgi Vesicle Transport","description":"Top terms reveal a clear focus on intracellular trafficking between the endoplasmic reticulum and Golgi (retrograde Golgi-to-ER transport and ER-to-Golgi vesicle transport), suggesting the core function is components of the secretory pathway. Although other terms touch on development and transcription, they are less cohesive across the cluster. Thus, the label reflects the strongest shared function with moderate confidence.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901998","count":3},{"id":"GO:0000278","count":2},{"id":"GO:0001403","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0006890","count":2}]},{"hash":"955268245037504410","title":"Central carbon metabolism and lipid biosynthesis","description":"GO terms point to lipid and central carbon metabolism (cholesterol biosynthetic and CoA biosynthetic processes) with broader carbohydrate flux (fructose metabolism, gluconeogenesis, PPP) and energy regulation (phosphorylation/dephosphorylation). A hint of mitochondrial translation (mitochondrial tyrosyl-tRNA aminoacylation) suggests a metabolic/mitochondrial context. Overall, the cluster appears to collect proteins involved in core metabolism and lipid biosynthesis rather than a single precise function.","confidence":"Medium","size":26,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006695","count":3},{"id":"GO:0015937","count":3},{"id":"GO:0016310","count":3},{"id":"GO:0016311","count":2}]},{"hash":"213973692973278314","title":"Cell Cycle and DNA Replication during Development","description":"The cluster is dominated by GO terms tied to DNA replication, the mitotic cell cycle, centrosome cycle, and DNA-templated transcription, indicating a core cell-cycle/DNA maintenance module. The presence of apoptotic processes and regulatory signals like positive regulation of Wnt signaling, along with developmental terms such as hippocampus development and embryonic cranial skeleton morphogenesis, suggests these proteins may coordinate proliferation with developmental signaling and morphogenesis, providing a cohesive, development-linked cell cycle theme.","confidence":"Medium","size":26,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":11},{"id":"GO:0048701","count":9},{"id":"GO:0010571","count":8},{"id":"GO:0007098","count":8},{"id":"GO:0000278","count":7}]},{"hash":"1237184581294621928","title":"Transcription and cell-cycle stress responses","description":"Top GO terms point to nuclear transcription machinery (DNA-templated transcription) and key cell-cycle components (centrosome duplication, mitotic cell cycle), along with multiple stress-response pathways (amino acid starvation, cadmium ion exposure, ER stress triggering intrinsic apoptosis). This mix suggests a cluster centered on transcriptional regulation coupled to cell-cycle control and broad stress responses, rather than a single narrow pathway.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0034198","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0048240","count":3},{"id":"GO:0006349","count":3}]},{"hash":"2287613307606452042","title":"Mitochondrial respiration and protein import","description":"Most frequent GO terms point to mitochondria: mitochondrial electron transport (ubiquinol to cytochrome c), aerobic respiration, and protein import/insertion into the mitochondrial matrix or inner membrane, plus proton transmembrane transport. Together these terms indicate a cluster of proteins involved in oxidative phosphorylation and mitochondrial protein targeting, with a couple of outliers that may reflect annotation noise.","confidence":"High","size":26,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006122","count":3},{"id":"GO:0030150","count":3},{"id":"GO:0001302","count":2},{"id":"GO:0042572","count":2}]},{"hash":"1975651553516858762","title":"Chromosome dynamics and mitosis","description":"The top GO terms are dominated by mitotic cell cycle and centromere-related processes (mitotic cycle, CENP-A chromatin assembly) plus microtubule severing, pointing to chromosome segregation and spindle dynamics as the core function. Other terms (mRNA transport, transcription, vesicle trafficking) are broad cellular processes often linked with dividing cells but do not redefine the cluster; the central theme remains mitosis and chromosome/chromatin organization.","confidence":"Medium","size":26,"edges":7,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0030433","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0051013","count":3},{"id":"GO:0051028","count":3}]},{"hash":"58863864262118293","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by GO terms tied to ribosome function and protein synthesis: translation (GO:0006412), ribosome biogenesis (GO:0042254), ribosomal large subunit export from nucleus (GO:0000055), translational initiation (GO:0006413), and tRNA modification (GO:0006400). The convergence on assembly, export, and initiation of translation suggests these proteins are core components or regulators of the ribosome/translation machinery, with a few auxiliary terms (e.g., response to antibiotic) likely reflecting related pathways or annotation overlap.","confidence":"High","size":26,"edges":6,"triangles":1,"max_degree":3,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":12},{"id":"GO:0042254","count":9},{"id":"GO:0046677","count":6},{"id":"GO:0000747","count":6},{"id":"GO:0051301","count":6}]},{"hash":"906679878969984364","title":"DNA Replication and Repair with Metabolic Pathways","description":"These proteins cluster around genome maintenance and expression (DNA replication, DNA-templated transcription, SOS response) alongside central metabolism and stress responses (TCA cycle, leucine biosynthesis, antibiotic response), with a note of mitochondrial translation suggesting organellar gene expression. The combination points to a module integrating DNA maintenance with core metabolic processes, hence the label.","confidence":"Medium","size":26,"edges":8,"triangles":2,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0019878","count":5},{"id":"GO:0032543","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0009432","count":3}]},{"hash":"1944784361927613761","title":"Ubiquitin-Dependent Proteostasis and Antiviral Immunity","description":"The cluster is dominated by GO terms for ubiquitin-mediated protein degradation (ubiquitin-dependent protein catabolic process, protein autoubiquitination, ERAD-related pathway), autophagy, and innate antiviral responses (innate immune response, defense response to virus). These points together suggest a group of proteins involved in proteostasis via ubiquitin and autophagy pathways that intersect with antiviral defense, with additional cell cycle-related terms that may reflect stress-related regulation. Overall, the theme centers on ubiquitin-dependent degradation and immune defense.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:0045087","count":6},{"id":"GO:0051607","count":6},{"id":"GO:0030433","count":5},{"id":"GO:0006914","count":5}]},{"hash":"1211674998889102999","title":"Amino acid and cofactor biosynthesis","description":"This cluster is dominated by GO terms tied to biosynthetic pathways for amino acids and cofactors (e.g., lysine biosynthesis via aminoadipic acid, oxaloacetate metabolism, biotin and heme-related porphyrinogen biosynthesis, antibiotic biosynthesis). While there are a few outliers (such as Notch signaling), the overall pattern points to metabolic production of amino acids and cofactors, with dense connectivity among proteins involved in these biosynthetic processes.","confidence":"Medium","size":25,"edges":221,"triangles":1010,"max_degree":24,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019878","count":7},{"id":"GO:0006107","count":7},{"id":"GO:0017000","count":7},{"id":"GO:0006782","count":6},{"id":"GO:0009102","count":6}]},{"hash":"1198573418048885259","title":"Spliceosome-Mediated mRNA Processing and Translation Initiation","description":"The GO terms show strong representation of spliceosome-mediated regulation of mRNA splicing (positive/negative, alternative splicing, cis splicing) and components of translation initiation (preinitiation complex formation and translation reinitiation). This indicates a functional cluster centered on RNA processing with ties to translation control, possibly modulated by regulatory ncRNAs and stress-related mRNA stability. Hence the label captures both core themes.","confidence":"High","size":25,"edges":179,"triangles":574,"max_degree":21,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":14},{"id":"GO:0031047","count":14},{"id":"GO:1901407","count":11},{"id":"GO:0010610","count":11},{"id":"GO:0048025","count":10}]},{"hash":"970494690369919916","title":"Amino acid and cofactor biosynthesis","description":"Top GO terms point to biosynthetic pathways for amino acids (lysine, histidine) and cofactors (biotin, heme precursor protoporphyrinogen IX), as well as related metabolic processes (lipoteichoic acid biosynthesis, fatty acid metabolism). The convergence on biosynthesis across several key metabolites suggests labeling the cluster as amino acid and cofactor biosynthesis, a representative high-level theme for these proteins.","confidence":"Medium","size":25,"edges":108,"triangles":202,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019878","count":6},{"id":"GO:0006782","count":6},{"id":"GO:0009102","count":6},{"id":"GO:0070395","count":6},{"id":"GO:0000105","count":5}]},{"hash":"1248687703015507701","title":"Nutrient-Responsive Transcription Regulation","description":"The top GO terms are all about DNA-templated transcription and positive regulation of transcription from RNA polymerase II promoter, under various nutrient- and carbon-source\u2013related conditions (gluconeogenesis, oleic acid, nonfermentable carbon sources, glyoxylate/glycolysis\u2013related regulation, pyrimidine biosynthesis). This points to a cluster of proteins involved in regulating gene expression in response to metabolic/nutrient signals, rather than a single metabolic enzyme complex. The lack of edges is compatible with a regulatory program where proteins act as transcriptional regulators coordinating metabolic gene expression.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":11},{"id":"GO:0035948","count":9},{"id":"GO:1900399","count":8},{"id":"GO:2001158","count":8},{"id":"GO:0061414","count":8}]},{"hash":"145900051327428795","title":"Chromatin and mitosis machinery","description":"The cluster centers on chromatin-related processes: DNA-templated transcription, CENP-A chromatin assembly, and cell division, with supporting involvement of microtubule severing and mRNA transport, pointing to chromatin dynamics and mitotic machinery as the core theme. Other vesicle-transport terms may reflect general cellular logistics but do not redefine the main function. ","confidence":"Medium","size":25,"edges":45,"triangles":42,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0030433","count":9},{"id":"GO:0051013","count":8},{"id":"GO:0051028","count":8},{"id":"GO:0061641","count":8}]},{"hash":"1576070347351300146","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0000466","count":2}]},{"hash":"290194944165225036","title":"Meiosis and Telomere Chromosome Dynamics","description":"These proteins cluster around meiosis- and chromosome-related processes: telomere localization to chromosome telomeric regions, meiotic attachment of telomeres to the nuclear envelope, spindle attachment during meiosis I, oocyte maturation, and broader cell-cycle regulation. Although one term references immunoglobulin V(D)J recombination, the dominant theme is meiotic chromosome dynamics and cell-cycle control, justifying a label focused on meiosis and telomere/chromosome functions.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033152","count":2},{"id":"GO:0070198","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0033147","count":2},{"id":"GO:0060743","count":2}]},{"hash":"1905646711609327434","title":"Unknown","description":"The top GO terms span transcription, RNA processing, protein repair, viral processes, development, and apoptosis, with several obsolete terms and no clear dominant function. The cluster lacks a cohesive biological theme or tightly connected pathway, so a specific functional label is not justifiable.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0030091","count":3},{"id":"GO:0032968","count":2},{"id":"GO:0000289","count":2},{"id":"GO:0051568","count":2}]},{"hash":"469361033887360594","title":"Heterochromatin formation and chromatin assembly","description":"This cluster is dominated by terms for heterochromatin formation (rDNA, pericentric, silent cassette) and centromeric chromatin assembly (CENP-A), with additional links to transcription regulation within a chromatin context and chromatin-related DNA processes. The common theme is chromatin organization and epigenetic silencing, including specialized centromeric chromatin maintenance.","confidence":"High","size":24,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000183","count":5},{"id":"GO:0000122","count":4},{"id":"GO:0042766","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0006351","count":4}]},{"hash":"77065227077299450","title":"Chloroplast and Mitochondrial Energy Metabolism","description":"This cluster centers on plastid (chloroplast) photosynthesis and mitochondrial respiration/assembly, with translation-related GO terms suggesting organelle protein synthesis; the combination points to energy production and redox regulation across plant organelles.","confidence":"Medium","size":24,"edges":276,"triangles":2024,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0055114","count":3},{"id":"GO:0032981","count":2},{"id":"GO:0019684","count":2},{"id":"GO:0006810","count":2}]},{"hash":"315786148812068900","title":"RNAP II Transcription Regulation","description":"The strongest signals are GO terms related to RNA polymerase II transcription regulation, including positive regulation of transcription elongation, preinitiation complex assembly, and transcription antitermination, which together point to a cluster of proteins involved in transcription control. Some redox/homeostasis terms and xenobiotic metabolism appear, suggesting additional roles or annotation noise, but they do not override the clear transcription-focused theme.","confidence":"Medium","size":24,"edges":20,"triangles":3,"max_degree":9,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0060065","count":4},{"id":"GO:0008584","count":3},{"id":"GO:0045454","count":3},{"id":"GO:0098869","count":3}]},{"hash":"2249737839630875974","title":"Ribosome biogenesis and mitotic machinery","description":"The cluster is dominated by translation-related terms (translation reinitiation; formation of translation preinitiation complex) and rRNA maturation (SSU/5.8S) along with cell division and mitosis-associated processes (microtubule severing; CENP-A chromatin assembly). While vesicle trafficking (ER to Golgi) and brain development appear, the core signal ties ribosome assembly to cell-cycle regulation, suggesting a functional cluster around ribosome biogenesis coupled to mitotic machinery.","confidence":"Medium","size":24,"edges":59,"triangles":92,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":6},{"id":"GO:0008283","count":5},{"id":"GO:0002188","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0000462","count":5}]},{"hash":"2036359821096504944","title":"Fungal metabolic transcription regulators","description":"This cluster\u2019s top GO terms consistently refer to positive regulation of transcription from RNA polymerase II promoter by various stimuli, many tied to fungal metabolism and secondary metabolism (e.g., sterol/ergosterol biosynthesis, aflatoxin biosynthesis, amino acid biosynthesis, respiration). This pattern points to a group of transcriptional regulators coordinating metabolic pathways in fungi.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035948","count":2},{"id":"GO:0035961","count":2},{"id":"GO:1904741","count":2},{"id":"GO:0061429","count":2},{"id":"GO:0043457","count":2}]},{"hash":"149774337766764149","title":"GTPase-Regulated Epithelial Polarity and Migration","description":"Most terms center on positive regulation of small GTPases and their signaling, plus establishment of epithelial cell polarity and cell migration (including podosome assembly). This points to a module coordinating cytoskeletal remodeling, polarity, and motility in epithelial contexts, likely via Rho/Rac/Cdc42-family GTPases and related pathways. Secondary terms about insulin and Fc receptor signaling appear as broader regulatory layers rather than defining a separate function.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0090162","count":3},{"id":"GO:0007264","count":3},{"id":"GO:0045737","count":3},{"id":"GO:0046626","count":3}]},{"hash":"1929062036978294410","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":15,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0006450","count":2},{"id":"GO:0044205","count":2},{"id":"GO:0006207","count":2}]},{"hash":"660967676319867105","title":"Cell cycle and chromosome segregation","description":"The dominant GO terms cluster around DNA replication and mitotic processes, including spindle-kinetochore attachment, kinetochore localization, G1/S transition, mitotic checkpoint signaling, and meiotic cell cycle. These strongly indicate cell cycle progression and chromosome segregation as the main theme of the cluster. A few terms related to neuronal development and drug response are present but appear as minor noise relative to the core signal.","confidence":"High","size":23,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0042220","count":2},{"id":"GO:0051315","count":2},{"id":"GO:0060079","count":2},{"id":"GO:0034501","count":2}]},{"hash":"1751656150471221614","title":"Nuclear transcription and RNA splicing regulation","description":"The GO terms are dominated by transcription-related processes (RNA Pol II/III activities, DNA-templated transcription, transcription elongation, preinitiation complex assembly) and RNA processing (alternative splicing via spliceosome, regulation of alternative splicing, mRNA export regulation), with some chromatin-associated activity (nucleosome disassembly). This suggests the cluster represents a nuclear gene expression regulation module focused on transcription and RNA processing/splicing.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000380","count":2},{"id":"GO:0000381","count":2},{"id":"GO:0051123","count":2},{"id":"GO:0010793","count":2},{"id":"GO:0006368","count":2}]},{"hash":"787598468502550394","title":"Embryonic development and morphogenesis","description":"The top GO terms cluster around developmental and morphogenetic processes, including embryonic placenta development, left-right pattern formation, cartilage morphogenesis, trophoblast differentiation, pancreas development, and endocrine system development, indicating a shared theme of embryo development and tissue formation. A couple of terms (mRNA splicing and translation reinitiation) relate to general cellular machinery and are less indicative of the cluster\u2019s core function. Overall, the group seems best described by embryonic development and morphogenesis.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":2},{"id":"GO:0060806","count":2},{"id":"GO:0003323","count":2},{"id":"GO:0060972","count":2},{"id":"GO:0003198","count":2}]},{"hash":"435013102627146461","title":"Meiosis and Cell Division","description":"This cluster is dominated by GO terms tied to meiotic processes and general cell division (meiotic spindle elongation, centromeric cohesion, and cell division). While there are additional terms related to intracellular trafficking (ER-to-Golgi transport, ribosomal protein import into the nucleus) and signaling (TORC1), the strongest signals point to meiosis and mitotic cell division as the core theme, with supporting roles from vesicle transport and protein synthesis regulation that facilitate these processes.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0051232","count":5},{"id":"GO:0006888","count":5},{"id":"GO:0051754","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0099590","count":4}]},{"hash":"2128671750355072352","title":"Ribosome biogenesis and translation","description":"The dominant GO terms relate to rRNA maturation (LSU and 5.8S), ribosome biogenesis, and translation, indicating the proteins cluster around ribosome assembly and protein synthesis. Some outlier terms touch RNA processing, transcription termination, or autophagy regulation, but the core signal is ribosome-related.","confidence":"High","size":23,"edges":12,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0014070","count":2},{"id":"GO:0000184","count":2},{"id":"GO:0006369","count":2}]},{"hash":"855416893768998109","title":"DNA Repair and RNA Pol II Transcription","description":"This cluster's top GO terms are DNA repair and DNA-templated transcription, pointing to nuclear maintenance and transcriptional control roles. Additional hits include ribosome biogenesis and rRNA maturation, consistent with nucleic-acid metabolism and ribosome assembly. Some terms are obsolete regulatory annotations, reflecting historical contexts but still aligning with transcription-centered functions. Overall, these proteins likely participate in genome maintenance and nucleic-acid processing rather than a single metabolic pathway.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006281","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0035948","count":3},{"id":"GO:1904741","count":3},{"id":"GO:0035969","count":3}]},{"hash":"1417393811804831354","title":"Brain development and neural tube closure","description":"Several top GO terms explicitly point to neurodevelopment, including brain development (GO:0007420) and neural tube closure (GO:0001843). Although there are also terms related to ribosomal RNA maturation and ER-Golgi transport among the list, these appear less central to the cluster\u2019s core signal. The dominant pattern across the enriched terms supports a neurodevelopmental theme, justifying this label.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043966","count":3},{"id":"GO:0006349","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0000466","count":3}]},{"hash":"1377254732118491715","title":"Membrane amino acid and polyamine transport","description":"This cluster is dominated by transmembrane transport terms for amino acids and related small molecules (methionine, D-serine, D-alanine, GABA, ammonium, leucine), as well as polyamine transport and osmotic response. The shared theme is transport across the membrane of amino acids and polyamines, so the label captures the core function represented.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006527","count":4},{"id":"GO:0044690","count":4},{"id":"GO:0035826","count":4},{"id":"GO:1902269","count":4},{"id":"GO:0070634","count":4}]},{"hash":"949392731694620595","title":"Metabolite and xenobiotic transmembrane transport","description":"Top GO terms indicate a cohesive theme of diverse transmembrane transport for xenobiotics, ions, vitamins, and metabolites, suggesting membrane transporters as the core function; a minority term on actin cytoskeleton organization is present but secondary to transport. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":3},{"id":"GO:0070634","count":2},{"id":"GO:0030036","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0015707","count":2}]},{"hash":"1987234808117041792","title":"Cyanobacterial sporulation and heterocyst differentiation","description":"The dominant GO terms point to sporulation and heterocyst development, with supporting signals for chemotaxis and flagellum-dependent motility, suggesting a cyanobacterial differentiation program involving spore formation, specialized cell differentiation, and environmental sensing. Some plant hormone signaling terms may reflect annotation noise or conserved signaling modules, but the core theme centers on cyanobacterial sporulation and heterocyst formation.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042173","count":1},{"id":"GO:0051606","count":1},{"id":"GO:0009736","count":1},{"id":"GO:0080117","count":1},{"id":"GO:0010105","count":1}]},{"hash":"528764102494193912","title":"Specialized lipid and secondary metabolite biosynthesis","description":"The top GO terms point to biosynthetic processes across lipids and numerous secondary metabolites (retinol/retinoic acid, sphingolipids, fatty acids, mycolic acids) as well as production of compounds like tropane alkaloids and antibiotics. This suggests a cohesive cluster centered on diverse lipid and specialized metabolite biosynthesis rather than a single pathway.","confidence":"Medium","size":22,"edges":138,"triangles":461,"max_degree":20,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009710","count":21},{"id":"GO:0017000","count":21},{"id":"GO:0055114","count":21},{"id":"GO:0042572","count":21},{"id":"GO:0006666","count":21}]},{"hash":"141437334094197516","title":"Mitochondrial energy metabolism and translation","description":"The dominant GO terms point to mitochondrial function\u2014protein import into the mitochondrial matrix, TCA cycle, mitochondrial electron transport, and translation\u2014together with redox homeostasis. This pattern suggests a cluster of proteins involved in mitochondrial energy production and mitochondrial protein synthesis, with a few developmental terms likely incidental.","confidence":"High","size":22,"edges":231,"triangles":1540,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0030150","count":3},{"id":"GO:0045454","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006120","count":2}]},{"hash":"2178315025629600479","title":"Cell Cycle and Cytoskeleton Regulation","description":"The cluster is enriched with terms tied to cell division and regulation of cyclin-dependent kinase (CDK) activity, as well as cytoskeletal and trafficking processes such as podosome assembly, actin cortical patch localization, and Golgi-to-plasma membrane transport. DNA-templated transcription and negative regulation of cell size further support proliferative control. Taken together, these terms point to coordinated control of cell cycle progression with cytoskeletal remodeling and vesicle trafficking, suggesting a functional theme around cell cycle coupled with cytoskeleton dynamics.","confidence":"High","size":22,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0097421","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0045737","count":2}]},{"hash":"1999302218961678438","title":"Prostate epithelial development and vesicle trafficking","description":"The top GO terms cluster around prostate gland\u2013specific epithelial maturation and differentiation, including epithelial maturation and secretory differentiation in prostate gland acini, complemented by vesicle trafficking (Golgi to ER), cilium assembly, and related secretory/cytoskeletal processes. This suggests a theme of prostate epithelium development paired with secretory and trafficking functions.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060743","count":3},{"id":"GO:0006890","count":2},{"id":"GO:0060271","count":2},{"id":"GO:0060038","count":2},{"id":"GO:0034316","count":2}]},{"hash":"927320612757530173","title":"Immune signaling and RNA processing","description":"The top GO terms point to immune signaling (GM-CSF stimulus, B cell and T cell homeostasis, T cell proliferation) and signaling pathways (EGF response, p38MAPK cascade), alongside RNA processing and proteostasis processes (proteasome assembly, mRNA splicing, localization, and translation). This suggests a cohesive cluster of proteins involved in immune signaling linked with RNA processing and protein turnover.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097011","count":2},{"id":"GO:0001782","count":2},{"id":"GO:0071364","count":2},{"id":"GO:0043248","count":2},{"id":"GO:0045292","count":1}]},{"hash":"1375117526810239230","title":"Unknown","description":"The top GO terms include a mix of iron metabolism, lipid/Cardiolipin metabolism, ion transport, mitosis, and diverse developmental processes with no single shared function, so there isn\u2019t a coherent theme tying these proteins together. ","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036086","count":2},{"id":"GO:0032048","count":2},{"id":"GO:0034758","count":2},{"id":"GO:0034087","count":2},{"id":"GO:2000185","count":2}]},{"hash":"842911851962417954","title":"Ribosome biogenesis and TORC1 signaling","description":"The top GO terms strongly point to ribosome production and maturation (ribosomal large subunit biogenesis; 5.8S rRNA maturation) together with growth regulation (TORC1 signaling) and cell-cycle processes (mitotic cell cycle; G0 to G1 transition; DNA damage checkpoint signaling). This combination indicates a module coordinating ribosome assembly with growth signals and division. While some terms are broader (transcription, GTPase regulation), they can be part of the same growth-and-growth-control program.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0000920","count":6},{"id":"GO:0035948","count":6},{"id":"GO:0042273","count":6}]},{"hash":"1276554829690319500","title":"Secretory vesicle trafficking (ER\u2013Golgi\u2013vacuole)","description":"The strongest signals in the GO terms are ER to Golgi vesicle-mediated transport and Golgi to vacuole transport, indicating a cohesive vesicle trafficking theme along the secretory pathway. Other terms (transcriptional regulation, methylation, biosynthesis, senescence) appear less represented and may reflect broader or secondary annotations, but do not outweigh the trafficking signal. Confidence: Medium","confidence":"","size":21,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0006896","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0009236","count":2}]},{"hash":"670717902097084311","title":"Ribosome Biogenesis and Translation","description":"The top GO terms are dominated by translation and ribosome biogenesis, including cytoplasmic translation, small and large subunit biogenesis/assembly, and rRNA maturation/export. This pattern points to proteins involved in ribosome production and function, with some linkage to general growth-related processes like the cell cycle. Overall, the cluster represents ribosome biogenesis and translation machinery.","confidence":"High","size":21,"edges":194,"triangles":1064,"max_degree":20,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":15},{"id":"GO:0042254","count":5},{"id":"GO:0042274","count":3},{"id":"GO:0002181","count":3},{"id":"GO:0007049","count":3}]},{"hash":"1598519644925015108","title":"Cell Cycle and Mitosis Regulation","description":"The terms cluster around cell cycle progression, DNA replication and checkpoint signaling, mitotic sister chromatid cohesion, and abscission, pointing to a coherent theme of cell cycle control and mitosis. A single term on insulin signaling regulation appears peripheral and does not define the cluster.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0046626","count":2},{"id":"GO:0009838","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0043111","count":1}]},{"hash":"1395547093579529747","title":"Unknown","description":"Top GO terms are highly diverse, including responses to cocaine, glucose metabolism, chemotaxis, fatty acid oxidation, peptide hormone signaling, FSH signaling, placenta development, sensory perception, and nucleus import regulation; with no dominant shared process or pathway across the cluster, a coherent label cannot be assigned.","confidence":"","size":21,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042220","count":2},{"id":"GO:0033160","count":2},{"id":"GO:0006006","count":2},{"id":"GO:0006935","count":2},{"id":"GO:0001890","count":2}]},{"hash":"1045473551485691847","title":"Lymphocyte signaling and cytoskeletal remodeling","description":"The Top Terms are largely immune-related, including T cell receptor signaling, NK/T cell differentiation, B cell maturation, and integrin signaling, as well as positive regulation of actin filament binding. This points to lymphocyte activation and cytoskeletal rearrangements as a unifying theme for the cluster, with actin dynamics supporting receptor signaling and cell movement. A few terms are less directly relevant (e.g., neuron development), but the dominant signal is immune signaling coupled with cytoskeletal dynamics.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0098761","count":3},{"id":"GO:0001865","count":3},{"id":"GO:1904531","count":3},{"id":"GO:0007229","count":3},{"id":"GO:0002344","count":3}]},{"hash":"1795832474739646425","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016441","count":2},{"id":"GO:1902039","count":2},{"id":"GO:0034063","count":2},{"id":"GO:0000056","count":2},{"id":"GO:0000480","count":2}]},{"hash":"376519276136643113","title":"Vertebrate organ development and metabolism","description":"The terms cluster around organ morphogenesis across multiple systems (inner ear, heart, ureter, gonad) and accompanying metabolic processes (retinol/retinal metabolism, GABA shunt, carbon utilization), suggesting a coherent theme of vertebrate organ development with metabolic context.","confidence":"High","size":20,"edges":171,"triangles":969,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":19},{"id":"GO:0042574","count":19},{"id":"GO:0035799","count":11},{"id":"GO:0042472","count":11},{"id":"GO:0008584","count":10}]},{"hash":"383792960973592023","title":"DNA replication and cell cycle regulation","description":"This cluster is dominated by GO terms related to DNA replication (GO:0006260), DNA-templated transcription (GO:0006351), the centrosome cycle, and positive regulation of nuclear cell cycle DNA replication, indicating a core role in genome duplication and cell-cycle control. Developmental terms (telencephalon development, cranial skeleton morphogenesis) may reflect pleiotropic roles of these proteins rather than a primary function of the cluster. ","confidence":"High","size":20,"edges":38,"triangles":25,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":19},{"id":"GO:0048701","count":18},{"id":"GO:0006351","count":15},{"id":"GO:0010571","count":15},{"id":"GO:0007098","count":15}]},{"hash":"608908154132206530","title":"Ribosome Biogenesis and Translation","description":"GO terms centered on translation and ribosome biogenesis (cytoplasmic/mitochondrial translation, ribosomal subunit assembly, initiation, termination, and disassembly), indicating these proteins belong to the protein synthesis machinery.","confidence":"High","size":20,"edges":95,"triangles":306,"max_degree":18,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":11},{"id":"GO:0042254","count":4},{"id":"GO:0046677","count":4},{"id":"GO:0000027","count":3},{"id":"GO:0006413","count":3}]},{"hash":"1855779324624067063","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000447","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0001731","count":4},{"id":"GO:0006446","count":3},{"id":"GO:0000480","count":3}]},{"hash":"1237290346483812373","title":"Ubiquitin-dependent proteolysis and stress signaling","description":"This cluster centers on ubiquitin-mediated protein turnover (ubiquitin-dependent proteolysis and autoubiquitination) and signaling pathways activated by stress, such as TNF signaling and JNK cascade with I-kappaB phosphorylation. While a few terms touch on peroxisomal import and chromatin regulation, the dominant theme is ubiquitin-regulated protein turnover linked to stress-responsive signaling. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016558","count":2},{"id":"GO:0042787","count":2},{"id":"GO:1903721","count":2},{"id":"GO:1903762","count":2},{"id":"GO:0009048","count":2}]},{"hash":"882390532985040443","title":"Metabolism and Hormone-Driven Immune Responses","description":"These proteins show links to core metabolic pathways (nitrate assimilation, cholesterol biosynthesis, fatty acid oxidation, amino acid transport/catabolism) and to cellular responses triggered by hormones and immune signaling (peptide hormone stimulus, FSH stimulus, cytokine production in inflammatory response). The common thread is metabolic processing coupled to signal-driven responses to hormonal and inflammatory cues.","confidence":"Medium","size":20,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":2},{"id":"GO:1904659","count":2},{"id":"GO:0006695","count":2},{"id":"GO:0071375","count":2},{"id":"GO:0071372","count":2}]},{"hash":"772048509643237350","title":"Ubiquitin-Proteasome and Translation Initiation Regulation","description":"This cluster centers on ubiquitin-related processes (deubiquitination and ubiquitination) and translation initiation, including proteasome-mediated protein turnover and mRNA stability elements. The co-occurrence of these terms suggests a coordinated role in regulating protein abundance and translation, potentially during development or stress responses.","confidence":"High","size":20,"edges":16,"triangles":0,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0070537","count":2},{"id":"GO:0035871","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0075522","count":2},{"id":"GO:0006446","count":2}]},{"hash":"1922254642019558011","title":"RNA processing and translational regulation","description":"GO terms indicate a strong focus on RNA-level processing and regulation, including mRNA splicing (cis, alternative), splice-site recognition, mRNA modification and stabilization, translation initiation and reinitiation, and miRNA-mediated translational repression; a related transcription regulation term is present but the dominant signal is RNA processing and post-transcriptional control.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0045292","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0000380","count":2},{"id":"GO:0001731","count":2}]},{"hash":"1064014752410963110","title":"Plant carbon metabolism and signaling","description":"The cluster\u2019s top GO terms cluster around carbohydrate handling (glucose transport, starch catabolism) and related metabolism (fatty acid biosynthesis) together with signaling/regulatory processes (protein kinase activity regulation, signal transduction) and circadian rhythm, pointing to a plant-centric set of metabolism tightly connected to signaling and temporal regulation. Pollen hydration hints at plant reproductive physiology but fits within broader plant metabolism context. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904659","count":2},{"id":"GO:0043562","count":1},{"id":"GO:0009744","count":1},{"id":"GO:0007165","count":1},{"id":"GO:0009859","count":1}]},{"hash":"1463832022829954770","title":"Mitochondrial respiration and redox regulation","description":"This cluster is dominated by GO terms related to mitochondrial electron transport, respirasome assembly, proton transmembrane transport, and regulation of cytochrome c release, all pointing to mitochondrial energy production and redox control; oxidative detoxification and response to toxic substances further support a role in redox homeostasis. An outlier like antibiotic biosynthetic process may be noise, but the core signal aligns with mitochondrial respiration functions.","confidence":"High","size":20,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0009060","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0019740","count":3},{"id":"GO:0009636","count":3}]},{"hash":"397054239961755427","title":"Metabolism and nitrosative stress signaling","description":"The cluster\u2019s GO terms point to broad metabolic activities (retinoid/retinol, galactose, sorbitol) alongside redox/nitrosative signaling processes (nitrosative stress response, S-nitrosylation), suggesting a theme of metabolism linked to redox regulation rather than a single precise pathway.","confidence":"Medium","size":19,"edges":106,"triangles":309,"max_degree":17,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0003016","count":11},{"id":"GO:0042573","count":11},{"id":"GO:0033859","count":11},{"id":"GO:0042572","count":11},{"id":"GO:0006069","count":11}]},{"hash":"64027624220552750","title":"Mitochondrial energy metabolism and redox cofactors","description":"The proteins group around mitochondrial energy production and redox balance, with terms covering NADH-driven electron transport, TCA-related metabolism (2-oxoglutarate), and cofactors like lipoate and thiamine that feed into pyruvate dehydrogenase and related complexes. Despite a few outliers (some obsolete or developmental terms), the dominant theme is mitochondrial energy metabolism and redox homeostasis.","confidence":"High","size":19,"edges":60,"triangles":73,"max_degree":18,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009228","count":15},{"id":"GO:0043046","count":12},{"id":"GO:0055114","count":12},{"id":"GO:0045454","count":12},{"id":"GO:0007568","count":11}]},{"hash":"1526317933900445338","title":"Mitochondrial translation and energy production","description":"This cluster is characterized by GO terms centered on protein synthesis and mitochondrial function, including positive regulation of mitochondrial translation, general translation, and cytosolic ribosome assembly, alongside energy-related processes such as proton motive force\u2013driven ATP synthesis and proton transmembrane transport. Additional terms like vacuolar acidification and sodium ion transport point to proton and ion homeostasis linked to energy production, supporting a cohesive theme of mitochondrially linked protein synthesis and energy generation.","confidence":"High","size":19,"edges":166,"triangles":887,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0070131","count":3},{"id":"GO:0006412","count":2},{"id":"GO:0006814","count":2},{"id":"GO:0007035","count":2},{"id":"GO:0042777","count":2}]},{"hash":"1797096844436718947","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":34,"triangles":14,"max_degree":9,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0071400","count":3},{"id":"GO:0006541","count":3},{"id":"GO:1903718","count":3},{"id":"GO:0000162","count":3},{"id":"GO:0070365","count":3}]},{"hash":"1276226439627286494","title":"DNA replication and repair","description":"The cluster's top GO terms are dominated by DNA replication-related processes: DNA replication, leading strand elongation, and error-free translesion synthesis, suggesting a core theme of genome duplication and maintenance. Other terms (vesicle transport, development, peroxisome import) are more peripheral, possibly reflecting ancillary roles or annotation noise, but the replication-centric terms anchor the label.","confidence":"Medium","size":19,"edges":16,"triangles":3,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0070987","count":3},{"id":"GO:0006272","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0007275","count":3}]},{"hash":"117427733693375696","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034063","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0032968","count":1}]},{"hash":"29853917735926013","title":"Lipid metabolism and palmitoylation","description":"The GO terms point to cholesterol homeostasis, triglyceride and VLDL biosynthesis, and multiple forms of protein palmitoylation, including N-palmitoylation, with a tangent to the smoothened signaling pathway. This pattern suggests a cluster of proteins involved in lipid metabolism and lipidation of proteins rather than a single narrow function.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061408","count":2},{"id":"GO:0042632","count":1},{"id":"GO:0060262","count":1},{"id":"GO:0007224","count":1},{"id":"GO:0034379","count":1}]},{"hash":"813244065535728274","title":"Unknown","description":"The top GO terms cover a wide and disparate range of functions (bicarbonate and oxygen transport, platelet aggregation, hepatic stellate cell regulation, brown fat differentiation, oxidative and nitrosative stress responses, endocytosis, vascular maintenance, and collagen regulation) with no evident common biological theme or interaction pattern, and there are no edges connecting proteins. This lack of a coherent shared function makes it inappropriate to assign a specific functional label beyond Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015701","count":1},{"id":"GO:0070527","count":1},{"id":"GO:2000490","count":1},{"id":"GO:0050873","count":1},{"id":"GO:0042542","count":1}]},{"hash":"1953910093774695345","title":"Ribosome Biogenesis and Translation","description":"The dominant GO terms are all about ribosome production and function: large subunit biogenesis, maturation of SSU/LSU rRNA, ribosome biogenesis in general, ribosomal subunit assembly, and translation. This points to a cluster of proteins involved in ribosome assembly, rRNA processing, and protein synthesis. A few RNA export and DNA-related terms appear as minor non-core associations, but the core signal remains ribosome-related.","confidence":"High","size":18,"edges":116,"triangles":494,"max_degree":15,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042273","count":6},{"id":"GO:0000463","count":4},{"id":"GO:0006412","count":4},{"id":"GO:0000462","count":4},{"id":"GO:0042254","count":3}]},{"hash":"353422394017871457","title":"DNA replication and centrosome cycle","description":"The cluster is dominated by GO terms for DNA replication, DNA-templated transcription, and centrosome cycle/mitotic centrosome separation, indicating a core module of replication and cell-cycle control. Additional terms point to nuclear transport regulation and developmental processes such as telencephalon development and cranial skeleton morphogenesis, suggesting some members may link replication with early development. Overall, the theme centers on DNA replication and centrosome dynamics with some developmental associations.","confidence":"Medium","size":18,"edges":25,"triangles":5,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":12},{"id":"GO:0006351","count":8},{"id":"GO:0010571","count":8},{"id":"GO:0048701","count":8},{"id":"GO:0007098","count":8}]},{"hash":"814949780077923547","title":"Ubiquitin-Dependent Innate Immune Signaling","description":"The cluster is enriched for innate immune and antiviral defense terms, together with ubiquitin-related processes (ubiquitination, polyubiquitination, ERAD), suggesting proteins that regulate immune signaling through ubiquitin-mediated degradation and quality control. Several terms also point to modulation of Toll-like receptor signaling and transcription/apoptosis, consistent with coordinated innate immune regulation.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045087","count":5},{"id":"GO:0051607","count":5},{"id":"GO:0000209","count":5},{"id":"GO:0042787","count":5},{"id":"GO:0071157","count":4}]},{"hash":"1305463365820818750","title":"Cell Cycle Control and Stress Signaling","description":"Top GO terms emphasize regulation of G0 to G1 transition, G1 DNA damage checkpoint signaling, TORC1 signaling, and intrinsic apoptotic signaling in response to ER stress. These together suggest a theme of coordinating cell cycle progression with cellular stress responses. Other terms on ribosome maturation, nuclear pore localization, and microtubule dynamics fit into the broader growth and division context, supporting a label for regulators of cell growth, division, and stress signaling rather than a single precise process.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0070317","count":2},{"id":"GO:0072432","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0038202","count":2}]},{"hash":"2134939857948154537","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000480","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0042254","count":2}]},{"hash":"1797415252122678141","title":"Developmental signaling and immune response","description":"The top GO terms span muscle and neural development (myotube differentiation, axon fasciculation), signaling (MAPK cascade), immune activity (type IV hypersensitivity, activated T cell proliferation), and general regulatory processes (apoptotic process, DNA repair, mRNA processing). The mix suggests a cluster of proteins involved in broad developmental regulation and signaling with immune and stress-related roles, rather than a single cohesive function. Confidence: Medium","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0014902","count":3},{"id":"GO:0032212","count":3},{"id":"GO:0000196","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0006397","count":3}]},{"hash":"2199370871897835792","title":"Cell cycle and apoptosis regulation","description":"The top GO terms include mitotic cell cycle and apoptotic process, indicating core involvement in proliferation and cell death. Additional terms point to transcriptional regulation and signaling, with some tissue-specific notes like keratinocyte differentiation and visual perception, suggesting the cluster houses proteins that coordinate cell fate, growth, and survival across contexts rather than a single pathway.","confidence":"Medium","size":18,"edges":150,"triangles":769,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":12},{"id":"GO:0000278","count":12},{"id":"GO:0034351","count":12},{"id":"GO:0001324","count":11},{"id":"GO:0090153","count":11}]},{"hash":"662605377097346464","title":"Unknown","description":"The top terms cover a wide range of processes from yeast vacuole fusion and growth forms to dopamine signaling, immune responses, and brain development, with no clear shared function or cohesive pathway linking them. The absence of edges further supports the lack of a common theme, so a meaningful cluster label cannot be assigned.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042144","count":3},{"id":"GO:0007124","count":2},{"id":"GO:0001403","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0032298","count":2}]},{"hash":"228325872417539839","title":"Mitochondrial Respiration and Translation","description":"This cluster is dominated by mitochondrial processes: electron transport chains and respiration (NADH to ubiquinone, cytochrome c to oxygen, respirasome assembly), mitochondrial translation, and protein import into the mitochondrial matrix. These terms together point to a cohesive mitochondrial bioenergetics module, with a few outliers like sporulation terms likely representing noise. ","confidence":"High","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0006123","count":2},{"id":"GO:0032543","count":2},{"id":"GO:0009060","count":1},{"id":"GO:1902600","count":1},{"id":"GO:0097250","count":1}]},{"hash":"1655020678951593856","title":"Transcription and Translation Regulation","description":"Based on the top GO terms, the cluster centers on regulation of gene expression, including DNA-templated transcription and regulation of translational initiation/translation reinitiation, with some related nuclear-periphery transcriptional tethering terms. Some entries are marked obsolete or peripheral (e.g., histone methylation, viral translation terms), but the recurring theme is control of gene expression at both transcriptional and translational levels.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0035948","count":3},{"id":"GO:0000973","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0075525","count":2}]},{"hash":"2230256809518942766","title":"Transmembrane amino acid and small-molecule transport","description":"The top GO terms cluster around transport across membranes for amino acids and small molecules (e.g., L-arginine, methionine, D-serine, D-alanine, GABA, ammonium, polyamines) and related processes like transepithelial transport and hypotonic salinity response. This pattern suggests a cohesive function centered on membrane transport rather than a single metabolic pathway, so a concise label focusing on transmembrane transport of amino acids and related small molecules is appropriate.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006527","count":1},{"id":"GO:0044690","count":1},{"id":"GO:0035826","count":1},{"id":"GO:1902269","count":1},{"id":"GO:0070634","count":1}]},{"hash":"2184419468884135848","title":"Ubiquitin-Dependent Proteolysis in Cell Cycle","description":"This cluster is driven by ubiquitin-proteasome\u2013mediated protein turnover, including autoubiquitination, K11-linked ubiquitination, SCF- and APC/C-dependent degradation, and neddylation. The presence of nucleotide-excision repair terms alongside cell-cycle regulators suggests a broader role for ubiquitin signaling in coordinating DNA repair with cell division.","confidence":"High","size":17,"edges":35,"triangles":18,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051865","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0031146","count":5},{"id":"GO:0070911","count":5},{"id":"GO:0070979","count":5}]},{"hash":"795649823183549765","title":"Metal stress response and proteostasis","description":"This cluster shows enrichment for responses to metal ions (cadmium and zinc) and ozone, indicating a metal- or oxidative-stress response. It also features terms related to the ubiquitin-proteasome system (proteasome core complex assembly, proteasomal ubiquitin-independent protein catabolic process, and protein deubiquitination), suggesting coordinated protein turnover during stress. Some regulatory and obsolete terms related to cell cycle stress responses are present, but the dominant theme points to proteostasis under metal/oxidative stress.","confidence":"Medium","size":17,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0010193","count":2},{"id":"GO:0006521","count":1},{"id":"GO:0010499","count":1},{"id":"GO:0051436","count":1},{"id":"GO:0080129","count":1}]},{"hash":"1732249080228945512","title":"Unknown","description":"The cluster's terms are scattered across mitochondrial energy generation (ATP synthase complex assembly, proton motive force) and various unrelated processes (auditory stereocilium organization, spermatogenesis, embryo implantation, antipsychotic response, sucrose stimulus). With no single dominant biological theme, it's not possible to assign a cohesive functional label.","confidence":"","size":17,"edges":14,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0035786","count":2},{"id":"GO:0033615","count":1},{"id":"GO:0015986","count":1},{"id":"GO:0097332","count":1},{"id":"GO:0060088","count":1}]},{"hash":"2073864003582723675","title":"Nuclear import/export and ribosome trafficking","description":"This cluster is dominated by GO terms tied to nucleus-focused transport and assembly: import of proteins bearing NLS, ribosomal protein import into the nucleus, nuclear pore complex assembly, and mRNA export, all pointing to a coordinated set of nuclear transport and ribosome-related processes that also intersect with cell division. A few outliers (e.g., proton transport) exist, but the core theme is cohesive around nuclear transport machinery and nuclear-cytoplasmic trafficking. ","confidence":"Medium","size":17,"edges":76,"triangles":162,"max_degree":16,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0042176","count":6},{"id":"GO:0006610","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0060188","count":5},{"id":"GO:0043547","count":5}]},{"hash":"1644335432800419113","title":"Cell cycle and cytoskeletal dynamics","description":"This cluster includes mitotic cell cycle terms, several apoptotic processes, ubiquitination, epithelial polarity, cell migration, and mechanotransduction (response to muscle stretch). The mix suggests a module coordinating cell division, apoptosis, and remodeling of cellular structure and polarity.","confidence":"Medium","size":17,"edges":6,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035994","count":3},{"id":"GO:0000278","count":3},{"id":"GO:2001275","count":2},{"id":"GO:2000171","count":2},{"id":"GO:0090162","count":2}]},{"hash":"2284834463297028667","title":"Neuronal endocytosis and receptor trafficking","description":"The cluster\u2019s top GO terms converge on endocytosis, targeting to vacuoles, and transport of neurotransmitter receptors from endosomes to postsynaptic membranes, which points to vesicular trafficking at synapses. Additional terms like nervous system development, Roundabout signaling, and Smoothened signaling reinforce a neuronal signaling/axonal guidance theme. Although a few terms (kidney development, mitochondrial outer membrane permeabilization) seem peripheral, the dominant pattern fits proteins involved in neuronal vesicle trafficking and synaptic receptor management.","confidence":"Medium","size":17,"edges":21,"triangles":1,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006897","count":3},{"id":"GO:0006623","count":2},{"id":"GO:0098887","count":2},{"id":"GO:0001822","count":2},{"id":"GO:0097345","count":2}]},{"hash":"1524309239529305068","title":"Cell Cycle and Proteostasis","description":"This cluster centers on mitotic/cytoskeletal functions (DNA-templated transcription, cell division, microtubule severing, centriole elongation) coupled with protein homeostasis and quality control (autophagosome maturation, chaperone-related folding, protein processing, ATP metabolism, and misfolded protein catabolic pathways). The blend suggests a cohesive theme around cell cycle progression supported by proteostasis and chaperone networks, rather than a single narrow process.","confidence":"Medium","size":17,"edges":65,"triangles":118,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0051301","count":9},{"id":"GO:0097352","count":8},{"id":"GO:0070389","count":8},{"id":"GO:0051013","count":8}]},{"hash":"157063630055466885","title":"Ribosome biogenesis and translation","description":"Most terms cluster around translation and ribosome biogenesis/assembly (translation, ribosome biogenesis, ribosomal subunit assembly, and related processes). Occasional terms about antibiotic response and stress-induced apoptosis may reflect cellular stress impacts on translation. Overall, the cluster is best described by ribosome function and protein synthesis.","confidence":"High","size":17,"edges":123,"triangles":516,"max_degree":16,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":17},{"id":"GO:0042254","count":5},{"id":"GO:0046677","count":5},{"id":"GO:0006407","count":4},{"id":"GO:0000027","count":4}]},{"hash":"1666351882166707866","title":"Energy metabolism and cellular stress responses","description":"This cluster shows enrichment for metabolism-related GO terms, including glycolytic and gluconeogenic processes and serine biosynthesis, alongside stress-related functions such as respiratory burst, autophagy, and apoptotic mitochondrial changes. The presence of cobalt ion response and cobalamin biosynthesis suggests a broader connection to metal handling and vitamin biosynthesis, which can tie into metabolic state. Brain development is less directly linked but can reflect tissue-specific roles of these pathways. Overall, the core theme appears to be metabolism coupled with cellular stress responses.","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045730","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0008637","count":3},{"id":"GO:0006564","count":2},{"id":"GO:0006096","count":2}]},{"hash":"226144585034940606","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0007420","count":2},{"id":"GO:0071480","count":2},{"id":"GO:0000466","count":2}]},{"hash":"1346720142682636307","title":"Cell Cycle and Vesicle Trafficking","description":"The cluster highlights G1/S transition and centrosome localization, complemented by vesicle transport and signaling processes (endosome-to-Golgi and phosphatidylinositol signaling) and secretory granule maturation. This pattern suggests proteins involved in coordinating cell cycle progression with intracellular trafficking and membrane dynamics, capturing a general theme of cell-cycle\u2013related organization and vesicle trafficking rather than a single precise pathway.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000082","count":2},{"id":"GO:0043666","count":1},{"id":"GO:0071539","count":1},{"id":"GO:0032005","count":1},{"id":"GO:0010252","count":1}]},{"hash":"1109094903446992335","title":"mRNA Splicing and Translation Regulation","description":"The top terms center on mRNA processing via spliceosome (cis and alternative splicing, splice site recognition, mRNA modification) and translation-related steps (translation reinitiation, preinitiation complex formation, miRNA-mediated translational inhibition, mRNA stabilization), indicating a cohesive cluster of post-transcriptional gene expression control spanning both splicing and translation.","confidence":"High","size":17,"edges":43,"triangles":29,"max_degree":10,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0000380","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0048255","count":3}]},{"hash":"1892809044700687832","title":"Neuronal chromatin regulation and ubiquitin turnover","description":"The cluster centers on transcriptional regulation in the nucleus (negative regulation of transcription by RNA polymerase II; establishment of protein localization to chromatin; regulation of histone methylation) and ubiquitin-related protein turnover (protein polyubiquitination; ubiquitin-dependent protein catabolic process), all within a neuronal context. Additional terms point to synaptic organization and dopamine responsiveness, suggesting these proteins link chromatin-level control to synaptic signaling via ubiquitin-mediated processes. This cohesive theme across nucleus and synapse supports a label centered on neuronal chromatin regulation coupled to ubiquitin pathways.","confidence":"Medium","size":17,"edges":9,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0071169","count":2},{"id":"GO:0061086","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0006516","count":1},{"id":"GO:0090394","count":1}]},{"hash":"828321141162816156","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048254","count":1},{"id":"GO:0000480","count":1},{"id":"GO:0000472","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0000244","count":1}]},{"hash":"1025629635630335182","title":"Photoreceptor Development","description":"This cluster includes GO terms linked to photoreceptor biology, notably photoreceptor cell outer segment organization and retinal rod cell development, which point to a retina/photoreceptor theme. Other terms are broad and mix with general processes, so the retina signal is present but not dominant; the label Photoreceptor Development captures the most specific shared function suggested by the data.","confidence":"Medium","size":17,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:1901215","count":1},{"id":"GO:0038108","count":1},{"id":"GO:1903646","count":1},{"id":"GO:0046661","count":1}]},{"hash":"1465103508641003870","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035948","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0000466","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0000398","count":3}]},{"hash":"2146026144196069713","title":"Unknown","description":"The top terms span both plant and animal biology (xylan catabolic process, systemic acquired resistance, mesonephros development) and include various proteolytic and immune-related processes (protein catabolic process, membrane protein proteolysis, antigen processing via MHC II, amyloid-beta metabolism, angiotensin maturation). This heterogeneity provides no single coherent function linking the proteins, and the lack of edges supports an Unknown cluster. ","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0045493","count":5},{"id":"GO:0001823","count":5},{"id":"GO:0042985","count":5},{"id":"GO:0030163","count":5},{"id":"GO:0002003","count":5}]},{"hash":"1118006971062082186","title":"Mitochondrial cofactor and metabolite transport","description":"These proteins show strong enrichment for transport of a range of cofactors and metabolites into mitochondria (NAD, PLP, alpha-ketoglutarate, CoA, heme, pyrimidine nucleotides) plus related mitochondrial functions like membrane potential regulation and oxidative stress response, suggesting a cohesive role in mitochondrial metabolite transport and redox homeostasis.","confidence":"High","size":16,"edges":57,"triangles":25,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0035352","count":9},{"id":"GO:0031921","count":9},{"id":"GO:0015742","count":9},{"id":"GO:0035349","count":9},{"id":"GO:0032869","count":9}]},{"hash":"1897229461904669219","title":"Protein acetylation and polyamine metabolism","description":"The GO terms show a strong emphasis on acetylation events, including N-terminal, peptidyl-lysine, and propionylation, as well as acetylation of polyamines (spermidine and spermine). Coupled with polyamine catabolic processes and related metabolic pathways (glucosamine and arginine biosynthesis) and mycothiol biosynthesis, the cluster appears to consist of proteins involved in acetylation-based modifications and polyamine metabolism, likely in a bacterial context. The mitotic chromatid cohesion term seems out of place and may be annotation noise. ","confidence":"Medium","size":16,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0018003","count":3},{"id":"GO:0046208","count":2},{"id":"GO:0061606","count":2},{"id":"GO:0032918","count":2},{"id":"GO:0032919","count":2}]},{"hash":"63967681815866065","title":"Detoxification and Stress Response","description":"The terms point to a theme of cellular defense and adaptation to chemical and metabolic stress: oxidant detoxification and toxin catabolic processes, response to toxic substances, starvation response, and insulin-related metabolic signaling. Additional terms (nitric oxide storage, aromatic amino acid metabolism, nucleotide-excision repair, and cytoplasmic translation) support a broader stress- and maintenance-oriented program rather than a single precise pathway, aligning well with a detoxification and stress-response label.","confidence":"Medium","size":16,"edges":119,"triangles":546,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":13},{"id":"GO:0032869","count":10},{"id":"GO:0060316","count":10},{"id":"GO:0009407","count":10},{"id":"GO:0035732","count":10}]},{"hash":"2056894747188467109","title":"Ribosome Biogenesis and Translation Initiation","description":"The terms cluster around maturation and processing of rRNA components (LSU, 5.8S, ITS1), ribosomal large subunit biogenesis, and steps in translation initiation (preinitiation complex formation, translation reinitiation). TORC1 signaling links to nutrient-regulated ribosome production, supporting a cohesive theme of ribosome assembly and initiation; peripheral terms like pigmentation or ER-Golgi transport may reflect broader cellular roles or annotation noise, but do not contradict the central ribosome-focused theme.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":4},{"id":"GO:0002188","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0043473","count":3}]},{"hash":"2012508797209484717","title":"Ribosome Biogenesis and Nucleolar RNA Processing","description":"The top GO terms cluster strongly around ribosome biogenesis and RNA processing, including maturation of 5.8S rRNA and rRNA processing, which point to nucleolar ribosome assembly functions. While other terms reference cell cycle regulation and stress responses, the dominant signal is nucleolar ribosome production and RNA maturation, justifying this label.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":7},{"id":"GO:0071456","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0000747","count":6},{"id":"GO:0042254","count":6}]},{"hash":"675751323034503989","title":"Mitochondrial respiration, translation, and genome maintenance","description":"The cluster is dominated by mitochondrial functions: electron transport and complex IV assembly point to respiration, while translation indicates mitochondrial protein synthesis; repair and genome maintenance terms (even if older/obsolete) further support a mitochondrial genome maintenance theme, with apoptosis and tumor-cell response reflecting mitochondria-related cell death signaling. Vitamin E biosynthesis may relate to oxidative stress context within mitochondria, reinforcing the overall mitochondrial functional theme.","confidence":"High","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006123","count":2},{"id":"GO:0033617","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0036297","count":1},{"id":"GO:0000725","count":1}]},{"hash":"782705301438300434","title":"RNA processing and chromatin regulation","description":"This cluster\u2019s top GO terms center on RNA metabolism and chromatin-related processes, including primary miRNA processing, rRNA catabolic processes, and RNA phosphodiester bond hydrolysis, plus chromatin organization. While several terms are obsolete or point to other catabolic activities (triglyceride, bradykinin, collagen), the strongest, non-obsolete signals point to nucleic acid processing and chromatin dynamics, suggesting a cluster of proteins involved in RNA maturation and chromatin-related regulation.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0019433","count":2},{"id":"GO:0034396","count":1},{"id":"GO:0010815","count":1}]},{"hash":"1433302283403093302","title":"Translation Initiation and Preinitiation Complex Regulation","description":"This cluster is dominated by GO terms tied to translation initiation and its regulation (formation of the translation preinitiation complex, positive regulation of eIF4F assembly, and negative regulation of translational initiation), with a couple of outliers (e.g., glycerophospholipid catabolic process, oligodendrocyte development) likely representing noise rather than core function.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046475","count":2},{"id":"GO:1905612","count":1},{"id":"GO:0001731","count":1},{"id":"GO:1905537","count":1},{"id":"GO:0045947","count":1}]},{"hash":"1850172833702367264","title":"Amino acid biosynthesis and central metabolism","description":"The dominant terms are several amino acid biosynthetic processes (leucine, aspartate, lysine) and core metabolism (TCA cycle), with supporting signals for fatty acid homeostasis and vitamin biosynthesis. Signaling terms like Notch and insulin response are comparatively fewer, suggesting the primary theme is metabolic pathways with some signaling links.","confidence":"Medium","size":15,"edges":91,"triangles":299,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019878","count":9},{"id":"GO:0006099","count":5},{"id":"GO:0009098","count":5},{"id":"GO:0007219","count":5},{"id":"GO:0042853","count":5}]},{"hash":"679227024091287097","title":"Amino acid biosynthesis and redox metabolism","description":"The cluster shows enrichment for amino acid biosynthetic processes (L-leucine, 2-oxoglutarate and lysine pathways) along with redox-related activities (NADP+/NADPH biosynthesis/regeneration, glutathione metabolism, and responses to oxidative stress). This combination points to proteins co-involved in balancing amino acid production with cellular redox homeostasis. Some terms related to development (female gonad development, response to steroid hormone, glial migration) appear less central to the core theme and may be incidental noise. Overall, the dominant theme is metabolic pathways tied to redox balance and amino acid supply.","confidence":"Medium","size":15,"edges":95,"triangles":339,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0009098","count":1},{"id":"GO:0008585","count":1},{"id":"GO:0006103","count":1},{"id":"GO:0006741","count":1},{"id":"GO:0019878","count":1}]},{"hash":"1846141822415030795","title":"Unknown","description":"The top GO terms cover xenobiotic response, plant hormone signaling, learning, multiple metabolic processes and development with no clear shared function, suggesting a heterogeneous cluster or cross-kingdom noise rather than a cohesive biological module.","confidence":"","size":15,"edges":12,"triangles":10,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":8},{"id":"GO:0009740","count":7},{"id":"GO:0007612","count":7},{"id":"GO:0046340","count":7},{"id":"GO:0042136","count":7}]},{"hash":"1088767300381187794","title":"Mitotic machinery and microtubule assembly","description":"The strongest signals are mitotic and cytoskeletal: nuclear envelope organization, cell division, mitotic cell cycle, and tubulin complex assembly. This points to roles in microtubule dynamics and mitotic spindle function. Other terms (Golgi-to-plasma membrane transport, cell adhesion, dopamine response, and interneuron development) suggest added involvement in trafficking, adhesion, and neural differentiation processes that can accompany cell division and cytoskeletal changes, but the core theme remains mitotic machinery and microtubule assembly.","confidence":"Medium","size":15,"edges":67,"triangles":112,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006998","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0007021","count":4},{"id":"GO:0003100","count":3}]},{"hash":"638868866325080692","title":"Nucleocytoplasmic mRNA and ribosome export","description":"These proteins show a cohesive pattern around nuclear transport: mRNA export from the nucleus, ribosomal large subunit export, ribosomal protein import, hnRNP/splicing-factor import, and tRNA transport, all pointing to the nuclear-cytoplasmic trafficking machinery. Ragged mentions of Ran signaling and intraciliary transport align with broader transport roles, supporting a core theme of nucleocytoplasmic transport and ribosome trafficking.","confidence":"High","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006406","count":6},{"id":"GO:0043547","count":5},{"id":"GO:0000055","count":5},{"id":"GO:0035048","count":4},{"id":"GO:0051031","count":4}]},{"hash":"2205334327507987598","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0000002","count":3},{"id":"GO:0032211","count":3},{"id":"GO:0070317","count":3},{"id":"GO:0034314","count":3}]},{"hash":"875065973443516543","title":"Unknown","description":"The GO terms are highly diverse with no single unifying process (plant hormone response, seed growth regulation, stress-related metabolism, chromatin and telomere biology, and basic cellular housekeeping), and there are no edges connecting proteins, making a coherent functional label unlikely.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":1},{"id":"GO:0046938","count":1},{"id":"GO:1904715","count":1},{"id":"GO:0043085","count":1},{"id":"GO:0055059","count":1}]},{"hash":"2293303721508227086","title":"Golgi Trafficking & Endocytosis","description":"The cluster shows several GO terms tied to intracellular transport and Golgi function: clathrin-dependent endocytosis, retrograde transport from endosome to Golgi, and protein retention in the Golgi. These collectively point to a membrane trafficking theme, possibly supported by GTPase regulation of trafficking processes. Some terms (osmotic stress, telomere maintenance, NK cell regulation, tRNA modification) appear more peripheral, suggesting noise or multi-function proteins; overall the core represents Golgi/vesicle trafficking biology.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0006970","count":2},{"id":"GO:0035435","count":2},{"id":"GO:0000722","count":1},{"id":"GO:0007329","count":1}]},{"hash":"1811180377690451267","title":"Embryonic Development and Tissue Morphogenesis","description":"These terms cluster around developmental differentiation and morphogenesis across multiple tissues\u2014placenta, pancreas, cartilage, and endocrine structures\u2014plus left-right patterning and EMT, with Rho signaling regulation and intracellular transport supporting cell movement and organization.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0060806","count":1},{"id":"GO:0003323","count":1},{"id":"GO:0060972","count":1}]},{"hash":"1910096865204515763","title":"Autophagy and mitophagy","description":"The top GO terms are dominated by autophagy-related processes (autophagosome assembly, autophagy of mitochondrion, Cvt pathway, and piecemeal microautophagy of nucleus) with links to mitophagy and stress-related programmed cell death, suggesting this cluster groups proteins involved in autophagy and mitochondrial turnover, potentially intersecting apoptosis signaling; minor terms like viral process or aerobic respiration may reflect broader cellular context but do not override the autophagy-centric theme.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009060","count":2},{"id":"GO:0016032","count":2},{"id":"GO:0000045","count":2},{"id":"GO:0032258","count":2},{"id":"GO:0098779","count":2}]},{"hash":"2135563102117299601","title":"Mitochondrial Metabolite and Ion Transport","description":"These proteins are linked by GO terms describing the transport of diverse metabolites and ions into mitochondria (NAD, alpha-ketoglutarate, pyridoxal phosphate, CoA, heme, manganese, pyrimidine nucleotides) and by related mitochondrial functions (membrane potential regulation, oxidative stress response). The concentration of mitochondrial transport-related terms with multiple substrates suggests a cohesive set of mitochondrial transporters maintaining metabolite supply and redox balance.","confidence":"High","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035352","count":8},{"id":"GO:0031921","count":8},{"id":"GO:0015742","count":8},{"id":"GO:0035349","count":8},{"id":"GO:0032869","count":8}]},{"hash":"1459452768943507698","title":"Organelle and Metabolite Transport","description":"The GO terms are dominated by transport activities for metabolites and vesicles between organelles, including NAD, alpha-ketoglutarate, pyridoxal phosphate, CoA, and pyrimidine nucleotides into mitochondria or across membranes, as well as ER-to-Golgi vesicle transport. This suggests the cluster centers on intracellular transport functionalities, with a note of metabolic regulation (insulin response, mitochondrial membrane potential) linked to these transport processes.","confidence":"Medium","size":14,"edges":13,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0035352","count":2},{"id":"GO:0031921","count":2},{"id":"GO:0015742","count":2},{"id":"GO:0035349","count":2}]},{"hash":"584783693688561689","title":"Epithelial Polarity and Tight Junction Assembly","description":"The top terms are dominated by epithelial organization, notably bicellular tight junction assembly and establishment of epithelial cell polarity, pointing to a core theme of epithelial cell structure. Some terms also relate to proteostasis and ER-stress\u2013driven translation, suggesting a supporting role of protein homeostasis in maintaining polarity, while a few (DNA replication, mesoderm formation) indicate broader developmental or housekeeping roles. Overall, the strongest cohesive signal is epithelial polarity and junction formation.","confidence":"Medium","size":14,"edges":85,"triangles":298,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070830","count":5},{"id":"GO:0090162","count":5},{"id":"GO:0071630","count":5},{"id":"GO:0032781","count":5},{"id":"GO:0001707","count":5}]},{"hash":"1327254472678993378","title":"Unknown","description":"The most recurrent terms are RNA modification (tRNA and rRNA methylation), but the cluster also includes lipid catabolic and glycolytic processes, along with various trafficking and regulatory terms (endosome transport, protein localization to cell surface, hypoxia response, angiogenesis regulation). The spread across unrelated biological themes provides no clear, cohesive function for all members, so the cluster cannot be confidently labeled with a specific, representative function.","confidence":"","size":14,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0030488","count":2},{"id":"GO:0031167","count":2},{"id":"GO:0016042","count":2},{"id":"GO:0031639","count":1},{"id":"GO:0006096","count":1}]},{"hash":"772499925797866659","title":"Unknown","description":"The GO terms show a highly diverse set of processes\u2014from metabolism (glycogen and sucrose), transcription and DNA recombination, to cytoskeletal regulation, neural signaling, development, and antibiotic biosynthesis\u2014without a single dominant theme. As a result, there isn\u2019t a coherent functional label that captures the cluster's function.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0005978","count":2},{"id":"GO:0000743","count":2},{"id":"GO:0031115","count":2},{"id":"GO:0090394","count":2},{"id":"GO:0006310","count":2}]},{"hash":"900267559065608530","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:1902987","count":4},{"id":"GO:0030435","count":3},{"id":"GO:0042572","count":3},{"id":"GO:0006633","count":3}]},{"hash":"590164363714790782","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006369","count":11},{"id":"GO:0071038","count":11},{"id":"GO:0000398","count":11},{"id":"GO:0000467","count":11},{"id":"GO:0034476","count":11}]},{"hash":"982351918265194009","title":"Metabolic and biosynthetic processes","description":"This cluster centers on metabolic and biosynthetic activity, with GO terms pointing to amino acid and fatty acid catabolism (L-leucine and fatty acids), glycogen biosynthesis, and starvation response. Additional terms touch on organelle-related processes (mitochondrial translation, ER organization) and tissue development (liver development), suggesting a broad energy- and biosynthesis-oriented theme across contexts. Overall, a single precise pathway isn\u2019t evident, but the core theme fits \"Metabolic and biosynthetic processes.\"","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006552","count":4},{"id":"GO:0042594","count":4},{"id":"GO:0001889","count":4},{"id":"GO:0005978","count":4},{"id":"GO:0032543","count":3}]},{"hash":"216197405108151284","title":"Proteostasis: translation and proteasome regulation","description":"The GO terms cluster around translation initiation and ribosome biogenesis (translation reinitiation, preinitiation complex formation, regulation of translational initiation, ribosome biogenesis) and the proteasome pathway (proteasome assembly, ubiquitin-dependent protein catabolic process), indicating a coordinated program for protein synthesis and turnover. While some development-related terms appear, the dominant signal is maintenance of proteostasis through both protein production and degradation.","confidence":"High","size":14,"edges":49,"triangles":76,"max_degree":13,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0002188","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0043248","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0051301","count":3}]},{"hash":"736530254852699694","title":"Fatty acid and sphinganine metabolism","description":"The top GO terms center on unsaturated fatty acid biosynthesis, sphinganine metabolism, and fatty acid response, indicating a cluster enriched for lipid metabolism, particularly fatty acid and sphingolipid pathways. Several other terms are obsolete or less related, suggesting annotation noise, but the lipid-related terms provide the most consistent theme for this group.","confidence":"Medium","size":14,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006636","count":1},{"id":"GO:0006667","count":1},{"id":"GO:0000001","count":1},{"id":"GO:0042128","count":1}]},{"hash":"1203828725869938915","title":"Membrane lipid biosynthesis and endocytosis","description":"This cluster is dominated by GO terms related to membrane processes: receptor-mediated endocytosis, GPI anchor biosynthetic process, and phospholipid biosynthesis pathways (CDP-choline and phosphatidylethanolamine), plus ethanolamine metabolism. These together point to proteins involved in lipid production and membrane trafficking; a few notes about stress response annotations (e.g., to antibiotics or 3-methylcholanthrene) may be incidental.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006898","count":2},{"id":"GO:0006506","count":2},{"id":"GO:0006657","count":1},{"id":"GO:0019509","count":1},{"id":"GO:0006646","count":1}]},{"hash":"372147949367082206","title":"Mitochondrial translation and respiratory chain assembly","description":"The dominant GO terms describe mitochondrial protein synthesis (translation, multiple tRNA aminoacylations, regulation of translational fidelity) and the assembly of mitochondrial respiratory chain complexes I and IV, pointing to a cohesive module of mitochondrial gene expression and respiratory complex assembly. A peripheral Group I intron splicing term may reflect mitochondrial RNA processing, while the fat cell differentiation term appears incidental. Overall, the cluster centers on mitochondrial translation machinery and respiratory complex assembly.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":1},{"id":"GO:0006428","count":1},{"id":"GO:0006438","count":1},{"id":"GO:0006429","count":1},{"id":"GO:0006412","count":1}]},{"hash":"1281260126162601690","title":"Unknown","description":"The top GO terms cover several unrelated areas (DNA-templated transcription, ER-Golgi trafficking, ribosomal RNA maturation, pigmentation, and cell cycle regulation), with no clear unifying function or interaction pattern in this cluster. Given the lack of a cohesive theme and edges, a single, interpretable label isn\u2019t apparent.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0043547","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0043473","count":2}]},{"hash":"1288159834538545812","title":"Xenobiotic and Phosphate Transporters","description":"Reason: enriched for membrane transport activities, especially xenobiotic transmembrane transport and phosphate ion transmembrane transport, with some related nutrient/stress response terms. This points to a cluster of transport proteins handling foreign compounds and phosphate ions across membranes, rather than a single enzyme pathway.","confidence":"Medium","size":14,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":2},{"id":"GO:0097421","count":2},{"id":"GO:0035435","count":2},{"id":"GO:0034198","count":2},{"id":"GO:0006817","count":2}]},{"hash":"2139193515782981729","title":"Neural development and signaling regulation","description":"The cluster includes neural development terms (cerebellar cortex formation, Bergmann glial differentiation, axon regeneration) alongside broad signaling pathway regulation (insulin receptor, T cell receptor, tyrosine dephosphorylation, VEGF signaling). This points to proteins involved in modulating signaling during neural development and growth, justifying the combined label.","confidence":"Medium","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035335","count":7},{"id":"GO:2001275","count":7},{"id":"GO:0008285","count":7},{"id":"GO:0048679","count":7},{"id":"GO:0021697","count":7}]},{"hash":"1145958531954300595","title":"Membrane Transporters","description":"The proteins are linked to diverse transmembrane transport processes (ions like K+, nitrite/nitrate, sugars such as arabinose, vitamins, xenobiotics, and neurotransmitter loading), indicating a cohesive theme of membrane transporter proteins across substrates.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":12},{"id":"GO:0015707","count":12},{"id":"GO:0098700","count":12},{"id":"GO:0015706","count":12},{"id":"GO:0006855","count":12}]},{"hash":"411545058827386641","title":"ER Stress and Protein Quality Control","description":"This cluster is dominated by terms tied to proteostasis: chaperone/cofactor-dependent protein refolding, response to unfolded protein, ER stress-regulated translation initiation, translation, and regulation of translational fidelity, along with nuclear proteasome-based quality control. Together, they point to cellular mechanisms that manage protein folding and degradation during stress, i.e., ER stress proteostasis. A few terms (mesoderm formation, DNA replication, tRNA import) are less directly related and may reflect broader or incidental annotations in this small cluster.","confidence":"Medium","size":14,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070389","count":2},{"id":"GO:0036494","count":2},{"id":"GO:0006986","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006450","count":2}]},{"hash":"2065189955255484080","title":"Proteasome-Mediated Protein Degradation and Deubiquitination","description":"The GO terms cluster strongly around proteasome function and ubiquitin-related turnover, including proteasome core complex assembly, ubiquitin-independent degradation, and deubiquitination, with additional ties to cell-cycle regulation and metal stress responses. This pattern points to a proteostasis-focused group of proteins coordinating degradation with regulatory processes.","confidence":"High","size":13,"edges":32,"triangles":39,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006521","count":5},{"id":"GO:0010499","count":5},{"id":"GO:0051436","count":5},{"id":"GO:0080129","count":5},{"id":"GO:0010043","count":5}]},{"hash":"1953684745222282216","title":"Mitochondrial metabolite transporters","description":"The cluster prominently features GO terms for transmembrane transport of cofactors and metabolites (NAD, \u03b1-ketoglutarate, pyridoxal phosphate, coenzyme A, heme) and processes related to mitochondrial function (mitochondrial membrane potential regulation, oxidative stress response) and insulin signaling, suggesting a group of proteins that transport key metabolites/cofactors across mitochondrial membranes and participate in redox/metabolic regulation. The mitotic cell cycle term is less consistent with the main theme.","confidence":"Medium","size":13,"edges":11,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0035352","count":1},{"id":"GO:0031921","count":1},{"id":"GO:0015742","count":1}]},{"hash":"1019607510432715928","title":"Golgi SNARE-mediated vesicle transport","description":"The cluster is dominated by GO terms for Golgi vesicle trafficking, SNARE complex assembly, and ER-Golgi transport, plus exocytic delivery to the plasma membrane and synaptic receptor trafficking, indicating a cohesive function in Golgi-centered vesicle transport and membrane fusion.","confidence":"High","size":13,"edges":33,"triangles":23,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0048280","count":7},{"id":"GO:0035493","count":6},{"id":"GO:0090161","count":6},{"id":"GO:0098967","count":6},{"id":"GO:0006888","count":6}]},{"hash":"793809207170584465","title":"Chromatin regulation and transcriptional control","description":"The cluster centers on chromatin state and transcriptional regulation, with GO terms for DNA-templated transcription, heterochromatin formation/maintenance, nucleosome density regulation, and histone deacetylation, plus developmental signals (endodermal fate, embryonic hematopoiesis) indicating broader regulatory roles in differentiation.","confidence":"High","size":13,"edges":27,"triangles":20,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0000183","count":4},{"id":"GO:0034983","count":4},{"id":"GO:0045668","count":4},{"id":"GO:0060303","count":4}]},{"hash":"1404696343786444258","title":"Ribosome and Translation Machinery","description":"Top terms are overwhelmingly translation- and ribosome-focused (translation, cytoplasmic and mitochondrial translation, ribosomal large subunit assembly, maturation of SSU-rRNA, translational termination, and translational fidelity). This suggests the proteins form a cohesive translation system across compartments, spanning both cytosolic and mitochondrial contexts. The antibiotic response term is a secondary signal; overall, the cluster represents protein synthesis machinery.","confidence":"High","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":10},{"id":"GO:0046677","count":3},{"id":"GO:0006450","count":3},{"id":"GO:0000462","count":2},{"id":"GO:0000027","count":2}]},{"hash":"1232720072597006477","title":"Transcription and Heterochromatin Formation with ER Stress Signaling","description":"This cluster is enriched for DNA-templated transcription and heterochromatin formation terms (pericentric and subtelomeric), together with ER stress-related signaling (unfolded protein response and apoptotic pathways). While a few terms touch development or immune signaling, the strongest common thread links transcription/chromatin regulation to ER stress responses.","confidence":"Medium","size":13,"edges":6,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0030702","count":2},{"id":"GO:0006348","count":2},{"id":"GO:1990502","count":2}]},{"hash":"2230606316747441471","title":"Development and Immune Differentiation","description":"The top GO terms point to developmental processes (segmental identity, outflow tract/eye/placenta morphogenesis) as well as immune differentiation (TH2 and dendritic cell differentiation). The terms are diverse with no single shared pathway, suggesting a broad theme of differentiation across developmental and immune contexts rather than a specific function. ","confidence":"Medium","size":13,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007381","count":1},{"id":"GO:0003151","count":1},{"id":"GO:1903984","count":1},{"id":"GO:0001892","count":1},{"id":"GO:0043011","count":1}]},{"hash":"2058810380093920087","title":"Amino acid biosynthesis and sulfur metabolism","description":"These proteins show enrichment across several amino acid biosynthetic pathways (tryptophan, D-serine, 2-oxobutyrate, pyruvate-derived biosynthesis) and sulfur-containing metabolism (hydrogen sulfide biosynthesis, homocysteine catabolism). Despite some obsolete terms, the remaining GO terms converge on amino acid biosynthesis with an emphasis on sulfur-containing compounds, supporting a single cohesive functional theme. ","confidence":"Medium","size":13,"edges":20,"triangles":30,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0042866","count":6},{"id":"GO:0070179","count":5},{"id":"GO:0043418","count":5},{"id":"GO:0046360","count":5},{"id":"GO:0000162","count":5}]},{"hash":"200996184557424304","title":"Xenobiotic and retinoid metabolism","description":"This cluster is driven by GO terms related to metabolism and breakdown of foreign compounds and retinoids (retinol/retinal), along with associated detox pathways (glutathione and glucuronate catabolic processes, bile acid metabolism, and aromatic compound degradation like naphthalene). Though a kidney development term appears, the dominant signals point to metabolic/detox functions, especially xenobiotic and retinoid processing, making this label representative and specific.","confidence":"High","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0042572","count":9},{"id":"GO:0055114","count":8},{"id":"GO:0046370","count":8},{"id":"GO:0042574","count":7},{"id":"GO:0006750","count":6}]},{"hash":"1713409900342256361","title":"Actin Cytoskeleton Dynamics and Vesicle Trafficking","description":"The Top Terms show a clear focus on actin cytoskeleton organization and remodeling (Arp2/3-mediated nucleation, postsynaptic actin organization, cortical patch localization) together with vesicle transport processes (COPII-coated vesicle loading, intracellular protein transport). Additional terms touch on muscle actin usage and developmental morphogenesis, supporting a cohesive theme around actin-driven cytoskeletal remodeling linked to vesicular trafficking. Therefore, this label captures the cluster\u2019s primary functions.","confidence":"High","size":13,"edges":10,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0060982","count":2},{"id":"GO:0090110","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0051666","count":1},{"id":"GO:0034314","count":1}]},{"hash":"1709670931850521107","title":"Neurodevelopment and Cell Cycle Regulation","description":"The top GO terms mix nervous system development and neuronal differentiation with core cell cycle transitions (G1/S, G2/M) and embryonic processes, suggesting a cluster of proteins that coordinate neural development with cell proliferation and differentiation. Insulin signaling and vitamin D receptor signaling appear as additional regulatory context, supporting a developmental and growth-promoting theme.","confidence":"Medium","size":13,"edges":7,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0045773","count":2},{"id":"GO:0000082","count":2},{"id":"GO:0007399","count":2},{"id":"GO:0030097","count":2}]},{"hash":"1672071276051806587","title":"Unknown","description":"The top GO terms span several unrelated processes (transcription elongation, translation initiation, protein folding, mitochondrial import and membrane regulation, triglyceride biosynthesis, cell cycle regulation, and DNA repair), with no single cohesive function linking the cluster. Therefore a specific, intuitive label isn\u2019t apparent.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070940","count":1},{"id":"GO:0010867","count":1},{"id":"GO:0030150","count":1},{"id":"GO:0046902","count":1},{"id":"GO:2000134","count":1}]},{"hash":"568740757986689267","title":"Mitotic Cell Cycle and Spindle Organization","description":"Most of the top GO terms cluster around mitosis, DNA replication, and spindle dynamics (mitotic cell cycle, DNA replication, pre-replicative complex assembly, mitotic spindle assembly, spindle orientation checkpoint). A broader cytoskeletal/polarity context is also present (cell shape regulation and actin cytoskeleton-related). The dominant signal is cell cycle progression and spindle organization, supporting this label.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0090394","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0031578","count":3},{"id":"GO:0031532","count":3}]},{"hash":"46279554120463161","title":"Nuclear RNA Processing and Surveillance","description":"The listed GO terms cluster around nuclear RNA metabolism and quality control, including nuclear mRNA surveillance, snoRNA catabolic and polyadenylation-dependent decay processes, and post-transcriptional tethering of RNA Pol II to DNA at the nuclear periphery, with supporting but looser connections to chromatin modification and DNA recombination within the nucleus. The emphasis on nuclear RNA processing and surveillance suggests a cohesive functional theme for this cluster, supporting the chosen label. ","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090503","count":1},{"id":"GO:0071044","count":1},{"id":"GO:0071036","count":1},{"id":"GO:0071049","count":1},{"id":"GO:0032066","count":1}]},{"hash":"762356304767112635","title":"Post-transcriptional RNA processing and translation regulation","description":"This cluster centers on RNA processing and regulation of gene expression at the post-transcriptional level, with prevalent GO terms for mRNA splicing, spliceosome activity, translation initiation/reinitiation, mRNA modification and stabilization, and miRNA-mediated translational silencing. A smaller signal for transcription elongation regulation is present but the dominant theme is RNA processing and control of translation.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032968","count":2},{"id":"GO:0045292","count":1},{"id":"GO:0002188","count":1},{"id":"GO:0000380","count":1},{"id":"GO:0001731","count":1}]},{"hash":"1507507420288983935","title":"Microbial RNA processing and energy metabolism","description":"The cluster shows strong signals for RNA-related processes (tRNA processing, ribosome disassembly, endoribonuclease regulation, tRNA queuosine biosynthesis) together with core metabolic pathways (TCA cycle, formate metabolism, methanogenesis, and even photosynthetic electron transport). This combination suggests a microbial context where RNA metabolism and energy production are tightly linked. The presence of some odd GO terms (e.g., sperm capacitation) likely reflects annotation noise rather than biology. Overall, the label captures the main themes: RNA processing/regulation and energy metabolism in microbes. ","confidence":"Medium","size":13,"edges":73,"triangles":238,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0008033","count":2},{"id":"GO:0006099","count":2},{"id":"GO:0048240","count":2},{"id":"GO:0008616","count":1}]},{"hash":"650217555817211856","title":"Cell Growth, DNA Repair, and Epigenetic Regulation","description":"The terms cluster around cellular proliferation and growth (inner cell mass proliferation, cell growth) alongside DNA repair (break-induced replication) and epigenetic/modification processes (histone H4 methylation, arginine methylation), with senescence as a related outcome. Some outliers (cobalamin biosynthesis, tellurium ion response) exist, but the dominant theme links growth control, genome maintenance, and chromatin regulation.","confidence":"Medium","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001833","count":2},{"id":"GO:0000727","count":2},{"id":"GO:0009236","count":2},{"id":"GO:0090398","count":2},{"id":"GO:0046690","count":2}]},{"hash":"828829334517892748","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":8,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006122","count":2},{"id":"GO:0006564","count":2},{"id":"GO:0007219","count":2},{"id":"GO:0019805","count":2},{"id":"GO:0001694","count":2}]},{"hash":"1828014400908500588","title":"Transmembrane solute transporters","description":"The top GO terms are dominated by diverse membrane transport activities: nitrite transport, nitrate transmembrane transport, selenite transport, sodium-dependent organic cation transport, xylose transmembrane transport, and glucose import in response to insulin stimulus, all pointing to a cluster of transporter proteins facilitating solute movement across the membrane. A few terms related to fructose stimulus response and intestinal epithelial maintenance appear as ancillary context, but the core theme remains membrane transporters handling varied substrates. Therefore, the label Transmembrane solute transporters captures the shared function.","confidence":"Medium","size":12,"edges":8,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":2},{"id":"GO:0097080","count":1},{"id":"GO:0070715","count":1},{"id":"GO:0015706","count":1},{"id":"GO:0071332","count":1}]},{"hash":"1794502210196991240","title":"Transcriptional Regulation of Metabolic Pathways","description":"Based on GO terms, the cluster centers on DNA-templated transcription and regulation of transcription from RNA polymerase II promoter, with accompanied signals for metabolic biosynthesis and regulation (cellular respiration, amino acid and nucleotide biosynthesis). This pattern points to proteins that influence transcriptional control of metabolic processes.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0035948","count":4},{"id":"GO:0035961","count":4},{"id":"GO:1904741","count":4},{"id":"GO:0061429","count":4}]},{"hash":"917861707548332395","title":"Unknown","description":"The terms span diverse themes: cellular responses to various stimuli (cAMP, hydrogen peroxide, oleic acid, ammonium), metabolic processes (glutamine and tryptophan biosynthesis), and development of multiple tissues (substantia nigra, skeletal muscle, hepatocytes). There isn\u2019t a single coherent function tying the cluster together, so a specific label isn\u2019t justifiable.","confidence":"","size":12,"edges":59,"triangles":156,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0071320","count":3},{"id":"GO:0006541","count":3},{"id":"GO:0021762","count":2},{"id":"GO:0070301","count":2},{"id":"GO:0048741","count":2}]},{"hash":"679288223525043464","title":"Fungal sterol and sphingolipid biosynthesis","description":"The cluster is enriched for ergosterol-related and sphingolipid metabolism terms (regulation of ergosterol biosynthetic process, mannosyl-inositol phosphorylceramide metabolic process) and fatty acid biosynthesis, plus mitochondrial energy production (mitochondrial ATP synthesis coupled electron transport), which together point to fungal lipid biosynthesis with connected energy metabolism.","confidence":"Medium","size":12,"edges":11,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":3},{"id":"GO:0035435","count":3},{"id":"GO:0006809","count":2},{"id":"GO:0006636","count":2},{"id":"GO:0006675","count":2}]},{"hash":"1353333957177743828","title":"Ubiquitin-Proteasome Immunity Pathways","description":"The cluster centers on ubiquitin-dependent protein catabolic processes (SCF- and ERAD-mediated) and proteasomal degradation, with accompanying innate immune and antiviral defense signals. This suggests a module where ubiquitin-proteasome machinery intersects with immune signaling, though a few terms are more peripheral to immunity (e.g., glycoprotein catabolic process, cell cycle regulation).","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":3},{"id":"GO:0045087","count":2},{"id":"GO:0045842","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0051607","count":2}]},{"hash":"188920829937902255","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042273","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0000463","count":4},{"id":"GO:0000747","count":4},{"id":"GO:0042254","count":4}]},{"hash":"900881017205641461","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":2},{"id":"GO:0016441","count":1},{"id":"GO:1902039","count":1},{"id":"GO:0034063","count":1},{"id":"GO:0000056","count":1}]},{"hash":"1948174254574415291","title":"Adaptive Immune Signaling and NK T Cell Differentiation","description":"The top GO terms cluster around adaptive immunity, Fc receptor\u2013mediated signaling, NK T cell differentiation, IL-7 response, and ubiquitination regulation, indicating proteins involved in immune signaling and T cell biology. Some terms about skeletal or neuronal development appear as minor outliers, but they do not dominate the cluster. Confidence: Medium","confidence":"","size":12,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0060368","count":2},{"id":"GO:0032005","count":2},{"id":"GO:1990441","count":2},{"id":"GO:1904888","count":2},{"id":"GO:1900044","count":2}]},{"hash":"1697222624683562405","title":"Acetylation-Driven Metabolism","description":"The cluster shows a strong enrichment for acetylation-related GO terms across different contexts (N-terminal acetylation, propionylation, spermidine/spermine acetylation, and histone H4 acetylation), suggesting a common theme of acetylation chemistry influencing protein and metabolite regulation. In addition, several metabolic processes appear (glucosamine metabolism, L-arginine biosynthesis, mycothiol biosynthesis), indicating associated metabolic pathways. A few terms related to chromatin regulation (centromeric cohesion, histone acetylation) may reflect broader regulatory roles of acetylation or annotation history, but the dominant signal remains acetylation-centered biology.","confidence":"Medium","size":12,"edges":57,"triangles":146,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0046208","count":9},{"id":"GO:0061606","count":9},{"id":"GO:0032918","count":9},{"id":"GO:0032919","count":9},{"id":"GO:0006041","count":9}]},{"hash":"38953980519154560","title":"Translation initiation and ribosome biogenesis","description":"This cluster shows strong enrichment for translation-related GO terms, including translation, initiation complex formation, translational initiation, and ribosome assembly, along with RNA processing steps tied to ribosome biogenesis (tRNA and snoRNA processing). The shared theme is proteins involved in starting translation and assembling ribosomes.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0090502","count":1},{"id":"GO:0000294","count":1},{"id":"GO:0034965","count":1},{"id":"GO:0008033","count":1}]},{"hash":"2022395102330414183","title":"Tissue Morphogenesis and Differentiation","description":"The top GO terms center on development and tissue formation, with lung epithelial differentiation, placenta morphogenesis, and coronary vasculature morphogenesis indicating a cross-tissue morphogenesis theme. Supporting processes like SMAD/TGF-\u03b2 signaling regulation and ubiquitin-mediated turnover point to common regulatory mechanisms in morphogenesis, while general processes such as GTPase activity regulation and transcriptional control align with differentiation. The cluster appears to be a network of proteins involved in tissue development and morphogenic signaling rather than a single specific pathway, justifying this label.","confidence":"Medium","size":11,"edges":52,"triangles":139,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0060487","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0045944","count":3},{"id":"GO:0032465","count":3},{"id":"GO:0043162","count":2}]},{"hash":"915265411621027826","title":"RNA splicing and mRNA decay machinery","description":"The top GO terms cluster around spliceosome-mediated mRNA processing (mRNA cis splicing via spliceosome, spliceosomal snRNP assembly), mRNA turnover (deadenylation-dependent decapping, P-body assembly), and transcription termination, with supporting hints of ribosomal RNA maturation and broader RNA metabolism. While a few terms touch on chromatin or cell-cycle regulation, the dominant theme is RNA processing and gene expression control.","confidence":"High","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":7},{"id":"GO:0033962","count":7},{"id":"GO:1990141","count":7},{"id":"GO:0000290","count":7},{"id":"GO:0042633","count":7}]},{"hash":"104446104872111258","title":"Bacterial cell envelope biosynthesis","description":"The cluster shows enrichment for teichoic and lipoteichoic acid biosynthesis (Gram-positive cell wall components), lipopolysaccharide biosynthesis (envelope-related), and fatty acid biosynthesis (membrane lipids), with supporting iron-sulfur cluster assembly in metabolism. Although several lysine biosynthesis terms are marked obsolete, the dominant theme is biosynthesis of cell envelope and membrane components in bacteria, suggesting a coherent envelope-related function for this group.","confidence":"Medium","size":11,"edges":54,"triangles":156,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0019878","count":4},{"id":"GO:0006633","count":3},{"id":"GO:0019518","count":3},{"id":"GO:0009236","count":3},{"id":"GO:0009097","count":2}]},{"hash":"470446179030881578","title":"Carbohydrate catabolism and amino acid biosynthesis with K+ transport","description":"This cluster centers on carbohydrate metabolism (pentose-phosphate shunt, glyoxylate, gluconate/galactarate, sulfoquinovose, formate catabolism) and amino acid biosynthesis (tyrosine; isoleucine), with a potassium ion transport term, suggesting a module of central carbon metabolism linked to amino-acid production and ion transport. Some terms are obsolete, but the core pattern supports this functional theme.","confidence":"Medium","size":11,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0016575","count":2},{"id":"GO:1902777","count":1},{"id":"GO:0006098","count":1},{"id":"GO:0042183","count":1},{"id":"GO:0046487","count":1}]},{"hash":"273063539385161683","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":48,"triangles":117,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0097310","count":2},{"id":"GO:0000453","count":2},{"id":"GO:0019062","count":2},{"id":"GO:0039654","count":2},{"id":"GO:0002128","count":2}]},{"hash":"1265257334985292549","title":"Neural development and translation machinery","description":"The terms show a strong presence of translation-related processes (multiple aminoacyl-tRNA synthetases, translation, translational fidelity) alongside chromatin-related activity (CENP-A chromatin assembly, histone H3 acetylation) and microtubule dynamics, plus a brain development term. This suggests a loosely connected theme around gene expression, chromatin regulation, and cytoskeletal remodeling in neural development, making this a best-fit but not tightly cohesive label.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061641","count":4},{"id":"GO:0006428","count":3},{"id":"GO:0006438","count":3},{"id":"GO:0006429","count":3},{"id":"GO:0006412","count":3}]},{"hash":"731516543292766547","title":"ER-Golgi protein processing during the cell cycle","description":"This cluster is enriched for cell division and cell cycle terms, along with ER-to-Golgi vesicle transport and ER protein folding, suggesting involvement in coordinating the secretory pathway with cell-cycle progression. A minor signal for autophagosome assembly also appears, supporting a broader role in cellular quality control during division.","confidence":"High","size":11,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0034975","count":1},{"id":"GO:0000045","count":1}]},{"hash":"1215947259345797009","title":"Unknown","description":"The terms span cofactor biosynthesis (NAD+ and CoA) and various intracellular transport processes, plus a scattered set of unrelated functions (cornified envelope assembly, retrograde signaling). This lack of a single cohesive theme across the cluster makes it difficult to assign a concise, representative label. None","confidence":"","size":11,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046939","count":1},{"id":"GO:0015937","count":1},{"id":"GO:0009435","count":1},{"id":"GO:0046940","count":1},{"id":"GO:0051469","count":1}]},{"hash":"2161411500641516819","title":"Chromatin modification and transcription initiation","description":"The proteins cluster around histone modification (acetylation, deubiquitination), RNA polymerase II preinitiation complex assembly, and DNA-templated transcription initiation, plus nuclear pore localization, with links to G1/S transition and cell cycle regulation. This suggests a cohesive theme of chromatin-based transcription control coupled with cell cycle entry and developmental signals.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043966","count":2},{"id":"GO:0035264","count":2},{"id":"GO:0051123","count":2},{"id":"GO:0031081","count":2},{"id":"GO:0000082","count":1}]},{"hash":"1305290323991530615","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":8,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0048813","count":2},{"id":"GO:0021954","count":2},{"id":"GO:0006486","count":2}]},{"hash":"1338446376705091023","title":"Glucose metabolism and insulin signaling","description":"The cluster\u2019s GO terms cluster around glucose handling and energy metabolism: canonical glycolysis, fructose-6-phosphate metabolism, detection of glucose, and negative regulation of gluconeogenesis, along with cellular/system responses to insulin and related metabolic stress (ROS regulation, ischemia). A transcription-initiation annotation (RNA polymerase II preinitiation complex assembly) may reflect broader transcriptional regulation of metabolic genes rather than a core metabolic function, but the dominant theme is glucose metabolism and insulin signaling. ","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051123","count":2},{"id":"GO:0045721","count":1},{"id":"GO:0051594","count":1},{"id":"GO:0061621","count":1},{"id":"GO:2000378","count":1}]},{"hash":"2169660542772596578","title":"Ubiquitin-Proteasome System","description":"The cluster shows strong enrichment for deubiquitination, proteasomal degradation (including ubiquitin-independent processes), and proteasome core complex assembly, pointing to components of the ubiquitin-proteasome pathway and protein turnover. Additional terms related to metal ion stress (zinc, cadmium), viral processes, and cell cycle regulation (G2/M) suggest links to stress responses and cell-cycle control that intersect with proteasome function. In short, the dominant theme is ubiquitin-proteasome\u2013mediated protein degradation and its regulation.","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":8},{"id":"GO:0006521","count":6},{"id":"GO:0010499","count":6},{"id":"GO:0051436","count":6},{"id":"GO:0080129","count":6}]},{"hash":"2255280876226957927","title":"Pol II Transcription Regulation","description":"The top GO terms are dominated by \"positive regulation of transcription from RNA polymerase II promoter\" with various regulatory cues (oleic acid, starvation, etc.), pointing to proteins that influence transcription initiation from Pol II. Although some entries are obsolete and a few terms touch on biosynthetic processes, the unifying theme is transcriptional regulation rather than a single metabolic pathway. Therefore the cluster is best labeled as Pol II transcription regulation, capturing the common function of regulating gene expression at the Pol II promoter level.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035948","count":5},{"id":"GO:0035961","count":5},{"id":"GO:1904741","count":5},{"id":"GO:0061429","count":5},{"id":"GO:0043457","count":5}]},{"hash":"2041423744568914520","title":"Unknown","description":"The GO terms are diverse (bacterial flagellum organization, cobalamin biosynthesis, SRP-dependent membrane targeting, cell division, plant shoot meristem formation, hemidesmosome assembly), with no clear shared function across organisms. This precludes a cohesive label; confidence None.","confidence":"","size":10,"edges":10,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":1},{"id":"GO:0009236","count":1},{"id":"GO:0006461","count":1},{"id":"GO:0006614","count":1},{"id":"GO:0044781","count":1}]},{"hash":"409973107107866231","title":"Nucleotide metabolism and turnover","description":"Many of the top terms cluster around pyrimidine ribonucleotide biosynthesis (dUTP, dUMP, dITP, dUTP biosynthesis), nucleotide biosynthesis in general (ppGpp/guanosine tetraphosphate biosynthesis), and related phosphorylation steps, with a touch of nucleotide-sugar pathways. This suggests the proteins share a common theme of nucleotide metabolism and nucleotide turnover rather than a single, more specific function. Confidence: Medium","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":2},{"id":"GO:0097171","count":2},{"id":"GO:0009220","count":1},{"id":"GO:0046081","count":1},{"id":"GO:0006226","count":1}]},{"hash":"53154632873930873","title":"Neural gene expression and epigenetic regulation","description":"These terms collectively point to regulation of gene expression by transcriptional control, RNA processing, and epigenetic marks, with additional links to neural development and stress signaling (corticosterone response, serotonin secretion). The cluster seems to group proteins involved in transcription, splicing, and chromatin modification, alongside neural signaling and stress-responsive processes, suggesting a cohesive theme around neural gene expression and its epigenetic control.","confidence":"Medium","size":10,"edges":4,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0051412","count":3},{"id":"GO:0009635","count":3},{"id":"GO:0019805","count":3}]},{"hash":"1152476075929790361","title":"Meiotic DNA Replication and Recombination","description":"The top terms strongly point to DNA synthesis and processing during meiosis, with frequent mentions of DNA replication, DNA recombination, DNA strand invasion, and reciprocal meiotic recombination, plus oocyte karyosome formation. Translation and xenobiotic response are present but seem ancillary, so the dominant theme is meiotic DNA replication/recombination machinery.","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0042493","count":4},{"id":"GO:0006412","count":4},{"id":"GO:2000269","count":2}]},{"hash":"428464390681748910","title":"Unknown","description":"The top GO terms include DNA-templated transcription, DNA replication, neural development/synapse assembly, sperm capacitation, dopamine- and LPS-related signaling, dsRNA response, and Gram-positive defense. With zero edges and no connectivity, there is no single cohesive function tying these terms together, suggesting the proteins do not form a meaningful, interpretable cluster. Therefore, a specific label cannot be assigned beyond Unknown.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006260","count":2},{"id":"GO:0048240","count":2},{"id":"GO:1903351","count":2},{"id":"GO:0071222","count":2}]},{"hash":"1409567870042507916","title":"Nuclear RNA processing and chromatin organization","description":"The proteins cluster around nuclear RNA metabolism (box H/ACA snoRNP assembly, negative regulation of rRNA processing, telomerase RNA localization to Cajal body) and chromatin architecture (heterochromatin organization, regulation of nucleus size). While some terms like redox homeostasis and pH regulation are general cellular constants, the dominant theme is nuclear RNA processing and chromatin organization, suggesting a cohesive role in ribonucleoprotein maturation within the nucleus and chromatin structure. ","confidence":"Medium","size":10,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0018279","count":2},{"id":"GO:0000493","count":1},{"id":"GO:2000233","count":1},{"id":"GO:1904874","count":1},{"id":"GO:0009826","count":1}]},{"hash":"1010006420154056370","title":"Plant metabolism and signaling proteins","description":"The GO terms show a mix of translation, metabolic processes (starch catabolic, fatty acid biosynthesis), circadian rhythm, signal transduction, and regulation of protein kinase activity, plus a pollen hydration term. This suggests a cluster of plant proteins involved in general metabolism and signaling with circadian regulation, rather than a single specific pathway. ","confidence":"Medium","size":10,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0043562","count":1},{"id":"GO:0009744","count":1},{"id":"GO:0007165","count":1},{"id":"GO:0009859","count":1}]},{"hash":"2165054797899254750","title":"Nucleobase and nucleoside transporters","description":"This cluster is dominated by GO terms for transport of various nucleobases and nucleosides across membranes (adenine, guanine, xanthine, hypoxanthine, uracil, urate), suggesting a shared role as nucleobase/nucleoside transporters. A couple of unrelated terms (ER membrane organization, steroid biosynthesis) likely reflect annotation noise or multifunctional proteins, but the clear transport pattern supports this label.","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042906","count":1},{"id":"GO:0098710","count":1},{"id":"GO:0035344","count":1},{"id":"GO:0098721","count":1},{"id":"GO:1903825","count":1}]},{"hash":"1833397472946372359","title":"Neuronal receptor trafficking and cytoskeleton dynamics","description":"The top GO terms point to tubulin folding/assembly and cytoskeletal organization (microtubule dynamics) together with endocytosis and transport of neurotransmitter receptors to the postsynaptic membrane, along with cell polarity and cytoskeletal remodeling. This suggests a cohesive module linking cytoskeleton assembly with vesicular trafficking and neuronal receptor localization, despite some obsolete terms. ","confidence":"Medium","size":10,"edges":12,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007021","count":2},{"id":"GO:0098887","count":2},{"id":"GO:0006897","count":2},{"id":"GO:0031532","count":2},{"id":"GO:0071963","count":2}]},{"hash":"2096251564425536172","title":"Gene Expression: Transcription, Splicing, and Translation Initiation","description":"The top GO terms indicate involvement across multiple stages of gene expression: DNA-templated transcription, mRNA processing and spliceosome-mediated splicing (including alternative splicing and splice site recognition), mRNA stabilization, and translation initiation features (preinitiation complex formation and translation reinitiation). This pattern suggests a coherent theme of RNA processing and initiation of protein synthesis, linking transcription, RNA maturation, and translation. ","confidence":"High","size":10,"edges":4,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0001731","count":4},{"id":"GO:0035948","count":3},{"id":"GO:0071276","count":3}]},{"hash":"971669467172189593","title":"Calcium-Dependent Signaling and NFAT Immunity","description":"The cluster is dominated by calcium signaling terms (store-operated calcium channel activation, intracellular calcium signaling, and positive regulation of the calcineurin-NFAT pathway) and general intracellular signal transduction, with accompanying immune-related terms (innate mucosal immunity, antibacterial humoral response). While heart development and visual perception appear, they are not central to the cluster\u2019s main theme; the core seems to be calcium-dependent signaling linked to NFAT activation and immune functions. ","confidence":"Medium","size":10,"edges":7,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":2},{"id":"GO:0045444","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0035556","count":2},{"id":"GO:0006412","count":1}]},{"hash":"1069259272839907345","title":"Unknown","description":"The GO terms cover immune regulation (negative regulation of inflammatory response; calcineurin-NFAT signaling cascade; T cell homeostasis), sphingolipid biosynthesis (globoside and mannosyl-inositol phosphorylceramide biosynthetic processes), and DNA repair (mitochondrial DSB repair via homologous recombination; SDSA-related processing), plus several obsolete terms. This mix lacks a single clear, cohesive function or pathway tying all proteins together, suggesting a heterogeneous set rather than a unified cluster.","confidence":"","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0050728","count":2},{"id":"GO:0036210","count":1},{"id":"GO:0051999","count":1},{"id":"GO:0001576","count":1},{"id":"GO:0033173","count":1}]},{"hash":"2254829603847391743","title":"Ribosome Biogenesis and Translation","description":"The top GO terms cluster around ribosome assembly and function: ribosome biogenesis, ribosomal subunit export from nucleus, small subunit biogenesis, and cytoplasmic translation. Together these indicate proteins involved in ribosome production and protein synthesis, justifying a label focused on ribosome machinery. Some terms (mitochondrial inheritance, GABAergic transmission) are less central to ribosome biology and may reflect broader cellular annotations.","confidence":"High","size":10,"edges":5,"triangles":0,"max_degree":2,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0051932","count":3},{"id":"GO:0000001","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0000055","count":3}]},{"hash":"935889214752160246","title":"Nucleotide Excision Repair and DNA Replication","description":"This cluster is dominated by terms related to DNA processing and repair, especially nucleotide-excision repair (NER) and transcription-coupled NER, along with DNA replication and UV protection. The presence of multiple NER-related terms (and UV response) suggests a cohesive role in DNA damage recognition and repair, with a possible ancillary link to developmental processes reflected by hair cell differentiation and embryonic organ development. Overall, the core theme is DNA repair/maintenance in the context of UV-induced damage and replication stress.","confidence":"High","size":9,"edges":32,"triangles":62,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0032508","count":3},{"id":"GO:0033683","count":2},{"id":"GO:0006283","count":2},{"id":"GO:0009650","count":2}]},{"hash":"936437558764533222","title":"Fatty acid metabolism and lipid development","description":"The cluster shows a strong enrichment for lipid-related processes: fatty acid beta-oxidation, ketone body catabolic process, fatty acid biosynthesis, lipid transport, and glyoxysome/peroxisomal organization, together with adipose and liver development and hormone response. These collectively point to lipid metabolism and its ties to organ development as the core theme of the cluster, with antibiotic biosynthesis likely an outlier. ","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":5},{"id":"GO:0006635","count":5},{"id":"GO:0060612","count":4},{"id":"GO:0009725","count":4},{"id":"GO:1901373","count":4}]},{"hash":"2128005032308555012","title":"Central Carbon Metabolism and Biosynthesis","description":"This cluster is dominated by core metabolic pathways: glycolysis, the TCA cycle, and pyruvate decarboxylation to acetyl-CoA, plus 2-oxoglutarate metabolism. It also includes biosynthetic processes such as thiamine biosynthesis, malonyl-CoA biosynthesis, long-chain fatty acid biosynthesis, and leucine catabolism, pointing to energy production and generation of biosynthetic precursors. Some terms like sodium ion transport and cellular response to sucrose starvation reflect regulatory responses under metabolic stress, but the dominant theme is central carbon metabolism and biosynthesis.","confidence":"High","size":9,"edges":35,"triangles":77,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006096","count":6},{"id":"GO:0006099","count":6},{"id":"GO:0006103","count":4},{"id":"GO:0009228","count":3},{"id":"GO:0042759","count":3}]},{"hash":"1383616291434138786","title":"Redox Balance and Nucleotide Metabolism","description":"This cluster is enriched for redox-related terms (redox homeostasis, oxidant detoxification) and nucleotide metabolism (nucleotide phosphorylation, CDP biosynthesis, purine ribonucleotide interconversion), with supporting methylamine metabolism; the brain development term appears incidental. Collectively, these proteins seem tied to maintaining cellular redox status while processing nucleotides and related metabolites, rather than a single, exclusive function.","confidence":"Medium","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0045454","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0030416","count":3},{"id":"GO:0046939","count":2}]},{"hash":"1321929571573081969","title":"Aromatic compound biosynthesis and carbohydrate metabolism","description":"Top terms cluster around shikimate-derived aromatic biosynthesis (chorismate, lignin, coumarin) and carbohydrate pathways (pentose-phosphate shunt, fructose metabolism), suggesting a shared role in producing aromatic metabolites linked to carbon flux. Translation appears incidental. ","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006098","count":1},{"id":"GO:0009052","count":1},{"id":"GO:0006000","count":1},{"id":"GO:0033587","count":1}]},{"hash":"1342700830519377052","title":"Proteostasis and Autophagy with Centrosome Links","description":"The cluster is dominated by protein folding/refolding, processing, and autophagy-related activities (autophagosome maturation, ER-associated degradation hints, chaperone-mediated assembly). ATP metabolism supports these energy-intensive processes. While there are hints of centrosome/centromere and microtubule-related roles, the clearest common theme is proteostasis and ER/autophagy quality control.","confidence":"Medium","size":9,"edges":21,"triangles":26,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0097352","count":3},{"id":"GO:0070389","count":3},{"id":"GO:0051013","count":3},{"id":"GO:1903724","count":3},{"id":"GO:0016485","count":3}]},{"hash":"508395282777714331","title":"Mitochondrial Metabolite Transport","description":"Proteins in this cluster are linked to transmembrane transport of diverse metabolites and cofactors (NAD, alpha-ketoglutarate, coenzyme A, pyridoxal phosphate, heme, pyrimidine nucleotides) with additional associations to mitochondrial membrane potential regulation, oxidative stress responses, and insulin signaling. The common thread is mitochondrial import of metabolites that support metabolic and redox functions, so this label appropriately reflects the group\u2019s function.","confidence":"High","size":9,"edges":9,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0035352","count":4},{"id":"GO:0031921","count":4},{"id":"GO:0015742","count":4},{"id":"GO:0035349","count":4},{"id":"GO:0032869","count":4}]},{"hash":"211385079640748891","title":"Translation Initiation Regulation & Stress Signaling","description":"The cluster shows enrichment in translational initiation control (GO:0006446, GO:0002183) and various stress-response signals (amino acid starvation, nitric oxide, ethylene) plus a chromatin-related term (rDNA heterochromatin formation) that can tie to gene expression regulation. Some terms (oligodendrocyte development, obsolete methionine salvage) seem less connected, but the core theme is regulation of protein synthesis under stress.","confidence":"Medium","size":9,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019509","count":2},{"id":"GO:1903833","count":2},{"id":"GO:0014003","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0071369","count":2}]},{"hash":"1668914869731276287","title":"Carbohydrate catabolic pathways","description":"The top GO terms cluster around catabolism of diverse sugars (rhamnose, lyxose, fucose, arabinose) and carbohydrate phosphorylation, indicating a shared function in sugar metabolism. A single pyroptotic inflammation term appears as an outlier but does not override the overall theme.","confidence":"High","size":9,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0019509","count":2},{"id":"GO:0019301","count":2},{"id":"GO:0019324","count":2},{"id":"GO:0070269","count":2},{"id":"GO:0042355","count":2}]},{"hash":"2190562854900773221","title":"Ribosome Biogenesis and Translation","description":"Based on the top GO terms, most of the proteins are linked to translation (GO:0006412) and the biogenesis of the ribosomal large subunit (GO:0042273), including LSU rRNA maturation (GO:0000463). This points to a cluster of ribosome assembly and protein synthesis factors. Additional terms about transcription regulation may reflect broader coordination of gene expression but do not contradict the main ribosome/translation theme.","confidence":"High","size":9,"edges":15,"triangles":11,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0042273","count":3},{"id":"GO:0000463","count":2},{"id":"GO:0045727","count":1},{"id":"GO:1902164","count":1}]},{"hash":"1267595386680649317","title":"Proteolytic processing and maturation","description":"This cluster is linked by proteolysis-related terms: protein catabolic processes, membrane and autoprocessing of proteins, angiotensin maturation, and amyloid precursor protein processing/metabolism. The presence of antigen processing via MHC II and amyloid-beta metabolism further supports a theme of peptide generation and maturation through proteolysis. Although there are no detected interactions in this dataset (Edges 0), the GO terms collectively point to proteolytic processing as the shared function.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045493","count":1},{"id":"GO:0001823","count":1},{"id":"GO:0042985","count":1},{"id":"GO:0030163","count":1},{"id":"GO:0002003","count":1}]},{"hash":"2237056364829080802","title":"Unknown","description":"Top terms span diverse processes including DNA replication, neural and muscle development, immune differentiation, dopamine signaling, and p53-related signaling, with no single cohesive function linking them. This likely represents a heterogeneous cluster rather than a specific biological module. ","confidence":"","size":9,"edges":5,"triangles":0,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0021537","count":3},{"id":"GO:0042523","count":3},{"id":"GO:2000811","count":3},{"id":"GO:1903351","count":3}]},{"hash":"649627078989570414","title":"Nuclear transport of ribosomal subunits","description":"The top GO terms center on import of ribosomal proteins into the nucleus, export of the ribosomal large subunit, NLS-bearing protein import, and nuclear pore complex assembly, indicating a cohesive module for nuclear transport and ribosome trafficking, with supporting nuclear regulatory processes like desumoylation and transcriptional control that fit the nuclear context.","confidence":"High","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0033674","count":3},{"id":"GO:0006610","count":3},{"id":"GO:0060188","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0000055","count":3}]},{"hash":"1331320664012778732","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060325","count":1},{"id":"GO:0070941","count":1},{"id":"GO:0045292","count":1},{"id":"GO:1904582","count":1},{"id":"GO:0043029","count":1}]},{"hash":"856590622173512165","title":"Transmembrane Transporters of Ions and Nutrients","description":"Top GO terms indicate broad transporter activity across membranes for nitrate, nitrite, sodium, potassium, phosphate, arabinose, xenobiotics, and neurotransmitter loading into synaptic vesicles. This coherent theme centers on transmembrane solute/ion transport, justifying a label as a transporter cluster.","confidence":"High","size":9,"edges":9,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0015706","count":9},{"id":"GO:0042128","count":9},{"id":"GO:0006855","count":9},{"id":"GO:0015751","count":9},{"id":"GO:0035725","count":9}]},{"hash":"1510729994029464886","title":"Transmembrane nutrient transporters","description":"This cluster is dominated by GO terms for transmembrane transport of diverse solutes (selenite, nitrate, xylose, glucose, organic cations) and related uptake, suggesting a membrane transporter function; some non-transport terms appear incidental. ","confidence":"High","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0097080","count":2},{"id":"GO:0070715","count":2},{"id":"GO:0015706","count":2},{"id":"GO:0071332","count":2},{"id":"GO:0015753","count":2}]},{"hash":"575149589397194504","title":"Cardiovascular and neural development","description":"Dominant GO terms center on organismal development with strong emphasis on heart development, angiogenesis, and neural/visual components (visual perception, excitatory postsynaptic potential). While some terms (e.g., G2/M transition, plant signaling) appear noisy, the overall pattern suggests proteins involved in organogenesis and neurovascular development across heart, vessels, and neural/retinal tissues. Therefore the label reflects a cohesive developmental theme rather than a single pathway.","confidence":"Medium","size":9,"edges":13,"triangles":6,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":9},{"id":"GO:0014850","count":9},{"id":"GO:0001525","count":8},{"id":"GO:0010800","count":8},{"id":"GO:0000086","count":8}]},{"hash":"173916392714876473","title":"Cardiac Development and Function","description":"The top GO terms are dominated by cardiac-related processes: outflow tract morphogenesis, regulation of SA node action potential, and positive regulation of the force of heart contraction. While there are also general cellular terms (actin cytoskeleton organization, calcium signaling, mitotic checks, Hippo pathway), the strongest signals point to heart development and function. Confidence: Medium.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035331","count":1},{"id":"GO:0000321","count":1},{"id":"GO:0030866","count":1},{"id":"GO:0031573","count":1},{"id":"GO:0003151","count":1}]},{"hash":"1307834825907469480","title":"Nucleotide Metabolism and RNA Modification","description":"The top GO terms cluster around nucleotide biosynthesis and salvage (UMP, uridine, cytidine, deoxycytidine) and RNA-related processing, including tRNA wobble adenosine to inosine editing, with additional but less central terms for riboflavin biosynthesis, glycerol-3-phosphate biosynthesis, and antibiotic response. This suggests a central theme of nucleotide metabolism intertwined with RNA modification, justifying a label focused on these processes.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046167","count":2},{"id":"GO:0009231","count":2},{"id":"GO:0044206","count":2},{"id":"GO:0019858","count":2},{"id":"GO:0046109","count":2}]},{"hash":"1462741326964488106","title":"Mitochondrial protein import and inner membrane insertion","description":"The cluster is dominated by GO terms related to mitochondrial targeting and import (protein targeting to mitochondrion, protein import into mitochondrial intermembrane space, protein insertion into mitochondrial inner membrane) and chaperone-mediated transport, pointing to mitochondrial protein handling. Additional terms on redox balance and iron homeostasis support a mitochondrial context, with a note of autophagy regulation possibly reflecting mitochondrial quality control. Together, these terms suggest a cohesive theme of mitochondrial protein targeting/assembly and associated redox maintenance.","confidence":"High","size":8,"edges":18,"triangles":17,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0072321","count":2},{"id":"GO:0006626","count":2},{"id":"GO:0045039","count":2},{"id":"GO:0045454","count":1},{"id":"GO:0016242","count":1}]},{"hash":"598177516808021316","title":"Mitochondrial Energy Metabolism","description":"The cluster is best characterized by GO terms tied to ATP synthesis driven by the proton motive force and ubiquinone biosynthesis/regulation, both hallmark components of mitochondrial energy production. Additional terms on lipid homeostasis and various metabolic processes align with broader mitochondrial-associated metabolism. Some neural-development terms (substantia nigra and Purkinje cell layer morphogenesis) appear in the set but do not define the core mitochondrial energy theme, suggesting possible tissue-specific annotations or ancillary roles in this cluster.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0015986","count":2},{"id":"GO:0035786","count":1},{"id":"GO:0021762","count":1},{"id":"GO:1902171","count":1},{"id":"GO:1901006","count":1}]},{"hash":"537396596506562755","title":"Chromatin Remodeling and RNA Pol II Transcription Regulation","description":"The cluster\u2019s GO terms center on transcription regulation by RNA polymerase II, chromatin-state modifiers like histone acetylation, and nucleosome mobility, along with preinitiation complex assembly. While a few terms touch plant-specific photomorphogenesis and metabolic regulation, the dominant theme ties to transcription control via chromatin remodeling and transcription machinery, justifying a cohesive label focused on RNA Pol II\u2013driven regulation and chromatin dynamics.","confidence":"Medium","size":8,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0043966","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0042766","count":1},{"id":"GO:0045898","count":1},{"id":"GO:2000306","count":1}]},{"hash":"42593349731672330","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006809","count":1},{"id":"GO:0006636","count":1},{"id":"GO:0006675","count":1},{"id":"GO:0032443","count":1},{"id":"GO:0001949","count":1}]},{"hash":"886151437562845798","title":"COPII vesicle formation and cargo loading","description":"This cluster is characterized by GO terms tied to COPII vesicle coating (GO:0048208) and its regulation (GO:0060088, GO:1901301), plus cargo loading into COPII-coated vesicles, pointing to a shared role in ER-to-Golgi trafficking and secretory pathway function. Additional terms related to morphogenesis and lumen formation suggest developmental contexts where secretory trafficking is critical. Overall, the dominant signal is COPII vesicle formation and cargo loading, with supporting membrane-related processes.","confidence":"High","size":8,"edges":5,"triangles":0,"max_degree":3,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0048702","count":3},{"id":"GO:0060088","count":3},{"id":"GO:0003400","count":3},{"id":"GO:0061156","count":3},{"id":"GO:0035909","count":3}]},{"hash":"662754712627362092","title":"Neural development and vesicle trafficking","description":"The top GO terms point to vesicle tethering in exocytosis and Golgi-to-plasma membrane transport, which reflect neuronal secretion and membrane trafficking. Several terms also highlight brain development (hippocampus and substantia nigra development) and neuron migration, plus neuronal excitability (membrane depolarization during action potential). While a few terms (insulin response, apoptotic signaling) are less central, the dominant signal ties neural development to synaptic vesicle trafficking and neuronal activity.","confidence":"Medium","size":8,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0090522","count":2},{"id":"GO:0006893","count":2},{"id":"GO:0008630","count":1},{"id":"GO:0032869","count":1},{"id":"GO:0021766","count":1}]},{"hash":"620580467620065964","title":"Metal Ion Transport and Homeostasis","description":"The cluster centers on transmembrane transport of metal ions (zinc, cadmium, iron) and export of potassium and sodium, plus intracellular ion homeostasis and cadmium detoxification, indicating a cohesive theme of metal ion transport and homeostasis with detoxification involvement.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071577","count":3},{"id":"GO:0070574","count":3},{"id":"GO:0097623","count":2},{"id":"GO:0036376","count":2},{"id":"GO:0030007","count":2}]},{"hash":"1467813847137629287","title":"Muscle development and regeneration","description":"The GO terms point to muscle biology: myoblast proliferation, myotube differentiation, skeletal muscle tissue regeneration, and angiogenesis involved in wound healing, indicating involvement in muscle formation and repair. The other terms (K11-linked ubiquitination, APC-dependent catabolic process, ERAD) reflect ubiquitin-proteasome and cell-cycle control that govern muscle cell proliferation and differentiation. Together, these suggest a cohesive cluster related to muscle development and regeneration, with ubiquitin-mediated regulation as a supporting context.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070979","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0031145","count":2},{"id":"GO:0051450","count":1}]},{"hash":"1542887780469846941","title":"Ribosome Biogenesis and rRNA Processing","description":"The proteins are enriched for translation and ribosome-related processes, including translation, ribosome biogenesis, maturation of SSU- and LSU-rRNA, and ribosomal subunit export, indicating a cluster of ribosome assembly and rRNA processing factors.","confidence":"High","size":8,"edges":27,"triangles":50,"max_degree":7,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0042254","count":3},{"id":"GO:0000462","count":2},{"id":"GO:0000055","count":1},{"id":"GO:0042273","count":1}]},{"hash":"1782649722038313443","title":"Ubiquitin-Proteasome Regulation and NF-\u03baB Signaling","description":"Top GO terms point to ubiquitin-dependent proteolysis (protein autoubiquitination, ubiquitin-dependent ERAD pathway, K48-linked ubiquitination, ubiquitin-dependent protein catabolic process) as the core function, implying this cluster centers on tagging and degrading proteins. Additional terms related to immune signaling (adaptive immune response, positive regulation of I-kappaB phosphorylation, negative regulation of RIG-I signaling) suggest modulation of NF-\u03baB and antiviral pathways by ubiquitin-related processes. A peroxisome matrix import term appears as a minor outlier; overall the theme is ubiquitin-driven protein turnover coupled with immune signaling regulation.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0070936","count":2},{"id":"GO:0016558","count":2},{"id":"GO:0042787","count":2}]},{"hash":"454693870692260729","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042407","count":1},{"id":"GO:0033108","count":1},{"id":"GO:0045292","count":1},{"id":"GO:0002188","count":1},{"id":"GO:0000380","count":1}]},{"hash":"2189243482087059494","title":"Spliceosome RNA Processing and Ribosome Biogenesis","description":"This cluster centers on RNA metabolism: splicing regulation by the spliceosome (positive regulation of mRNA splicing; spliceosome conformational changes) and RNA processing such as RNA-protein cross-linking, ncRNA-mediated gene silencing, and mRNA export. It also includes ribosome biogenesis and rRNA maturation, suggesting coordination between RNA processing and ribosome assembly. Some terms are obsolete, but the core theme remains RNA splicing/processing and ribosome biogenesis.","confidence":"High","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0006306","count":2},{"id":"GO:0000466","count":2}]},{"hash":"1774455824474009552","title":"Cell stress response and growth regulation","description":"The cluster combines signals of cellular stress responses (ER stress\u2013induced apoptosis, DNA damage signaling, TORC1 pathway) with proteostasis processes (ubiquitin\u2013proteasome\u2013dependent degradation, rRNA maturation) and cell cycle/growth control (G0\u2192G1 transition, regulation of hemocyte proliferation), pointing to a cohesive theme of how cells manage stress while regulating proliferation and growth. Immune defense terms appear but do not dominate the set, so the overarching theme remains stress and growth regulation.","confidence":"Medium","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0050830","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0070317","count":1},{"id":"GO:0035206","count":1},{"id":"GO:0072432","count":1}]},{"hash":"2118990661105645254","title":"Chromatin regulation and DNA repair","description":"The cluster is mainly tied to nuclear processes: DNA-templated transcription, histone methylation (H3K4 and H3K79), and ubiquitin-dependent protein turnover, all pointing to chromatin modification and transcription control with some links to DNA repair. A few terms (dynein arm assembly, aging) are less connected, but the core signal remains chromatin regulation and genome maintenance.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006469","count":2},{"id":"GO:0006511","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0007568","count":2}]},{"hash":"1564438530313988454","title":"Autophagy and organelle-specific degradation","description":"The top GO terms are dominated by autophagy-related processes, including autophagosome assembly and selective autophagy pathways targeting organelles (nucleus via piecemeal microautophagy, peroxisomes via pexophagy, glycogen via glycophagy, ER via reticulophagy, and in the Cvt pathway). This concerted pattern indicates a cluster centered on autophagy and its organelle-specific degradation routes, with a few transcription or apoptotic regulation terms accompanying. ","confidence":"High","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0045793","count":1},{"id":"GO:0034727","count":1},{"id":"GO:0000045","count":1},{"id":"GO:0035096","count":1}]},{"hash":"325219540781502842","title":"Mitochondrial Translation and Dynamics","description":"Most of the top GO terms point to mitochondrial processes\u2014translational initiation, ribosomal large subunit biogenesis, cristae formation, and mitochondrial fusion\u2014suggesting a theme of mitochondrial protein synthesis and organization. The other terms are diverse and less clearly connected, which may reflect annotation noise, but the dominant mitochondrial signature supports the chosen label.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006413","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0042407","count":1},{"id":"GO:0008053","count":1},{"id":"GO:0046661","count":1}]},{"hash":"705192198078365202","title":"Unknown","description":"The top GO terms are highly mixed: mitochondrial complex IV assembly and aerobic respiration hint at metabolic roles, while transcription initiation components, histone acetylation, and diverse immune-related processes (humoral response, germinal center formation, follicular dendritic cell differentiation, IL-10 regulation) and plant cytokinin signaling suggest no single coherent function linking all proteins. This appears to be annotation noise or multifunctional proteins, so the cluster is best labeled Unknown.","confidence":"","size":8,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":3},{"id":"GO:0006352","count":1},{"id":"GO:0051123","count":1},{"id":"GO:0009736","count":1},{"id":"GO:0043966","count":1}]},{"hash":"769230439095781367","title":"RNA Processing and Decay Machinery","description":"The cluster centers on RNA metabolism: rRNA maturation, tRNA processing, mRNA splicing and spliceosome assembly, P-body formation, and deadenylation-dependent decapping, plus transcription termination signals. These terms together suggest a cohesive group of proteins involved in RNA maturation, processing, and turnover, with a broader link to RNA surveillance and turnover pathways.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0030490","count":3},{"id":"GO:0008033","count":3},{"id":"GO:0045292","count":2},{"id":"GO:0033962","count":2},{"id":"GO:1990141","count":2}]},{"hash":"459716900006212836","title":"DNA Damage Response and Ubiquitination","description":"The top terms point toward genome maintenance and stress signaling, notably meiotic double-strand break formation, telomere recombination, ER-stress\u2013induced apoptosis, and K63-linked ubiquitination, suggesting a shared role in ubiquitin-mediated DNA damage response and proteostasis. Some terms appear as outliers (e.g., fungal cell wall organization, neuronal development), indicating mixed functionality in the cluster. Overall, the strongest linkage is to DNA damage response and ubiquitin signaling, hence the label.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:1990920","count":7},{"id":"GO:1903955","count":7},{"id":"GO:0000722","count":7},{"id":"GO:0071347","count":7},{"id":"GO:0010976","count":7}]},{"hash":"2147604250290745521","title":"ER Proteostasis and Quality Control","description":"The GO terms cluster around ER-associated protein handling: targeting to membranes, ubiquitin-dependent ERAD, proteasome-mediated nuclear quality control, and translation upregulation under ER stress. These collectively indicate proteostasis management at the ER and related quality-control pathways, with a few terms (mesoderm formation, DNA replication) seeming less representative.","confidence":"Medium","size":7,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0031204","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0071630","count":2},{"id":"GO:0032781","count":2},{"id":"GO:0001707","count":2}]},{"hash":"44981956489531734","title":"Diverse biosynthetic pathways","description":"The top GO terms point to multiple, distinct biosynthetic processes (RNA methylation; vitamin E, cobalamin, sterol, ubiquinone, chlorophyll, and antibiotic biosynthesis), suggesting a cluster of proteins involved broadly in biosynthesis rather than a single pathway. The lack of interactions (Edges 0) supports an umbrella grouping across several related metabolic routes, hence the label \u201cDiverse biosynthetic pathways.\u201d","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036265","count":3},{"id":"GO:0043547","count":2},{"id":"GO:0010189","count":2},{"id":"GO:0009236","count":2},{"id":"GO:0016126","count":2}]},{"hash":"1653106925531614790","title":"Protein Folding Stress Response","description":"The cluster centers on protein quality control under stress: unfolded protein response, chaperone-assisted refolding, and post-translational targeting to membranes, with related terms on inclusion body regulation and oxidative stress signaling. While a few terms touch on DNA replication or development, the strongest connected theme is managing misfolded proteins and cellular stress, suggesting a protein folding/stress-response module.","confidence":"Medium","size":7,"edges":16,"triangles":20,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0070389","count":5},{"id":"GO:1903751","count":5},{"id":"GO:0070880","count":5},{"id":"GO:0034620","count":5}]},{"hash":"822263015534353352","title":"Unknown","description":"The GO terms mix DNA repair (base-excision repair) with xenobiotic response and developmental processes across heart, muscle, neuron, and lung; there is no clear shared function tying these proteins together, so the cluster appears heterogeneous.","confidence":"","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009410","count":2},{"id":"GO:0006284","count":1},{"id":"GO:0097510","count":1},{"id":"GO:0071400","count":1},{"id":"GO:0061100","count":1}]},{"hash":"43661668498054051","title":"Multilineage Development and Growth Regulation","description":"This cluster shows GO terms spanning multiple tissues and developmental processes (osteoblast, cardiac, neuron, skeletal muscle, lung neuroendocrine differentiation) along with regulation of cell cycle and signaling pathways, suggesting a broad role in developmental differentiation and growth control across tissues.","confidence":"Medium","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0045668","count":4},{"id":"GO:0060766","count":4},{"id":"GO:0071400","count":3},{"id":"GO:0061100","count":3},{"id":"GO:0003218","count":3}]},{"hash":"815623591644475785","title":"Vertebrate Development and Hormone-Driven Differentiation","description":"The cluster centers on developmental processes (eyelid development, outflow tract morphogenesis, R3/R4 cell fate commitment, vitellogenesis) and hormonal signaling (response to estradiol), with additional immune differentiation terms (dendritic cell and Th2 differentiation). This suggests a shared theme of development and lineage specification modulated by hormones, with some immune differentiation context.","confidence":"Medium","size":7,"edges":19,"triangles":26,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007296","count":3},{"id":"GO:0000183","count":3},{"id":"GO:0071392","count":2},{"id":"GO:0003151","count":2},{"id":"GO:0043011","count":2}]},{"hash":"2021613693556716849","title":"Steroid and lipid metabolism","description":"GO terms point to biosynthesis and modification of lipid and steroid compounds (aldosterone and bile acid biosynthesis, lipid hydroxylation, methylation, oxidative demethylation), indicating a shared function in lipid/steroid metabolic pathways. A few development-related terms appear incidental, but the dominant pattern supports a lipid/steroid metabolism theme.","confidence":"Medium","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032342","count":5},{"id":"GO:0060137","count":5},{"id":"GO:0061298","count":5},{"id":"GO:0002933","count":5},{"id":"GO:0033072","count":5}]},{"hash":"898621435749454183","title":"Nutrient and Ion Transporters","description":"This cluster is dominated by GO terms for transport across membranes of various nutrients and ions (nitrite, nitrate, selenite, D-xylose, sodium-dependent organic cations, fructose-related responses, etc.), suggesting a shared role in membrane transport for nutrient uptake. A few terms (e.g., ribosome biogenesis, protein kinase activation) appear as outliers and do not define the core theme. Therefore, labeling it as Nutrient and Ion Transporters appropriately captures the main function represented by the cluster.","confidence":"High","size":7,"edges":8,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":2},{"id":"GO:0061420","count":1},{"id":"GO:0001300","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0032147","count":1}]},{"hash":"884918238896172722","title":"Spliceosome-Mediated RNA Processing","description":"The cluster is dominated by RNA processing and splicing-related terms, including mRNA splicing via spliceosome, spliceosomal snRNP assembly, and P-body assembly, as well as decay-related processes like deadenylation-dependent decapping. Additional terms for transcription termination and rRNA maturation fit the broader theme of RNA biogenesis and turnover. Some unrelated terms (e.g., chromatin-related) may be incidental, but the core signal is spliceosome-driven RNA processing.","confidence":"High","size":7,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":1},{"id":"GO:0033962","count":1},{"id":"GO:1990141","count":1},{"id":"GO:0000290","count":1},{"id":"GO:0042633","count":1}]},{"hash":"1969331916531646363","title":"Spliceosome-driven mRNA processing and translation initiation","description":"This cluster is dominated by GO terms related to spliceosome-mediated mRNA splicing and processing (including alternative and cis splicing, splice-site recognition, and mRNA modification), along with terms tied to translation initiation and reinitiation (formation of preinitiation complex, translation reinitiation, and mRNA stabilization). The common theme is post-transcriptional RNA processing and regulation of translation, making this name representative of the cluster\u2019s function.","confidence":"High","size":7,"edges":12,"triangles":7,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":4},{"id":"GO:0031047","count":4},{"id":"GO:0006378","count":4},{"id":"GO:0045292","count":3},{"id":"GO:0002188","count":3}]},{"hash":"1420157294742789553","title":"Large Subunit Ribosome Biogenesis","description":"Dominated by GO terms for maturation and export of the large ribosomal subunit (LSU) and assembly of preribosomes, this cluster clearly centers on ribosome biogenesis, specifically LSU maturation and assembly. A few cholesterol/isoprenoid-related terms appear but do not define the cluster.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000055","count":1},{"id":"GO:0000463","count":1},{"id":"GO:0000466","count":1},{"id":"GO:0000027","count":1},{"id":"GO:1902626","count":1}]},{"hash":"657417646698333421","title":"Diverse Solute Transporters","description":"GO terms indicate transmembrane transport of a wide range of substrates (ions, sugars, vitamins, xenobiotics, neurotransmitters), suggesting proteins that function as membrane transporters with diverse substrates.","confidence":"High","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":3},{"id":"GO:0015707","count":3},{"id":"GO:0098700","count":3},{"id":"GO:0015706","count":3},{"id":"GO:0006855","count":3}]},{"hash":"1338751741555452413","title":"RNA splicing and mRNA processing","description":"This cluster is dominated by RNA-centric terms: mRNA splicing via the spliceosome, spliceosomal snRNP assembly, deadenylation-dependent decapping, P-body assembly, and maturation of rRNA, along with transcription termination. These point to a cohesive theme of RNA processing and post-transcriptional regulation, with a few additional terms (heterochromatin formation, hair cycle, water deprivation) that are less directly tied but do not override the core RNA metabolism signal.","confidence":"Medium","size":7,"edges":8,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0070317","count":2},{"id":"GO:0045292","count":1},{"id":"GO:0033962","count":1},{"id":"GO:1990141","count":1},{"id":"GO:0000290","count":1}]},{"hash":"1331154375172501467","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":8,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006289","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0000717","count":1},{"id":"GO:0006363","count":1},{"id":"GO:0006295","count":1}]},{"hash":"303265127481253746","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000466","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0000472","count":3},{"id":"GO:0000462","count":3}]},{"hash":"861533385561586611","title":"Viral Translation Initiation Regulation","description":"The top GO terms are dominated by translation initiation and viral translation processes (regulation of translational initiation, formation of preinitiation complex, IRES-dependent viral initiation, and viral termination-reinitiation), suggesting a cohesive theme around how translation initiation is regulated, including viral contexts. A few non-translation terms (jasmonic acid response, seed growth, chromatin-related processes) appear but do not form a clear, cohesive alternative function, so the core signal remains translation initiation regulation, potentially in a viral setting.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006446","count":2},{"id":"GO:0075525","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0075522","count":2},{"id":"GO:0009753","count":1}]},{"hash":"253135844147457108","title":"Mitotic DNA replication and repair","description":"The GO terms cluster around DNA replication (leading/lagging strand elongation, general replication) and multiple DNA repair pathways (NER, UV-damage excision, HR with double-strand break repair), plus cell-cycle milestones (G2/M transition, cell division). This combination points to proteins involved in DNA synthesis and repair during mitosis and the preceding S/G2 phases, representing a coherent functional theme for the cluster.","confidence":"High","size":7,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1903459","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0006297","count":1},{"id":"GO:0043150","count":1},{"id":"GO:1903460","count":1}]},{"hash":"2060246130083181858","title":"Central Carbon and Nucleotide Metabolism","description":"The top GO terms point to core energy and nucleotide turnover: canonical glycolysis and gluconeogenesis, adenine catabolic process, and DNA catabolic process. Additional metabolism-related terms like methionine biosynthetic process support a metabolic theme. A few other terms (vacuole fusion regulation, apoptosis regulation, muscle regeneration) seem to reflect broader cellular maintenance contexts rather than a single pathway. Overall, the cluster is best described as central metabolic and nucleotide turnover functions rather than a single dedicated pathway.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009086","count":2},{"id":"GO:0006146","count":2},{"id":"GO:0061621","count":1},{"id":"GO:0009405","count":1},{"id":"GO:0032889","count":1}]},{"hash":"1824569013992341456","title":"Ion and Metabolite Transporters","description":"The top GO terms are dominated by transport activities for ions and small metabolites (sodium ion transport, succinate transport, citrate transport, arsenite transport) and a related metabolic process (polyphosphate biosynthesis), suggesting the cluster centers on transporter or transporter-associated functions. Some terms (mitotic spindle assembly checkpoint signaling, cellular response to cold) appear less related and may reflect annotation noise or multi-functional proteins, but overall transport-related terms best explain the group.","confidence":"Medium","size":7,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0032516","count":1},{"id":"GO:0032515","count":1},{"id":"GO:0007094","count":1},{"id":"GO:0006814","count":1},{"id":"GO:0070417","count":1}]},{"hash":"596204133336578125","title":"tRNA charging and wobble modification","description":"This cluster is dominated by GO terms relating to tRNA aminoacylation (lysyl-, aspartyl-, and general lysyl-tRNA charging) and tRNA wobble cytosine modification, including mitochondrial tRNA charging. These terms point to a cohesive theme around tRNA biosynthesis, charging, and modification, spanning both cytosolic and mitochondrial contexts. A few terms pertain to DNA replication/repair and telomere maintenance, which are less central to the core theme but may reflect secondary roles or annotations; overall, the strongest signal is tRNA biology.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071915","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0070200","count":1},{"id":"GO:0002101","count":1},{"id":"GO:0070146","count":1}]},{"hash":"1562815418372432081","title":"Transcriptional and Cell Cycle Regulation","description":"The top GO terms cluster around control of transcription by RNA Pol II and coordination of the cell cycle, including meiosis-related processes (homologous chromosome pairing, syncytial blastoderm mitotic cell cycle). While some terms reference specific tissues or stress responses, the dominant theme is transcriptional regulation linked to cell-cycle/meiotic events, indicating a regulatory module rather than a single tissue function.","confidence":"Medium","size":7,"edges":4,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":4},{"id":"GO:0071157","count":3},{"id":"GO:0035186","count":3},{"id":"GO:0060749","count":3},{"id":"GO:0007129","count":3}]},{"hash":"107480007501726406","title":"Ubiquitin-Dependent Protein Degradation","description":"The top GO terms center on ubiquitination and ubiquitin-protein catabolic processes (including K48-linked ubiquitination and autoubiquitination), plus pathways like ERAD; a peroxisomal protein import term is also present, which can relate to ubiquitin-mediated turnover in peroxisomes. This suggests a coherent cluster driven by ubiquitin-dependent proteolysis and quality-control pathways.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070936","count":2},{"id":"GO:0016558","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0060816","count":2},{"id":"GO:0046621","count":2}]},{"hash":"333871540909269145","title":"Post-translational modification and protein targeting","description":"The cluster shows enrichment for ubiquitin-like modifications (ISG15 conjugation, SUMOylation) and a lipidation process (C-terminal lipidation), which tie to protein regulation, localization, and interactions. The presence of the Cvt autophagy pathway term suggests trafficking to organelles or turnover. While t6A biosynthesis relates to RNA modification and some developmental terms appear, the common thread is protein modification and targeting rather than a single metabolic function. Medium","confidence":"Medium","size":6,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0061504","count":1},{"id":"GO:0032020","count":1},{"id":"GO:0016925","count":1},{"id":"GO:2000220","count":1},{"id":"GO:0006501","count":1}]},{"hash":"269764235764737721","title":"Stress-response signaling cluster","description":"The cluster is driven by GO terms related to cellular responses to chemical stimuli and signal transduction, such as cellular response to cAMP, response to corticosterone, and response to herbicide, indicating a core theme of stress- and signaling-related responses. Other terms (metabolic and neural-related) are present but appear peripheral, suggesting heterogeneity with a primary emphasis on signal response.","confidence":"Low","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071320","count":3},{"id":"GO:0046168","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0051412","count":2},{"id":"GO:0009635","count":2}]},{"hash":"1046944233121980837","title":"Adaptive immune signaling and cytoskeletal remodeling","description":"The cluster is enriched for adaptive immune response terms, NK T cell differentiation, IL-7 signaling, and integrin-mediated signaling with actin filament regulation, indicating immune cell activation alongside cytoskeletal remodeling; insulin pathway term may reflect cross-talk rather than core function.","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":3},{"id":"GO:0060368","count":2},{"id":"GO:0032005","count":2},{"id":"GO:1990441","count":2},{"id":"GO:0002250","count":2}]},{"hash":"134632743043949032","title":"Biosynthesis and Energy Metabolism","description":"The GO terms point to multiple biosynthetic pathways (KDO, chorismate, aromatic amino acids, LPS) alongside energy-generation processes (proton motive force-driven ATP synthesis, mitochondrial ATP synthesis coupled electron transport, NADH dehydrogenation to ubiquinone) and transport. This suggests a broad cluster of proteins involved in core metabolite production coupled to cellular energy production, rather than a single, cohesive pathway. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019294","count":1},{"id":"GO:0009073","count":1},{"id":"GO:0009423","count":1},{"id":"GO:0009103","count":1},{"id":"GO:0015986","count":1}]},{"hash":"1633763459547122482","title":"Metabolic biosynthesis and transcription regulation","description":"This cluster shows a mix of terms related to regulation of metabolism (e.g., regulation of cellular respiration) and multiple biosynthetic pathways (ergosterol, aflatoxin, pyrimidine nucleotides, leucine, proline), as well as transcriptional regulation by RNA polymerase II under metabolic cues. The small number of edges and presence of several obsolete terms suggest a broad, regulatory/metabolic theme rather than a single cohesive pathway, making a combined label most representative.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043457","count":4},{"id":"GO:0035948","count":4},{"id":"GO:0035961","count":3},{"id":"GO:1904741","count":3},{"id":"GO:0061429","count":3}]},{"hash":"1852576732603475018","title":"TCA Cycle and Redox Metabolism","description":"GO terms strongly point to central carbon metabolism and redox maintenance, with the tricarboxylic acid cycle, 2-oxoglutarate metabolism, NADPH regeneration, and glutathione metabolism dominating. Beta-alanine and lysine biosynthesis terms further support a metabolic cluster, while a few development-related terms appear less represented. This suggests a cohesive metabolic module centered on energy production and redox balance rather than signaling or development.","confidence":"Medium","size":6,"edges":13,"triangles":12,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":3},{"id":"GO:0006103","count":2},{"id":"GO:0019483","count":2},{"id":"GO:0006740","count":2},{"id":"GO:0006749","count":2}]},{"hash":"271075116893393101","title":"Histone deacetylation\u2013driven chromatin silencing","description":"GO terms highlight histone deacetylation (H3/H4), rDNA heterochromatin formation, and negative regulation of transcription by RNA polymerase I, indicating chromatin-level gene repression as the core function. Some terms about proteostasis and stress signaling may be secondary, but the dominant signal is histone deacetylation and chromatin silencing.","confidence":"High","size":6,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016479","count":2},{"id":"GO:0070932","count":2},{"id":"GO:0000183","count":2},{"id":"GO:0070933","count":2},{"id":"GO:0034983","count":2}]},{"hash":"2032765669297329079","title":"Nucleotide salvage and interconversion","description":"The cluster\u2019s GO terms predominantly describe nucleotide metabolism: AMP salvage, purine nucleoside interconversion, nucleotide catabolic processes, and deoxyguanosine catabolism, with additional but related terms for NAD and riboflavin biosynthesis salvage. A single term about T cell differentiation appears unrelated and may reflect annotation noise. Overall, the proteins seem to function in nucleotide and cofactor turnover, justifying the label.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":2},{"id":"GO:0009231","count":1},{"id":"GO:0046638","count":1},{"id":"GO:0019509","count":1},{"id":"GO:0009166","count":1}]},{"hash":"1281963092352231699","title":"Ribosome Biogenesis and Translation","description":"Dominant terms relate to ribosomal large subunit biogenesis/assembly and translation, indicating a ribosome/protein-synthesis role. Retina-related terms are few and likely incidental; thus the core theme is ribosome biogenesis and translation.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031290","count":1},{"id":"GO:0010458","count":1},{"id":"GO:0060041","count":1},{"id":"GO:0032781","count":1},{"id":"GO:0021554","count":1}]},{"hash":"500677180714652407","title":"Multi-Substrate Membrane Transporters","description":"The cluster centers on diverse transmembrane transport activities for substrates such as nitrate, xylose, glucose, selenite, and organic cations, with related sugar sensing and insulin-responsive uptake signals, suggesting a cohesive set of membrane transporters with broad specificity. A minority of terms reference senescence but do not redefine the main theme.","confidence":"High","size":6,"edges":10,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0090398","count":2},{"id":"GO:0097080","count":2},{"id":"GO:0070715","count":2},{"id":"GO:0015706","count":2},{"id":"GO:0071332","count":2}]},{"hash":"241044681702968419","title":"Ubiquitin-Dependent Protein Catabolism","description":"Based on the dominant GO terms, the cluster centers on ubiquitin-mediated proteolysis, including ubiquitin-dependent protein catabolic process, autoubiquitination, and K48-linked ubiquitination, which are hallmarks of proteasomal degradation and ERAD. Some auxiliary terms (peroxisome import, Wnt receptor catabolic process, dosage compensation-related terms) appear ancillary or historical, but the core signal is ubiquitin-driven protein turnover; thus this label is representative of the cluster's function.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0051865","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0070936","count":3},{"id":"GO:0016558","count":3}]},{"hash":"399396955117926634","title":"GTPase-regulated actin remodeling","description":"This cluster shows a coherent theme around actin cytoskeleton dynamics and small GTPase signaling, with terms like filopodium assembly, actin filament branching, small GTPase\u2013mediated signal transduction, and positive regulation of synapse structural plasticity. These suggest proteins that coordinate cytoskeletal remodeling in response to signaling to support processes such as filopodia formation, synaptic changes, and cell spreading; phagocytic engulfment can also involve actin remodeling. The subtelomeric heterochromatin formation term is less connected to this core theme, but the dominant pattern points to cytoskeletal regulation via GTPases. ","confidence":"Medium","size":6,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006348","count":3},{"id":"GO:0051835","count":2},{"id":"GO:0046847","count":2},{"id":"GO:0034260","count":2},{"id":"GO:0090135","count":2}]},{"hash":"1105428735828354993","title":"Ribosome biogenesis and RNA processing","description":"This cluster centers on GO terms related to ribosomal RNA maturation (5.8S, SSU, LSU), ribosomal large subunit biogenesis, RNA methylation, and mRNA splicing, pointing to a shared role in ribosome assembly and RNA processing. While ubiquitin-proteasome\u2013mediated protein turnover and developmental terms appear, the strongest signal is in RNA processing and ribosome biogenesis, supporting a coherent functional theme.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":3},{"id":"GO:0071276","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0036265","count":2}]},{"hash":"1943042832371337128","title":"RNA processing and chromatin regulation","description":"Dominant GO terms center on mRNA splicing and spliceosome regulation, with supporting signals of transcription initiation by RNA Pol II, ncRNA-mediated gene silencing, ribosomal subunit biogenesis, and chromatin processes such as heterochromatin formation; together this suggests a nuclear RNA processing and chromatin-regulation theme. ","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0006367","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0042273","count":2}]},{"hash":"2268923886234309584","title":"Amino Acid Transport","description":"The GO terms are dominated by transmembrane transport of amino acids and related small molecules (methionine, D-serine, D-alanine, GABA, arginine-related processes) and transepithelial transport, with additional polyamine transport hints. This points to a cluster of amino acid transporters/channels that mediate uptake/export across membranes and epithelia. ","confidence":"High","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006527","count":2},{"id":"GO:0044690","count":2},{"id":"GO:0035826","count":2},{"id":"GO:1902269","count":2},{"id":"GO:0070634","count":2}]},{"hash":"1907765313570683679","title":"Viral entry, latency, and life cycle","description":"The GO terms center on viral processes: membrane fusion and entry, viral life cycle, proviral latency, viral release, and RNA-templated DNA biosynthesis, suggesting a viral infection/replication theme; a few unrelated terms appear, but the dominant pattern is viral-host interactions and lifecycle steps.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034389","count":1},{"id":"GO:0019064","count":1},{"id":"GO:0030260","count":1},{"id":"GO:1901407","count":1},{"id":"GO:0010849","count":1}]},{"hash":"66557810033471983","title":"Ribosome biogenesis and proteostasis","description":"The cluster shows enrichment for ribosome-related processes: ribosome biogenesis, translation, maturation of SSU rRNA; and for protein turnover: ubiquitin-dependent protein catabolic process and proteasome assembly, with regulation of catalytic activity. A plausible unified theme is proteostasis centered on ribosome production and protein turnover, despite one odd term (platelet formation) that may be noise.","confidence":"Medium","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":1},{"id":"GO:0032147","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0031564","count":1},{"id":"GO:0000462","count":1}]},{"hash":"2143300844411088251","title":"Unknown","description":"The terms cover a broad mix of cellular processes (protein unfolding, peroxisome import, Golgi retention, N-linked glycosylation, DNA damage tolerance, mtDNA replication regulation, development, and neuronal vesicle transport) with no single cohesive function linking all six proteins. Therefore, no clear cluster label can be assigned.","confidence":"","size":6,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0043335","count":1},{"id":"GO:0030420","count":1},{"id":"GO:0072389","count":1},{"id":"GO:0018279","count":1},{"id":"GO:0016558","count":1}]},{"hash":"143418227348041290","title":"Neural, immune, and muscle differentiation signals","description":"This cluster includes GO terms for telencephalon development, NK T cell differentiation, and myotube differentiation, along with signaling-related terms (STAT phosphorylation, p53-mediated signaling, dopamine response), indicating a broad theme of differentiation linked by cellular signaling across neural, immune, and muscle contexts.","confidence":"Medium","size":6,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006813","count":3},{"id":"GO:0021537","count":2},{"id":"GO:0042523","count":2},{"id":"GO:2000811","count":2},{"id":"GO:1903351","count":2}]},{"hash":"75131699911977508","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006295","count":1},{"id":"GO:0006298","count":1},{"id":"GO:0070987","count":1},{"id":"GO:2000001","count":1},{"id":"GO:0006310","count":1}]},{"hash":"1968532381977961536","title":"Unknown","description":"The top GO terms are diverse and include obsolete terms as well as unrelated processes (photoreceptor maintenance, circulatory development, viral process, ER protein folding, etc.), with no clear shared function tying the proteins together. This prevents a concise, representative label beyond Unknown.","confidence":"","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006662","count":1},{"id":"GO:0080058","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0045494","count":1},{"id":"GO:0033158","count":1}]},{"hash":"1448861347006158806","title":"Glycosylation and mannan biosynthesis","description":"The top GO terms point to glycosylation and glycan biosynthesis, including vacuolar protein processing, mannan biosynthetic process, globoside biosynthesis, and mannosyl-inositol phosphorylceramide biosynthetic process. This suggests a cohesive theme around carbohydrate modification and assembly, especially relating to glycoprotein maturation and fungal cell-wall\u2013related mannans and glycosphingolipids. While a few terms are obsolete, the shared glycosylation/glycan biosynthesis signal supports this label.","confidence":"Medium","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006624","count":1},{"id":"GO:0036210","count":1},{"id":"GO:0051999","count":1},{"id":"GO:0001576","count":1},{"id":"GO:0006486","count":1}]},{"hash":"1002449920372816445","title":"Ribosome Targeting and Cell Cycle Regulation","description":"The cluster\u2019s top GO terms emphasize translation and SRP-dependent cotranslational targeting to membrane, indicating ribosome-associated protein synthesis and targeting to the ER/membrane. Additionally, terms related to mitotic spindle organization and G1/S transition suggest links to cell cycle control and protein localization. Together, these imply a theme around ribosome- and membrane-targeted protein production with concurrent cell cycle/localization roles, justifying this label.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0006614","count":1},{"id":"GO:0006616","count":1},{"id":"GO:0030472","count":1},{"id":"GO:1904785","count":1}]},{"hash":"1830183943587765661","title":"Unknown","description":"This cluster's top GO terms span a wide range of regulatory processes (transcription regulation, signaling pathways such as NF-kappaB and Rap, vesicle transport, chromatin formation, hormone biosynthesis, and ion channel regulation) with no clear single theme. The diversity suggests no cohesive function tying all members together, so Unknown is the safest label.","confidence":"","size":5,"edges":7,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0010950","count":2},{"id":"GO:0090419","count":1},{"id":"GO:0072383","count":1},{"id":"GO:0090055","count":1},{"id":"GO:1905150","count":1}]},{"hash":"581547052269134618","title":"Calcineurin-NFAT Calcium Signaling and T Cell Homeostasis","description":"The cluster\u2019s top GO terms are dominated by the calcineurin-NFAT signaling cascade and its regulation, along with T cell homeostasis, indicating a core theme of calcium-dependent transcriptional control in immune cells. Although some terms touch DNA repair and ER-Golgi transport, the most coherent and specific function tying these proteins together is calcium-mediated NFAT signaling that governs T cell homeostasis.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0033173","count":4},{"id":"GO:0043029","count":4},{"id":"GO:0010791","count":4},{"id":"GO:0061587","count":4},{"id":"GO:0097552","count":4}]},{"hash":"14996566267745740","title":"Cellular stress response and metabolic regulation","description":"The proteins show GO terms tied to stress and metabolic processes, including cellular responses to insulin, lipopolysaccharide, arsenic, and nitric oxide; regulation of mitochondrial membrane potential and calcium-release channels; toxin catabolic processes; and aromatic amino acid metabolism, suggesting a broad stress-response and metabolic regulation cluster rather than a single, cohesive pathway.","confidence":"Low","size":5,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0060315","count":1},{"id":"GO:0051881","count":1},{"id":"GO:0032869","count":1},{"id":"GO:0060316","count":1},{"id":"GO:0071243","count":1}]},{"hash":"287661895497349959","title":"Ribosome Biogenesis and Translation Regulation","description":"Top terms are dominated by ribosome assembly and translation-related processes (ribosomal biogenesis, cytoplasmic translation, ribosome disassembly, selenocysteine incorporation, translation elongation) with supporting signals like nonfunctional rRNA decay and cell division context. The cluster appears to group proteins involved in ribosome construction and regulation of protein synthesis, rather than unrelated functions.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042274","count":1},{"id":"GO:0002181","count":1},{"id":"GO:0032790","count":1},{"id":"GO:0001514","count":1},{"id":"GO:0070651","count":1}]},{"hash":"974311815059148525","title":"Amino acid and one-carbon metabolism","description":"The listed GO terms cluster around amino acid turnover (methionine catabolic, valine biosynthetic) and one-carbon metabolism, with selenium metabolism as a related nutrient-processing term. While a few terms (circadian rhythm, hypoxia response, host cell entry) are unrelated to metabolism, the dominant signal is amino acid and one-carbon metabolism, suggesting a functional theme in these proteins.","confidence":"Medium","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0001887","count":1},{"id":"GO:0009087","count":1},{"id":"GO:0035635","count":1},{"id":"GO:0042745","count":1}]},{"hash":"1541541568438321648","title":"Shikimate pathway and aromatic amino acid biosynthesis","description":"The top GO terms point to the shikimate pathway and production of aromatic amino acids, e.g., chorismate biosynthetic process and aromatic amino acid biosynthetic process, with related 3,4-dihydroxybenzoate biosynthesis. While a couple of terms are unrelated or obsolete, the strongest shared theme across most terms is aromatic compound biosynthesis via the shikimate pathway, suggesting this cluster centers on aromatic amino acid production. ","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030416","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009073","count":1},{"id":"GO:0046279","count":1},{"id":"GO:0040007","count":1}]},{"hash":"198882904567231855","title":"Nucleotide metabolism and RNA editing","description":"The dominant GO terms cluster around nucleotide metabolism (UMP salvage, uridine and cytidine metabolism, deoxycytidine catabolism, ribonucleotide/cytidine related processes) and a notable RNA modification event (tRNA wobble adenosine to inosine editing), with a few outliers like riboflavin biosynthesis and antibiotic response that reduce cohesion but do not override the core theme.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009231","count":1},{"id":"GO:0044206","count":1},{"id":"GO:0019858","count":1},{"id":"GO:0046109","count":1},{"id":"GO:0009972","count":1}]},{"hash":"2023493102958716648","title":"Spliceosome and rRNA processing","description":"Most terms point to RNA processing and splicing functions: mRNA cis splicing via spliceosome, spliceosomal snRNP assembly, and maturation/processing of various rRNAs (LSU, 5.8S, 5S). This strongly suggests a cluster of spliceosome/rRNA processing proteins; a couple of terms related to plant tissue patterning and T cell differentiation appear unrelated noise.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":2},{"id":"GO:0000470","count":1},{"id":"GO:0000466","count":1},{"id":"GO:0006364","count":1},{"id":"GO:0000387","count":1}]},{"hash":"657444100741540088","title":"Meiosis and cell cycle checkpoint signaling","description":"The top GO terms point to meiosis- and cell-cycle\u2013related processes, including meiotic recombination checkpoint signaling, G1/S transition in the cell cycle, and double-strand break repair via NHEJ, as well as megagametogenesis and asymmetric neuroblast division. Additional terms on phosphatase regulation, protein dephosphorylation, and ribosome-associated proteostasis suggest broader cellular regulation linked to cell division and genome maintenance. Taken together, the cluster appears focused on meiosis and cell-cycle checkpoint control with supporting roles in protein quality control and metabolism, making this label a concise reflection of the dominant theme.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000082","count":1},{"id":"GO:0043666","count":1},{"id":"GO:0009561","count":1},{"id":"GO:0072344","count":1},{"id":"GO:1990116","count":1}]},{"hash":"1778423054926923167","title":"Fatty acid metabolism (biosynthesis & degradation)","description":"The top terms show several fatty acid\u2013related processes (biosynthesis and catabolism of medium- and long-chain fatty acyl-CoAs, palmitic acid biosynthesis), indicating a core theme of fatty acid metabolism. A few outliers (enterobactin biosynthesis, transcriptional regulation, phosphorylation) exist but are less represented, so the label captures the dominant function of the cluster.","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051792","count":1},{"id":"GO:0045892","count":1},{"id":"GO:0010124","count":1},{"id":"GO:0009239","count":1},{"id":"GO:1900535","count":1}]},{"hash":"1512727552503911352","title":"ER Protein Folding and UPR","description":"The top GO terms strongly point to ER-associated proteostasis: protein folding in the endoplasmic reticulum, response to unfolded protein, and translation changes during ER stress, together with chaperone/refolding activity. While there are a few generic or nuclear-related terms, the dominant theme centers on ER quality control and the unfolded protein response.","confidence":"High","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071630","count":1},{"id":"GO:0032781","count":1},{"id":"GO:0001707","count":1},{"id":"GO:0070389","count":1},{"id":"GO:0006260","count":1}]},{"hash":"2130346613243654754","title":"Meiosis and Early Embryogenesis","description":"The cluster\u2019s GO terms cluster around oocyte maturation and spindle assembly in female meiosis I, with supporting microtubule dynamics and proteasomal degradation processes, suggesting meiotic/oogenesis activity. The presence of neural development terms (initiation of neural tube closure, third ventricle development) points to involvement in early embryogenesis and brain development, while other terms reflect general remodeling during development. Overall, the proteins appear linked to meiosis/oogenesis and early embryonic development.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0008285","count":1},{"id":"GO:0006516","count":1},{"id":"GO:0007057","count":1},{"id":"GO:0021678","count":1},{"id":"GO:0001556","count":1}]},{"hash":"804945476121091802","title":"Transmembrane Transporters","description":"The GO terms are dominated by transmembrane transport across diverse substrates (xenobiotics, vitamins, nitrates, arabinose, ions like Na+/K+/phosphate), with an additional note on neurotransmitter loading into synaptic vesicles, all pointing to a shared function in moving substances across membranes. This suggests a cluster of transporter proteins with broad substrate specificity or related transporter families.","confidence":"High","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":5},{"id":"GO:0042891","count":5},{"id":"GO:0035461","count":5},{"id":"GO:0015706","count":4},{"id":"GO:0042128","count":4}]},{"hash":"1085720682509690124","title":"RNA processing and nuclear export","description":"Most GO terms point to nucleic acid metabolism and nuclear functions: tRNA processing, mRNA export, transcription by RNA polymerase I, nucleotide-excision repair, and nuclear envelope organization. The cytokinin-related terms (isopentenyl adenine biosynthesis) likely reflect a tRNA modification connection rather than core nuclear processes, while lipid homeostasis and obsolete terms are less related. Overall, the cluster centers on RNA processing and nuclear transport with some peripheral metabolic hints.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006289","count":1},{"id":"GO:0070816","count":1},{"id":"GO:0006360","count":1},{"id":"GO:0009691","count":1},{"id":"GO:0034265","count":1}]},{"hash":"1616180103037275886","title":"Unknown","description":"Top terms are diverse: dopamine response, GABAergic interneuron development, endothelin-regulated blood pressure, and several basic cellular processes. This mix lacks a clear single function or pathway, so a cohesive label cannot be determined.","confidence":"","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1903206","count":2},{"id":"GO:0003100","count":1},{"id":"GO:1903351","count":1},{"id":"GO:0090136","count":1},{"id":"GO:0006893","count":1}]},{"hash":"577752311922496475","title":"Unknown","description":"The top GO terms are a mix of developmental (placenta, thymus), metabolic (glucose metabolism), stress/drug-response (cadmium, cocaine, antipsychotic), signaling (MAPK), and cellular processes (chemotaxis) with no clear shared function across all proteins. This lack of a cohesive theme makes it hard to assign a precise, representative label. ","confidence":"","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0001890","count":3},{"id":"GO:0000187","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0048538","count":2},{"id":"GO:0042220","count":2}]},{"hash":"1499188636391558067","title":"ER-Golgi trafficking and secretion","description":"The top GO terms cluster around intracellular trafficking and the secretory pathway, especially ER-to-Golgi transport (including COPI vesicles, Golgi ribbon formation, and regulation of protein exit/retention in the ER) and Wnt secretion. A few developmental terms (placenta development, axis specification, egg-laying behavior) may reflect broader roles or cross-species annotation, but the dominant signal is ER-Golgi transport and cargo routing across the secretory pathway.","confidence":"High","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0001893","count":1},{"id":"GO:0032525","count":1},{"id":"GO:0002121","count":1},{"id":"GO:0061357","count":1},{"id":"GO:0048205","count":1}]},{"hash":"13004147252355697","title":"Fatty-acyl-CoA metabolism and cholesterol transport","description":"The top GO terms point to fatty-acyl-CoA metabolism for both very long- and medium-chain forms, along with lipid transport and cholesterol handling (including intracellular cholesterol transport and lipid hydroperoxide transport). While there are mentions of reproductive development and transcription/kinase activity, the lipid metabolism terms are dominant and cohesive, suggesting a cluster centered on lipid processing and cholesterol transport with possible contextual ties to steroid metabolism. Overall, a lipid metabolism\u2013driven cluster is most representative. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001824","count":1},{"id":"GO:0032147","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0036111","count":1},{"id":"GO:0008209","count":1}]},{"hash":"965545939003672426","title":"Cell Division and Cytoskeletal Regulation","description":"Top GO terms emphasize cell cycle progression and septin/cytoskeletal organization (mitotic exit and septin ring), pointing to roles in cytokinesis and cytoskeletal dynamics. While transcription and translation terms are present, the strongest signal centers on cell division and related structural remodeling.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0010458","count":1},{"id":"GO:0032186","count":1},{"id":"GO:0042274","count":1},{"id":"GO:0002181","count":1}]},{"hash":"2283279000888663346","title":"DNA damage response and ubiquitin signaling","description":"The top GO terms center on telomere maintenance via recombination, meiotic double-strand break formation, and K63-linked ubiquitination, all of which align with genome maintenance and ubiquitin-mediated signaling. There are also signals of cellular stress responses (ER stress\u2013related apoptotic signaling) that support a broader theme of stress response and protein quality control. Some terms appear noisy or less coherent, but the core cluster seems to reflect genome maintenance and ubiquitin-driven quality control under stress.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:1990920","count":4},{"id":"GO:1903955","count":4},{"id":"GO:0000722","count":4},{"id":"GO:0071347","count":4},{"id":"GO:0010976","count":4}]},{"hash":"1870428228388978009","title":"RNA processing and mRNA decay","description":"The cluster is enriched for RNA-related processes: splicing and spliceosome assembly, mRNA turnover via deadenylation-dependent decapping and P-body formation, plus transcription termination, which together point to roles in RNA maturation and gene expression regulation. Some terms like pericentric heterochromatin formation and hair cycle are less directly tied, but may reflect broader chromatin and cell-cycle regulation contexts.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0033962","count":2},{"id":"GO:1990141","count":2},{"id":"GO:0000290","count":2}]},{"hash":"146103486552772034","title":"Shikimate-Phenylpropanoid Aromatic Biosynthesis","description":"The GO terms point to the core shikimate pathway and downstream aromatic metabolism, including chorismate and phenylpropanoid biosynthesis, which are characteristic of plant aromatic compound production. The presence of a transcription-related term suggests possible regulatory coordination, but the strongest, non-obsolete signals are aromatic biosynthesis-related, justifying this label. ","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006541","count":1},{"id":"GO:0019878","count":1},{"id":"GO:0019632","count":1},{"id":"GO:0006730","count":1}]},{"hash":"336952053358820880","title":"Unknown","description":"GO terms point to miscellaneous metabolic processes (inositol, galactose, sorbitol catabolic/biosynthetic) and some regulatory activities, but there is no coherent theme tying the four proteins together; the term set includes several obsolete GO entries and there are no edges to form a functional cluster, so a precise function cannot be inferred.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019310","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0000122","count":1},{"id":"GO:0006012","count":1},{"id":"GO:0043433","count":1}]},{"hash":"719482956299917572","title":"Yeast autophagy and vacuolar targeting","description":"The top GO terms cluster around autophagy- and vacuole-directed processes (mitophagy, Cvt pathway) and related protein modifications (sumoylation, lipidation) that regulate such pathways, with additional references to growth and cell-cycle regulation. The strongest shared theme is autophagy- and vacuolar targeting-\u2013associated turnover in yeast, making the label concise and representative.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0061504","count":1},{"id":"GO:0016925","count":1},{"id":"GO:2000220","count":1},{"id":"GO:0006501","count":1},{"id":"GO:0045892","count":1}]},{"hash":"2137099272942175968","title":"Unknown","description":"The GO terms are very diverse, including various embryonic development processes, meiosis, DNA repair regulation, and an immune-related term, with no evident shared pathway or function connecting all four proteins. This lack of a cohesive theme supports labeling the cluster as Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007493","count":1},{"id":"GO:0003142","count":1},{"id":"GO:0043046","count":1},{"id":"GO:0030538","count":1},{"id":"GO:2000819","count":1}]},{"hash":"1412188209771722288","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042450","count":1},{"id":"GO:0006108","count":1},{"id":"GO:0014850","count":1},{"id":"GO:0001666","count":1},{"id":"GO:0019619","count":1}]},{"hash":"37342188345608877","title":"Purine and Folate Biosynthesis","description":"The cluster is dominated by GO terms related to purine nucleotide biosynthesis and folate metabolism (10-formyltetrahydrofolate biosynthesis, tetrahydrofolate interconversion, purine nucleotide biosynthetic process, purine nucleobase biosynthetic process). These connect to one-carbon metabolism and nucleotide production, suggesting a cohesive theme around nucleotide and folate biosynthesis. Some terms (neutrophil homeostasis, embryonic neurocranium morphogenesis, obsolete biosynthetic terms) appear less related and may reflect annotation noise or broader metabolic roles in certain contexts. Overall, the core function appears to center on nucleotide and folate biosynthesis.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001780","count":2},{"id":"GO:0048702","count":2},{"id":"GO:0009086","count":2},{"id":"GO:0009257","count":2},{"id":"GO:0035999","count":2}]},{"hash":"2038082868498559964","title":"Calcineurin-NFAT signaling in T cells","description":"This cluster is dominated by GO terms for the calcineurin-NFAT signaling cascade and T cell homeostasis, pointing to calcium-dependent transcriptional regulation in immune cells as the core function. Other terms present (DNA repair, vesicle transport, responses to cocaine) seem secondary or unrelated, suggesting some annotation noise alongside the main NFAT/T cell theme.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0033173","count":4},{"id":"GO:0043029","count":4},{"id":"GO:0010791","count":4},{"id":"GO:0061587","count":4},{"id":"GO:0097552","count":4}]},{"hash":"1039606294248813621","title":"NAD and Thiamine Biosynthesis with Stress Responses","description":"The dominant GO terms point to cofactor biosynthesis (quinolinate/NAD and thiamine) as a core function, with several terms indicating responses to environmental stimuli ( xenobiotic stimulus, lipopolysaccharide, aluminum ion, corticosterone ). This suggests a cluster centered on metabolism of essential cofactors coupled with general stress/adaptation responses; a few dopamine-related terms and obsolete entries are likely annotation noise.","confidence":"Medium","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019805","count":3},{"id":"GO:0043046","count":3},{"id":"GO:0042493","count":3},{"id":"GO:0032496","count":3},{"id":"GO:0042135","count":3}]},{"hash":"2123098054090364346","title":"Brain development and neural signaling","description":"Reasoning: The most represented terms point to neural processes\u2014sensory perception of pain, telencephalon development, and dopamine-related cellular responses\u2014suggesting brain development and neurotransmission as core functions. Additional terms involve broader signaling and survival pathways (STAT phosphorylation, p53 regulation, TLR4 signaling), which can intersect with neural signaling. This supports a concise label of brain development and neural signaling, with some cross-talk to immune and cell-survival signaling.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019233","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0010744","count":1},{"id":"GO:0042523","count":1},{"id":"GO:2000811","count":1}]},{"hash":"1813135264988551888","title":"Unknown","description":"The top GO terms span megagametogenesis, sugar/nitrogen responses, circadian rhythm, pollen hydration, protein kinase regulation, and starch catabolic processes, with no single biological process uniting them. Coupled with zero edges among the proteins, the cluster lacks a cohesive functional theme, so the safe label is Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009561","count":1},{"id":"GO:0043562","count":1},{"id":"GO:0009744","count":1},{"id":"GO:0007165","count":1},{"id":"GO:0009859","count":1}]},{"hash":"1005054956505309061","title":"Aminoacyl-tRNA Synthetases","description":"The dominant GO terms point to tRNA aminoacylation activities (aspartyl- and lysyl-tRNA aminoacylation) and mitochondrial-specific aminoacylation, which together identify aminoacyl-tRNA synthetases as the core function of this cluster. Some DNA replication/repair and telomere maintenance annotations may reflect incidental or moonlighting associations, but the strongest signal is the tRNA charging function across mitochondrial and cytosolic contexts.","confidence":"Medium","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0071915","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0070200","count":4},{"id":"GO:0070146","count":4},{"id":"GO:0002101","count":4}]},{"hash":"1358203817267506171","title":"Transmembrane Sugar and Ion Transporters","description":"This cluster is driven by multiple GO terms for plasma membrane transport of diverse substrates (selenite, organic cations, nitrate, xylose, and glucose), plus a fructose-related response, indicating a core function in transmembrane nutrient/ion transport. Some unrelated terms appear (e.g., regulatory processes) and may reflect ancillary roles or annotation noise, but the dominant theme is transport across the membrane. ","confidence":"Medium","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0097080","count":4},{"id":"GO:0070715","count":4},{"id":"GO:0015706","count":4},{"id":"GO:0071332","count":4},{"id":"GO:0015753","count":4}]},{"hash":"859236944366153530","title":"Organelle assembly and trafficking","description":"The top GO terms cluster around organelle maintenance and membrane-related processes: microautophagy, vacuolar transport and fusion, along with membrane organization in muscle cells (T-tubules, sarcoplasmic reticulum calcium handling) and mitochondrial ribosome assembly. This suggests a broad theme of organelle biogenesis, turnover, and trafficking.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016237","count":1},{"id":"GO:0007034","count":1},{"id":"GO:0042144","count":1},{"id":"GO:2000769","count":1},{"id":"GO:0006799","count":1}]},{"hash":"1504375508001379503","title":"Diverse Microbial Catabolic and Biosynthetic Processes","description":"The GO terms are dominated by microbial metabolism and cell processes\u2014lignin and cellulose catabolism, nutrient transport (copper, iron, arsenate), denitrification, antibiotic biosynthesis, sporulation, and FtsZ-dependent cytokinesis\u2014suggesting a cluster of bacterial metabolic and division activities rather than a single pathway. An outlier term for platelet activation may reflect annotation noise or cross-domain mapping.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046274","count":1},{"id":"GO:0030168","count":1},{"id":"GO:1901684","count":1},{"id":"GO:0043093","count":1},{"id":"GO:0030435","count":1}]},{"hash":"630347497888113828","title":"Ion Transport and Salt Stress Response","description":"These proteins cluster around membrane ion transport and osmoregulation, with GO terms for sodium export, proton transmembrane transport, potassium homeostasis, and cell volume regulation, plus a response to salt stress and vacuolar acidification. While a couple terms (BDNF signaling, cardiac conduction) may be annotation noise, the dominant theme is ion transport and salt/osmotic balance, supporting this label.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1903281","count":1},{"id":"GO:0009651","count":1},{"id":"GO:0036376","count":1},{"id":"GO:0007035","count":1},{"id":"GO:0031547","count":1}]},{"hash":"1877108045425671427","title":"Neuronal development and RNA processing","description":"The terms point most strongly to neuronal-related functions (neuron projection extension; regulation of serotonin secretion) while also highlighting RNA processing steps (alternative splicing; tRNA wobble base modification) and miscellaneous stress/metabolic terms. The shared theme appears to be neural development and regulation of neuronal gene expression, with RNA processing as a supporting mechanism.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051412","count":1},{"id":"GO:0009635","count":1},{"id":"GO:0019805","count":1},{"id":"GO:0008283","count":1},{"id":"GO:0014063","count":1}]},{"hash":"1204558069403807074","title":"mRNA Splicing and Translation Regulation","description":"Based on the top GO terms, this cluster centers on RNA processing and control of translation: spliceosome-mediated mRNA splicing (cis/alternative), splice site recognition, and mRNA modification/stabilization, together with translation initiation/reinitiation and miRNA-mediated translational repression. The co-occurrence suggests a functional module coordinating mRNA maturation with translation efficiency.","confidence":"High","size":4,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":2},{"id":"GO:0045292","count":1},{"id":"GO:0002188","count":1},{"id":"GO:0000380","count":1},{"id":"GO:0001731","count":1}]},{"hash":"1736884170996180390","title":"Neurodevelopment and Dopamine Signaling","description":"The top GO terms include telencephalon development and cellular response to dopamine, pointing to brain development and dopaminergic signaling as core functions of this cluster. Additional terms related to tyrosine phosphorylation of STAT, p53-mediated signaling, and differentiation processes suggest broader developmental signaling activity, but the recurrence of brain-related terms supports a neurodevelopmental/dopaminergic theme. Thus the label captures the dominant function while acknowledging some non-brain terms.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0021537","count":2},{"id":"GO:0042523","count":2},{"id":"GO:2000811","count":2},{"id":"GO:1903351","count":2},{"id":"GO:2001275","count":2}]},{"hash":"1339697332412095004","title":"Fungal cell wall biosynthesis and trafficking","description":"Based on GO terms, the cluster centers on cell wall formation and transport of wall components: endocytic recycling, Golgi to plasma membrane transport, and biosynthesis of beta-D-glucan, which are key steps in assembling fungal cell walls. The presence of fungal-type cell wall organization and cell wall biogenesis supports this theme. A few unrelated terms (dopamine response, endothelin signaling, neuron development) likely reflect annotation noise and do not override the core cell-wall trafficking signal.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032456","count":2},{"id":"GO:0031505","count":1},{"id":"GO:0042546","count":1},{"id":"GO:0006078","count":1},{"id":"GO:0003100","count":1}]},{"hash":"113375389494450003","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0035975","count":1},{"id":"GO:0002188","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0032790","count":1}]},{"hash":"1753287904577228191","title":"Sphingolipid and Phospholipid Metabolism","description":"The cluster\u2019s GO terms are dominated by lipid-related processes, especially sphingolipid pathways (regulation of sphingolipid signaling, sphingosine and sphinganine-1-phosphate metabolism) and phospholipid turnover (phosphatidylglycerol biosynthesis, phospholipid dephosphorylation, and catabolic processes). This suggests a cohesive lipid metabolism module centered on sphingolipids and phospholipids, with a few unrelated terms that may reflect annotation noise.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1902068","count":1},{"id":"GO:0006670","count":1},{"id":"GO:0006655","count":1},{"id":"GO:0046839","count":1},{"id":"GO:0044330","count":1}]},{"hash":"1224185732698406865","title":"Nuclear ubiquitin-proteasome quality control","description":"The strongest signal is nuclear proteostasis mediated by the ubiquitin-proteasome system, including ubiquitin-dependent protein catabolic processes. This suggests the cluster\u2019s proteins participate in nuclear quality control and turnover of misfolded or damaged proteins, especially under stress conditions. Some terms reflect broader or incidental nuclear processes (DNA replication, tRNA import, nuclear membrane fusion), but the core theme appears to be UPS-driven nuclear protein quality control and turnover.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071630","count":2},{"id":"GO:0032781","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0001707","count":2},{"id":"GO:0070389","count":2}]},{"hash":"1938045444984372086","title":"Unknown","description":"The top GO terms span mitochondrial/chloroplast protein import, mitochondrial genome maintenance, and diverse membrane trafficking processes (endocytosis, vesicle budding) with no single unifying function among the proteins; plus there are no interactions observed, suggesting no coherent cluster function. ","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":2},{"id":"GO:0045039","count":1},{"id":"GO:0045037","count":1},{"id":"GO:0030150","count":1},{"id":"GO:0032094","count":1}]},{"hash":"2214550547869618975","title":"Nuclear Transport and Telomere Tethering","description":"The cluster shows strong signals for nuclear import/export processes (NLS import into nucleus; ribosomal subunit and mRNA export; nuclear pore organization) and for chromatin/telomere association at the nuclear periphery (telomere tethering, periphery gene DNA tethering). This suggests a cohesive theme around nuclear transport machinery and perinuclear chromatin/telomere organization, with some ancillary roles in chromatin silencing at telomeres. Confidence: Medium","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035392","count":2},{"id":"GO:0036228","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0034398","count":2},{"id":"GO:0035080","count":2}]},{"hash":"314775016426478609","title":"Nuclear transport and mRNA export","description":"The cluster\u2019s GO terms cluster strongly around nuclear pore localization, import into/export from the nucleus, and poly(A)+ mRNA export, pointing to a cohesive set of proteins involved in nuclear transport and RNA trafficking; a few outliers (light absorption, imaginal disc growth) are less related.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090204","count":1},{"id":"GO:1904046","count":1},{"id":"GO:0016037","count":1},{"id":"GO:0045571","count":1},{"id":"GO:2000156","count":1}]},{"hash":"1324837856396034114","title":"Arp2/3-Mediated Actin Assembly and Cytoskeleton Organization","description":"The dominant GO terms describe actin cytoskeleton assembly and organization, especially Arp2/3-mediated actin nucleation, cortical patch localization, and postsynaptic actin dynamics, with some muscle-related actin filament terms. This suggests a cohesive focus on actin dynamics and cytoskeletal architecture, though a few obsolete terms appear as noise.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051666","count":3},{"id":"GO:0034314","count":3},{"id":"GO:0098974","count":3},{"id":"GO:1904623","count":3},{"id":"GO:0001300","count":3}]},{"hash":"447947531365446180","title":"Ribosome Biogenesis and Translation","description":"Based on the top GO terms, the cluster centers on ribosome-related processes: ribosomal small subunit biogenesis, ribosomal large subunit export from nucleus, and cytoplasmic translation. Additional terms for cell division and cell cycle may reflect coordination between growth and protein synthesis, but the strongest signal is ribosome assembly and function.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903833","count":1},{"id":"GO:0055072","count":1},{"id":"GO:0000747","count":1},{"id":"GO:1901001","count":1},{"id":"GO:0051301","count":1}]},{"hash":"459116396011612321","title":"Cytoskeletal regulation of cell division and development","description":"The cluster is dominated by microtubule- and centrosome-related division processes (mitotic centrosome separation, cytokinesis by cell plate formation, actomyosin contractile ring assembly) and plus-end-directed vesicle transport, with additional developmental and junctional terms (root development, epidermal stem cell homeostasis, zonula adherens maintenance). This points to a shared theme of cytoskeletal control underpinning cell division and tissue development, across contexts. ","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007100","count":3},{"id":"GO:0072383","count":3},{"id":"GO:0036334","count":3},{"id":"GO:0000911","count":3},{"id":"GO:0009904","count":3}]},{"hash":"220814952586157429","title":"Microtubule-driven cytokinesis and transport","description":"The cluster\u2019s GO terms converge on microtubule-based processes: centrosome separation, plus-end-directed vesicle transport along microtubules, and actomyosin contractile ring assembly during cytokinesis, with additional terms pointing to broader cytoskeletal and developmental roles (including plant-related processes). This suggests a cohesive theme around microtubule dynamics governing cell division and transport, albeit with some cross-kingdom terms.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007100","count":1},{"id":"GO:0072383","count":1},{"id":"GO:0036334","count":1},{"id":"GO:0000911","count":1},{"id":"GO:0009904","count":1}]},{"hash":"927166911244712649","title":"p53-Mediated DNA Damage Response and Proteostasis","description":"The GO terms cluster around p53 signaling and cell cycle regulation (including positive regulation of p53 mediator signaling and regulation of the cell cycle), with evidence of proteostasis control (protein stabilization and negative regulation of ubiquitin-dependent proteolysis/ubiquitin ligase activity) and a stress response to DNA-damaging agents like actinomycin D; translation-related terms may reflect a broader stress-associated translational regulation, together suggesting a cohesive response to DNA damage requiring cell cycle control and proteostasis.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0050821","count":2},{"id":"GO:0071157","count":2},{"id":"GO:1904667","count":2},{"id":"GO:2000059","count":2}]},{"hash":"1818284038429768489","title":"B cell immune activation and cytokine production","description":"The top GO terms emphasize B cell\u2013related functions: isotype switching to IgG, B cell cytokine production, and TNF production, indicating activation and inflammatory signaling in B cells. Other terms (e.g., response to ischemia, response to cocaine, Cajal body localization, mitochondrial import) appear less directly tied to this theme and may reflect broader cellular processes, giving a cautious but identifiable immune-focused signal.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048291","count":3},{"id":"GO:0051086","count":3},{"id":"GO:1904871","count":3},{"id":"GO:0002931","count":3},{"id":"GO:0002368","count":3}]},{"hash":"355745695176199340","title":"Unknown","description":"The GO terms cover a mix of immune-related activities (IgG isotype switching, B cell cytokine production, TNF production) and general cellular processes (protein folding/stabilization, mitochondrial protein import, Cajal body localization, cell division), with no clear unified function or pathway linking all three proteins. Because there isn't a coherent, shared theme across these annotations, a single, distinct label isn\u2019t justifiable.","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048291","count":3},{"id":"GO:0051086","count":3},{"id":"GO:1904871","count":3},{"id":"GO:0002931","count":3},{"id":"GO:0002368","count":3}]},{"hash":"9017815986219010","title":"Oxidative stress\u2013induced mitochondrial apoptosis","description":"These proteins show a cohesive pattern around intrinsic apoptotic signaling in response to oxidative stress and regulation of mitochondrial membrane potential, with support from inositol phosphoceramide metabolism (a sphingolipid pathway linked to stress-induced cell death). An ER-to-Golgi transport term is present but does not dominate the signal, so the dominant theme is stress-responsive, mitochondria-mediated apoptosis. ","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":1},{"id":"GO:0002037","count":1},{"id":"GO:0008631","count":1},{"id":"GO:0010917","count":1},{"id":"GO:0006673","count":1}]},{"hash":"1820486241225867322","title":"GPI-anchor biosynthesis and attachment","description":"This cluster is centered on GPI-anchor biosynthesis and attachment to proteins, evidenced by GO:0006506 and GO:0016255. Related terms like dolichol-linked oligosaccharide biosynthesis support the lipid-linked precursor steps; a few other terms may reflect broader, context-dependent annotations but do not override the core function.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":2},{"id":"GO:0006488","count":1},{"id":"GO:0010183","count":1},{"id":"GO:0050976","count":1},{"id":"GO:0016255","count":1}]},{"hash":"687119803834058007","title":"Unknown","description":"The top GO terms span DNA-templated transcription, various signaling and developmental processes (neurodevelopment, dopamine response, NK T cell differentiation), and cell-cycle regulation, with no single cohesive function linking all three proteins. Given this spread and small cluster size, there isn\u2019t a clear, representative theme to name the group.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0097011","count":3},{"id":"GO:0021537","count":2},{"id":"GO:0042523","count":2},{"id":"GO:2000811","count":2}]},{"hash":"981615365374355238","title":"Mitochondrial lipid regulation and inheritance","description":"Top terms point to mitochondrial functions, notably positive regulation of cardiolipin metabolic process and mitochondrion inheritance, with related terms on mitochondrial morphogenesis (obsolete). While other terms touch on membrane rafts, excretion, cholesterol regulation, and peptidase activity, the strongest signal is mitochondrial lipid metabolism and inheritance, suggesting these proteins may influence mitochondrial membrane dynamics and lipid homeostasis.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070584","count":3},{"id":"GO:1900210","count":3},{"id":"GO:0007588","count":3},{"id":"GO:1903044","count":3},{"id":"GO:0034141","count":3}]},{"hash":"1114696011726626721","title":"Unknown","description":"The GO terms are highly diverse, spanning otolith development, various biosynthetic processes (cholesterol, L-cysteine, sulfate assimilation), ion transport, organofluorine metabolism, and redox-related apoptotic signaling. With only three proteins and a single edge, there is no clear, unifying function linking these terms, so a cohesive cluster label cannot be confidently assigned.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048840","count":1},{"id":"GO:1904042","count":1},{"id":"GO:0006695","count":1},{"id":"GO:0019344","count":1},{"id":"GO:0045726","count":1}]},{"hash":"2273380139346933714","title":"Protein catabolic remodeling in development and bone","description":"The Top Terms show multiple catabolic proteolysis processes (neuropeptide, bradykinin, collagen catabolic) plus bone remodeling activities (bone resorption, intramembranous ossification) and proteasome-related components, with additional development/morphogenesis signals (lung branching, neural precursor proliferation). This points to a theme of proteolytic remodeling across tissues and developmental contexts, justifying a label centered on protein catabolism and remodeling. ","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051603","count":1},{"id":"GO:1990237","count":1},{"id":"GO:2000179","count":1},{"id":"GO:0010815","count":1},{"id":"GO:0030574","count":1}]},{"hash":"452571322101169740","title":"Mitotic progression and APC/C ubiquitination","description":"The terms cluster around mitosis and ubiquitin-mediated proteolysis: mitotic spindle checkpoint signaling, mitotic cell cycle, meiosis I, and general cell division, together with APC/C-dependent and K11-linked ubiquitination processes. This pattern points to proteins that orchestrate mitotic progression by targeted degradation, notably during metaphase-to-anaphase transitions.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032516","count":1},{"id":"GO:0032515","count":1},{"id":"GO:0007094","count":1},{"id":"GO:0000278","count":1},{"id":"GO:0007127","count":1}]},{"hash":"1245351042504068025","title":"Neural Dopamine Signaling and Glucose Metabolism","description":"The GO terms cluster around dopamine response and glucose metabolism, with neural development terms hinting at a brain context. Some terms are peripheral or obsolete, and the small cluster size yields modest confidence in a single cohesive function. Overall, the shared theme is neural signaling tied to metabolic processes.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006006","count":2},{"id":"GO:0021537","count":1},{"id":"GO:0042523","count":1},{"id":"GO:2000811","count":1},{"id":"GO:1903351","count":1}]},{"hash":"1232109529094567833","title":"Bacterial LPS core and lipid biosynthesis","description":"The top GO terms are dominated by lipopolysaccharide biosynthetic processes, including core region synthesis and ADP-L-glycero-beta-D-manno-heptose biosynthesis, plus phospholipid dephosphorylation. This strongly suggests a function related to bacterial cell envelope lipid assembly and LPS production. Some terms like epoxygenase P450 pathway and stilbene catabolic process are less directly connected and may reflect broader metabolic capabilities or annotation noise, but they do not outweigh the LPS/lipid biosynthesis signal. Confidence: Medium","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019373","count":3},{"id":"GO:0097755","count":3},{"id":"GO:0046839","count":3},{"id":"GO:0046272","count":3},{"id":"GO:0006564","count":2}]},{"hash":"575561381340099317","title":"Purine Nucleotide Salvage","description":"The Top Terms cluster around salvage and interconversion of nucleotides (AMP salvage, purine nucleotide interconversion, nicotinate nucleotide salvage, deoxyguanosine catabolic process, nucleotide catabolic process), indicating a nucleotide salvage/metabolic module. Immune-related terms (interleukin-2 production, T cell differentiation) appear but likely reflect broader annotations rather than the primary function of the cluster.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046638","count":1},{"id":"GO:0019509","count":1},{"id":"GO:0009166","count":1},{"id":"GO:0034356","count":1},{"id":"GO:0044209","count":1}]},{"hash":"1477525022688068145","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032543","count":1},{"id":"GO:0070681","count":1},{"id":"GO:0006425","count":1},{"id":"GO:0035690","count":1},{"id":"GO:0071257","count":1}]},{"hash":"1793436052818433156","title":"Meiotic Recombination and Synaptonemal Complex","description":"Predominant GO terms relate to meiotic processes: double-strand break formation, recombination, synaptonemal complex assembly, chiasma formation, and telomere clustering. These indicate a cluster of proteins involved in meiotic chromosome pairing and DNA repair, with some plant-reproductive terms (oogenesis, seed development) possibly reflecting broader roles in gamete formation. ","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007131","count":1},{"id":"GO:0048477","count":1},{"id":"GO:1990918","count":1},{"id":"GO:0045141","count":1},{"id":"GO:0048316","count":1}]}]