[{"hash":"702848935206457177","title":"Neural development and signaling","description":"This cluster is dominated by terms related to neural development and function, including CNS projection neuron axonogenesis, dorsal/ventral neural tube patterning, and dopaminergic synaptic transmission, suggesting a core theme around neural development and neuronal signaling. Endosome transport may reflect cellular trafficking relevant to neurons, while a few terms (cartilage condensation, pseudohyphal growth, NK T cell differentiation) appear as outliers, but do not override the central neural-developmental signal.","confidence":"Medium","size":29,"edges":317,"triangles":1862,"max_degree":27,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":29},{"id":"GO:0007124","count":29},{"id":"GO:1901621","count":29},{"id":"GO:1904637","count":29},{"id":"GO:0001963","count":29}]},{"hash":"486940134962698704","title":"Cerebellar development and neural signaling","description":"The cluster is dominated by cerebellum-related development terms (Bergmann glial cell differentiation and cerebellar cortex formation) and axon regeneration regulation, suggesting a cohesive theme around cerebellar development and neural signaling. While other high-count terms involve cell cycle regulation and broader signaling pathways, these cerebellar terms provide the strongest, most specific linkage to function for this cluster.","confidence":"Medium","size":29,"edges":398,"triangles":3448,"max_degree":28,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0034501","count":27},{"id":"GO:0045736","count":27},{"id":"GO:0008286","count":18},{"id":"GO:0060020","count":18},{"id":"GO:0021697","count":18}]},{"hash":"1123092643515675843","title":"Chromatin maintenance and proteostasis","description":"The enrichment includes heterochromatin formation and nucleosome organization, as well as regulation of protein stability and aggresome/chaperone-mediated assembly, pointing to a theme of preserving chromatin structure and ensuring protein quality; a couple of unrelated terms (mitochondrion inheritance, nitrate assimilation) are peripheral.","confidence":"Medium","size":29,"edges":63,"triangles":79,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030466","count":7},{"id":"GO:0000183","count":7},{"id":"GO:0070842","count":5},{"id":"GO:0000001","count":5},{"id":"GO:0006348","count":5}]},{"hash":"89936959933678975","title":"Mitotic progression and ER-Golgi trafficking","description":"The cluster is dominated by GO terms for cell division and cell cycle, along with vesicle trafficking from the ER to the Golgi (COPII) and spindle/kinetochore attachment, indicating a cohesive module where mitosis is coordinated with intracellular transport and cytoskeletal rearrangements; additional terms related to migration and other processes appear as broader context rather than defining features.","confidence":"High","size":29,"edges":174,"triangles":620,"max_degree":23,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":26},{"id":"GO:0003400","count":26},{"id":"GO:0006888","count":26},{"id":"GO:0007049","count":25},{"id":"GO:0001667","count":25}]},{"hash":"854850881878015984","title":"Drosophila oogenesis and maternal processes","description":"The top GO terms cluster around germline development and maternal provisioning (lymph gland development, female germline ring canal formation, maternal process involved in female pregnancy), with supporting cellular regulation terms (proteasome localization, NLS-bearing protein import into nucleus). This pattern suggests a group of proteins functioning in Drosophila oogenesis and maternal biology, possibly coupled with general cellular control mechanisms reflected by RNA silencing and chromatin-related terms. Overall, a germline-maternal development theme best fits the data, though some terms point to broader housekeeping roles.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048542","count":2},{"id":"GO:0007301","count":2},{"id":"GO:0031144","count":2},{"id":"GO:0060135","count":2},{"id":"GO:0015991","count":2}]},{"hash":"272437934640469127","title":"Neuronal development and signaling","description":"This cluster is dominated by GO terms related to neural development and neuronal signaling, including CNS projection neuron axonogenesis, dopaminergic synaptic transmission, and dorsal/ventral neural tube patterning regulation. Intracellular transport and calcium-responsive signaling (endosome transport, cellular response to ionomycin) align with neuronal growth and communication. A few terms (NK T cell differentiation, cartilage condensation) are less directly connected and may reflect broader developmental processes or annotation noise, but the overall theme centers on neurons and their signaling networks.","confidence":"Medium","size":29,"edges":206,"triangles":555,"max_degree":20,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":28},{"id":"GO:0007124","count":28},{"id":"GO:1901621","count":28},{"id":"GO:1904637","count":28},{"id":"GO:0001963","count":28}]},{"hash":"919463055870378577","title":"Negative regulation of TGF-\u03b2/BMP signaling","description":"The cluster is dominated by GO terms for negative regulation of transforming growth factor beta receptor signaling and BMP signaling, as well as related SMAD regulation and peptidyl-threonine dephosphorylation, pointing to a common function: inhibition of TGF-\u03b2/BMP pathway activity. Some terms (e.g., photosystem stoichiometry adjustment, meristem identity maintenance) suggest plant context, but the central theme is regulatory suppression of TGF-\u03b2/BMP signaling. This label is specific and representative of the cluster\u2019s core function.","confidence":"High","size":29,"edges":25,"triangles":36,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042347","count":8},{"id":"GO:0071560","count":8},{"id":"GO:0080005","count":8},{"id":"GO:0061191","count":8},{"id":"GO:0010991","count":8}]},{"hash":"2105382232302996060","title":"Golgi-ER trafficking and cell proliferation","description":"This cluster centers on vesicle transport between the Golgi and ER (COPII-coated budding, retrograde transport) and core cell-cycle processes (mitotic division, spindle assembly, proliferation). While ribosome biogenesis and brain development appear, the strongest shared theme is ER-Golgi trafficking coupled with proliferative cell growth, making this a concise, representative label for the group.","confidence":"Medium","size":29,"edges":105,"triangles":59,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0090114","count":6},{"id":"GO:0051301","count":6},{"id":"GO:0090307","count":6},{"id":"GO:0007420","count":6}]},{"hash":"201955427440869373","title":"Endomembrane Trafficking and Signaling","description":"The cluster is enriched for vesicle-related processes (COPII-coated vesicle budding, phagosome maturation) and membrane-associated signaling (Wnt signalosome assembly), alongside cell migration and adhesion functions. This points to a core role in endomembrane trafficking coupled with signaling that governs movement and membrane dynamics, with additional hints of broader membrane-related activities in immunity and differentiation. ","confidence":"Medium","size":29,"edges":255,"triangles":1069,"max_degree":26,"top_function":null,"top_go_terms":[{"id":"GO:0090114","count":3},{"id":"GO:1903215","count":2},{"id":"GO:0001667","count":2},{"id":"GO:0006878","count":2},{"id":"GO:0043316","count":2}]},{"hash":"1186619117269854320","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071276","count":10},{"id":"GO:0000278","count":10},{"id":"GO:0031145","count":9},{"id":"GO:2001162","count":9},{"id":"GO:0001843","count":9}]},{"hash":"586949918557650990","title":"Muscle development and transcription regulation","description":"Top GO terms indicate transcriptional control (positive regulation of DNA binding, DNA-templated transcription) and a pronounced muscle-development signal (skeletal muscle fiber development), with supporting processes in cytoskeletal organization (microtubule nucleation) and signaling regulation. ER protein folding and redox homeostasis may reflect proteostasis requirements during differentiation. Overall, the cluster appears driven by transcription programs steering muscle development, with associated cellular remodeling.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043388","count":5},{"id":"GO:0034975","count":4},{"id":"GO:0045454","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0006469","count":3}]},{"hash":"927675712456721022","title":"Male germline meiosis and spermatogenesis","description":"The cluster shows strong representation of GO terms tied to male germline development and meiotic processes: male germ-line cyst formation, male meiosis chromosome segregation, spermatocyte division, and stem cell population maintenance, pointing to functions in spermatogenesis and germline maintenance. Some annotations (e.g., viral process, negative regulation of neuron differentiation) may be incidental, but the core signal is germline meiosis and spermatogenesis.","confidence":"High","size":29,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":2},{"id":"GO:0035066","count":2},{"id":"GO:0048136","count":1},{"id":"GO:0007060","count":1},{"id":"GO:0000082","count":1}]},{"hash":"1661924007898918873","title":"NF-\u03baB/TNF signaling via ubiquitination","description":"The cluster is dominated by GO terms related to ubiquitination (autoubiquitination, K63-linked ubiquitination, ubiquitin-dependent proteolysis) and to TNF signaling/NF-\u03baB activation (TNF-mediated signaling, NF-\u03baB-inducing kinase activation, I\u03baB phosphorylation). This points to a coherent theme where ubiquitin modifications regulate TNF/NF-\u03baB pathways. Some terms are less relevant or obsolete, but the core pattern supports a function in ubiquitin-mediated control of NF-\u03baB signaling. ","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":8},{"id":"GO:0090073","count":7},{"id":"GO:0033209","count":7},{"id":"GO:0042787","count":7},{"id":"GO:1903721","count":7}]},{"hash":"1613066115215063580","title":"Neural development and cellular stress responses","description":"The top terms include brain development and glial apoptotic processes, suggesting a neural context, while other terms point to fundamental cellular stress responses and protein regulation (COPII vesicle budding, mRNA processing, ubiquitination, chromatin assembly, and cell cycle control). This mix indicates proteins involved in neural development with accompanying stress response and protein quality control mechanisms.","confidence":"Medium","size":29,"edges":8,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007420","count":8},{"id":"GO:0090114","count":6},{"id":"GO:2000728","count":5},{"id":"GO:1904668","count":5},{"id":"GO:0000398","count":5}]},{"hash":"1032775382807510060","title":"Unknown","description":"The GO terms are varied and cover processes from GPI-anchor biosynthesis and secretion to JAK-STAT signaling, ubiquitin-related regulation, apoptosis, pH response, mechanosensory detection, and DNA-binding regulation. There isn\u2019t a single cohesive biological theme that unifies the cluster, suggesting the proteins do not represent one clear functional module. Confidence: None","confidence":"","size":29,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0090116","count":2},{"id":"GO:0009268","count":2},{"id":"GO:0050976","count":1},{"id":"GO:0046425","count":1},{"id":"GO:0016255","count":1}]},{"hash":"414562953996787647","title":"Glutamatergic Synaptic Transmission and Endosomal Recycling","description":"The top GO terms point to neuronal signaling, especially glutamatergic synaptic transmission, along with receptor recycling and regulation of endosome size, suggesting a core function in synaptic vesicle trafficking and endocytic recycling. The presence of Rho signaling regulation supports cytoskeletal changes linked to trafficking. Some transcription- and cell-cycle-related terms appear less central, likely reflecting broader or housekeeping roles. Overall, the cluster appears focused on neuronal synaptic activity and endosomal trafficking.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0060316","count":8},{"id":"GO:0006355","count":8},{"id":"GO:0035249","count":7},{"id":"GO:0001881","count":7},{"id":"GO:0051036","count":7}]},{"hash":"1492334276013776","title":"Endomembrane trafficking and receptor recycling","description":"This cluster is characterized by GO terms pointing to Golgi retention, intralumenal vesicle formation, endosome size regulation, and receptor recycling, indicating a cohesive role in endomembrane trafficking and vesicle recycling processes.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0045053","count":2},{"id":"GO:0070676","count":2},{"id":"GO:0034968","count":1},{"id":"GO:0001881","count":1}]},{"hash":"1915339387932588655","title":"Nutrient and xenobiotic transporters","description":"Top GO terms point to transmembrane transport of nutrients, vitamins, and xenobiotics, suggesting a core role in moving small molecules across membranes. Additional terms related to mRNA transport and ER-to-Golgi trafficking support a broader transport/trafficking context, but the dominant signal is membrane transport for nutrients and xenobiotics, consistent with a cluster of transporter proteins. Confidence reflects a coherent but not exclusive transport theme.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007584","count":6},{"id":"GO:0006855","count":6},{"id":"GO:0042891","count":6},{"id":"GO:0035461","count":6},{"id":"GO:0006351","count":4}]},{"hash":"1112722687632760876","title":"Unknown","description":"The top GO terms span transcription, cell cycle, stress and metal response, endosomal transport, fungal morphology, signaling pathways, and neuronal communication, showing no single cohesive function across the cluster. ","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046827","count":7},{"id":"GO:0071276","count":7},{"id":"GO:0006351","count":7},{"id":"GO:0000278","count":7},{"id":"GO:0045087","count":7}]},{"hash":"2247009123528136113","title":"Ubiquitin-dependent TNF and NF-kappaB signaling","description":"Top GO terms cluster around ubiquitination processes (autoubiquitination, K48- and K6-linked ubiquitination) and ubiquitin-dependent protein catabolic process, together with TNF-mediated signaling and NF-kappaB activation steps (I-kappaB phosphorylation, NIK activation). This indicates a cohesive function where ubiquitination modulates TNF signaling and NF-kappaB pathway.","confidence":"High","size":29,"edges":3,"triangles":0,"max_degree":3,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":21},{"id":"GO:1903265","count":21},{"id":"GO:0090073","count":20},{"id":"GO:0033209","count":20},{"id":"GO:0042787","count":20}]},{"hash":"1964886682301742351","title":"Chromatin assembly and mitosis regulators","description":"The prominent terms point to chromosome-level organization (CENP-A chromatin assembly, histone deacetylation) and mitotic processes (spindle orientation, mitotic cell cycle). This suggests a cluster enriched for chromatin dynamics and cell-cycle control proteins, with some RNA processing and trafficking annotations likely incidental.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":5},{"id":"GO:0000132","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0016575","count":4},{"id":"GO:0043547","count":4}]},{"hash":"245579254524042740","title":"Transcription Regulation and Signaling Proteins","description":"Top terms center on regulation of DNA-templated transcription and various signaling pathways (cytokinin-activated signaling, Rho signal transduction), with additional hints of cell cycle processes and cellular fusion. Although neural terms appear among the annotations, the core signal is regulatory rather than a single metabolic pathway. Thus, labeling this cluster as transcription regulation and signaling proteins captures the main shared function with reasonable specificity.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:0009736","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0035023","count":2}]},{"hash":"1516199163141949751","title":"Lipid catabolism and endocannabinoid signaling","description":"This cluster is enriched for lipid-centric catabolic processes, including triglyceride, diacylglycerol, monoacylglycerol, and phosphatidylserine catabolism, along with regulation of endocannabinoid signaling. These converging lipid metabolism terms point to a common theme of lipid turnover and lipid mediator dynamics, making a lipid metabolism-focused label appropriate. Some unrelated terms (e.g., biotin/antibiotic biosynthesis) may reflect annotation noise or multifunctional proteins, but the lipid-related terms dominate.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019433","count":7},{"id":"GO:2000124","count":7},{"id":"GO:0009102","count":7},{"id":"GO:0017000","count":7},{"id":"GO:0009636","count":6}]},{"hash":"1515108253603419784","title":"Heat-stress RNA processing and cell cycle regulation","description":"This cluster centers on nuclear processes like mRNA splicing and export, chromatin assembly involving CENP-A, and regulation of the cell cycle, all in the context of stress responses (heat). Ubiquitination and cytoskeletal changes accompany these processes, suggesting coordinated control of gene expression, protein turnover, and cell division under stress, with some inflammatory signaling. Overall, the dominant theme is how cells adjust RNA processing and cell cycle control during heat-induced stress.","confidence":"Medium","size":29,"edges":16,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030042","count":3},{"id":"GO:0043547","count":3},{"id":"GO:2000728","count":2},{"id":"GO:1904668","count":2},{"id":"GO:0000398","count":2}]},{"hash":"104215717133293115","title":"Ubiquitin-regulated transcription and protein turnover","description":"This cluster is dominated by ubiquitination-related GO terms (protein ubiquitination, negative regulation of protein ubiquitination, and ubiquitin-dependent protein catabolic process) and transcriptional regulation (positive regulation of transcription by RNA polymerase II, plus NF-kappaB activity regulation). These together suggest a cohesive theme around ubiquitin signaling controlling gene expression and protein degradation. Some related terms like stress fiber assembly or viral release hint broader signaling roles but do not outweigh the central ubiquitin/transcription focus.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0033138","count":3},{"id":"GO:0032088","count":3},{"id":"GO:0045944","count":3},{"id":"GO:0031397","count":3}]},{"hash":"2024161526315381302","title":"Mitotic spindle and chromatin assembly","description":"This cluster is dominated by GO terms tied to mitosis and chromosome handling: mitotic spindle assembly, mitotic cell cycle, and CENP-A\u2013containing chromatin assembly point to a core function in chromosome segregation and spindle dynamics. Supporting terms like regulation of kinase and GTPase activity suggest coordination of signaling during cell division. Some other terms (mRNA processing, stress-related export) appear as broader cellular processes accompanying division. Overall, the theme centers on mitosis-associated machinery and chromatin organization.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001845","count":4},{"id":"GO:0071902","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0090307","count":4},{"id":"GO:0070306","count":4}]},{"hash":"137927417900148034","title":"Chromatin Regulation and Transcription","description":"Top GO terms are dominated by DNA-templated transcription and chromatin remodeling, indicating a core role in gene expression control via chromatin state. Additional terms touch on cell morphogenesis, mitotic cell cycle, telomere dynamics, and development, with some plant-specific annotations (cytokinin signaling, secondary cell wall biogenesis) that may reflect annotation cross-talk. Overall, this cluster likely represents nuclear regulators of transcription and chromatin architecture.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0043044","count":5},{"id":"GO:0000902","count":4},{"id":"GO:0090090","count":4},{"id":"GO:0045819","count":4}]},{"hash":"693226189221399746","title":"Vesicle trafficking and mitosis regulation","description":"The cluster prominently features endocytic recycling, Golgi-to-ER retrograde transport, and COPII vesicle budding, indicating a strong emphasis on membrane trafficking. It also includes mitosis-related terms such as mitotic cell cycle, mitotic spindle assembly, cell division, and organismal growth, suggesting links to cell proliferation and division. Together, these themes imply proteins that coordinate trafficking with cell-cycle progression, justifying a label that captures both aspects, even in the absence of direct interaction data.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032456","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0090114","count":2}]},{"hash":"1615992908615439946","title":"Mitosis and cytoskeleton remodeling","description":"Top GO terms emphasize actin filament depolymerization and mitotic spindle assembly, along with mitotic cell cycle processes, suggesting the proteins mainly regulate cell division and cytoskeletal dynamics; while there are additional terms related to signaling or development, the dominant signal supports a mitosis/cytoskeleton theme.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030042","count":3},{"id":"GO:0090307","count":3},{"id":"GO:0016055","count":2},{"id":"GO:0048549","count":2},{"id":"GO:0046784","count":2}]},{"hash":"2302906489194519793","title":"Ubiquitin-Dependent Signaling and Regulation","description":"The top GO terms point to ubiquitin-related processes (ubiquitin-dependent ERAD pathway, autoubiquitination) and signaling pathways (NF-kappaB, nuclear receptor signaling such as retinoic acid and vitamin D receptors), with a note of cytoskeletal movement. This pattern suggests proteins involved in ubiquitin-mediated regulation that impacts diverse signaling and cellular processes, even if some terms reflect annotation noise. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0001782","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0007018","count":2},{"id":"GO:1900458","count":1}]},{"hash":"1891633291390322216","title":"Mitotic cell cycle, chromatin organization, and DNA repair","description":"Dominant GO terms center on mitosis and chromosome maintenance: mitotic cell cycle, cell division, APC-dependent mitotic catabolic process, chromatin organization, and homologous recombination\u2013mediated DNA repair. Vesicle trafficking terms are present but peripheral. Overall, the cluster appears to group proteins involved in cell-cycle progression and genome integrity.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007420","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0031145","count":3},{"id":"GO:0031497","count":3}]},{"hash":"1752478461726734704","title":"ER Protein Folding and Redox Homeostasis","description":"Top GO terms show a strong emphasis on protein folding in the endoplasmic reticulum, redox processes, and oxidative stress response, suggesting a cluster of proteins involved in ER-associated protein maturation and maintaining redox balance. Some ancillary terms related to transcription regulation and nuclear transport are present but less central. Overall, the theme is ER protein folding linked to redox homeostasis.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034975","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0045454","count":3},{"id":"GO:0042128","count":2},{"id":"GO:0033158","count":2}]},{"hash":"1737867884103439121","title":"Mitochondrial import and metabolism regulation","description":"This cluster is dominated by terms related to mitochondrial function, notably regulation of mitochondrial membrane permeability and protein import into the mitochondrial matrix, suggesting a group of proteins involved in mitochondrial maintenance and transport. Additional terms point to lipid metabolism (triglyceride biosynthesis) and cAMP signaling, indicating broader metabolic regulation linked to mitochondria. The connection to cell-cycle regulation appears secondary, making mitochondrial import/metabolic regulation the most representative theme. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":4},{"id":"GO:2000134","count":4},{"id":"GO:0070940","count":4},{"id":"GO:1903740","count":4},{"id":"GO:0010867","count":4}]},{"hash":"394304717725785466","title":"Mitotic division and chromosome segregation","description":"The top GO terms emphasize cell division, mitotic spindle assembly, sister chromatid cohesion, and mitotic DNA replication, pointing to a core theme of mitosis and chromosome dynamics. Some items are obsolete or broader, but the dominant signal is proteins involved in mitotic progression and chromosome handling, so the label captures the cluster\u2019s function well.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0090307","count":6},{"id":"GO:0030433","count":5},{"id":"GO:0090344","count":5},{"id":"GO:0031081","count":5}]},{"hash":"341918163554866225","title":"Synaptic vesicle cycling and endocytosis","description":"The prominent GO terms describe clathrin-dependent endocytosis, synaptic vesicle coating, receptor recycling, intracellular protein transport, and glutamatergic synaptic transmission, all pointing to vesicle trafficking and recycling at synapses. A couple of transcription-related terms are present but appear incidental; the core theme is neuronal vesicle recycling and endocytosis.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0034968","count":1},{"id":"GO:0001881","count":1},{"id":"GO:0051036","count":1},{"id":"GO:0035023","count":1}]},{"hash":"482739806101499071","title":"Cardiac muscle signaling and gene regulation","description":"The cluster\u2019s top GO terms cluster around muscle structure and function (sarcomere organization, cardiac muscle cell proliferation) alongside signaling and regulatory processes (regulation of membrane potential, cAMP/PKA signaling, guanylyl cyclase pathways) and transcription-related activity (DNA-templated transcription, nuclear transport). This combination suggests a cohesive theme of muscle-related signaling that integrates gene regulation and excitation-contraction processes, making a cardiac muscle signaling and gene regulation label appropriate.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":5},{"id":"GO:0045214","count":5},{"id":"GO:0006351","count":5},{"id":"GO:2000480","count":4},{"id":"GO:0098719","count":4}]},{"hash":"2317044842613427","title":"Neuronal development and synaptic plasticity","description":"This cluster is enriched for brain development and synaptic signaling terms (brain development, regulation of glutamatergic transmission, long-term synaptic depression, habituation), plus cilium assembly, which can relate to neuronal signaling, and PKC signaling. Lipid metabolism/signaling terms (sphingosine, cholesterol, phosphatidic acid biosynthesis) suggest involvement of lipid-mediated signaling pathways that modulate neuronal function, aligning with a theme of neuronal development and synaptic plasticity.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0060271","count":2},{"id":"GO:0046512","count":1},{"id":"GO:0070528","count":1},{"id":"GO:0090181","count":1}]},{"hash":"684487451105077163","title":"Endocytic-Golgi-Vacuolar Trafficking","description":"The top GO terms revolve around endosome-to-lysosome transport, endocytic recycling, retrograde transport from endosomes to the Golgi, and Golgi-to-vacuole trafficking, with related protein targeting to vacuole and membrane remodeling signals (GTPase activity, plasma membrane tubulation). This points to a cohesive cluster of proteins involved in intracellular trafficking along endosomal\u2013Golgi\u2013vacuole routes. ","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008333","count":4},{"id":"GO:1990126","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0000902","count":3},{"id":"GO:0042147","count":2}]},{"hash":"1879566213434153409","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000244","count":2},{"id":"GO:0048254","count":1},{"id":"GO:0071166","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0000398","count":1}]},{"hash":"1394973215612964964","title":"Unknown","description":"There are no GO terms or network connections in this cluster to suggest a shared function; the top terms are empty and the graph has no edges, so a coherent theme cannot be inferred.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1216655284349621332","title":"Proliferation and Signaling Regulation","description":"The cluster\u2019s top GO terms span negative regulation of cell proliferation and CDK activity, along with multiple signaling pathways (T cell receptor, insulin receptor) and development-related terms (cerebellar cortex formation, Bergmann glial differentiation). This suggests a broad regulatory theme centered on controlling proliferation and signaling across diverse biological contexts, rather than a single, narrow function.","confidence":"Medium","size":28,"edges":335,"triangles":2343,"max_degree":27,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0034501","count":27},{"id":"GO:0045736","count":27},{"id":"GO:0050852","count":25},{"id":"GO:0008285","count":25},{"id":"GO:0008286","count":25}]},{"hash":"416915472105069189","title":"Unknown","description":"The top GO terms cover very different biological areas, including growth factor response, kinetochore localization, cell cycle regulation, endosome transport, yeast pseudohyphal growth, developmental signaling, calcium-related responses, dopaminergic synaptic transmission, p53-mediated signaling, and NK T cell differentiation. There isn't a single coherent biological theme linking these terms, so a unified, specific label is not supported.","confidence":"","size":28,"edges":240,"triangles":981,"max_degree":27,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035729","count":28},{"id":"GO:0034501","count":28},{"id":"GO:0045736","count":28},{"id":"GO:2000641","count":27},{"id":"GO:0007124","count":27}]},{"hash":"442165495374165073","title":"Neuronal transcription regulation and glutamatergic signaling","description":"The cluster\u2019s top GO terms cluster around regulation of DNA-templated transcription and transcription itself, with a strong signal for glutamatergic synaptic transmission. Additional terms point to endosomal/receptor trafficking (receptor recycling, endosome size) and cytoskeletal signaling (Rho), which together suggest a theme of how gene expression interfaces with neuronal synaptic signaling and vesicle trafficking. Some terms are obsolete or stress-related, but the core pattern supports a neuronal transcription\u2013synaptic trafficking link.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":7},{"id":"GO:0006351","count":6},{"id":"GO:0035249","count":6},{"id":"GO:0034968","count":5},{"id":"GO:0001881","count":5}]},{"hash":"820774759959998006","title":"Unknown","description":"The GO terms for this cluster are highly heterogeneous, spanning endosome transport, pseudohyphal growth, neural patterning, ionomycin response, dopaminergic synaptic transmission, p53 signaling, NK T differentiation, neuron axonogenesis, aging-related response, and cartilage condensation. There isn\u2019t a single coherent biological function tying these together, so no intuitive, specific label can capture the cluster.","confidence":"","size":28,"edges":347,"triangles":2560,"max_degree":27,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":28},{"id":"GO:0007124","count":28},{"id":"GO:1901621","count":28},{"id":"GO:1904637","count":28},{"id":"GO:0001963","count":28}]},{"hash":"1751951546705036279","title":"Heat Stress and Growth Regulation","description":"The cluster combines heat response with signals of cell proliferation, transcriptional regulation, translation initiation, and lipid signaling (SREBP pathway), plus membrane ion transport and protein oligomerization. Together, these terms point to a coordinated program where heat stress modulates growth and metabolism via transcriptional/ translational control and membrane/lipid signaling.","confidence":"Medium","size":28,"edges":116,"triangles":224,"max_degree":26,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":3},{"id":"GO:0007049","count":3},{"id":"GO:0097623","count":3},{"id":"GO:1990573","count":3},{"id":"GO:0000122","count":3}]},{"hash":"364549636314287995","title":"Developmental Signaling & Trafficking","description":"The cluster shows a mix of developmental and signaling GO terms, including endosome transport regulation, neural development (axonogenesis, neural tube patterning), dopaminergic synaptic transmission, p53-mediated signaling, NK T cell differentiation, and cartilage condensation. Endosomal trafficking often underpins receptor signaling across tissues, so this points to a shared theme of developmentally driven signaling coordinated by intracellular trafficking, despite the diversity of body systems represented.","confidence":"Medium","size":28,"edges":231,"triangles":769,"max_degree":20,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":28},{"id":"GO:0007124","count":28},{"id":"GO:1901621","count":28},{"id":"GO:1904637","count":28},{"id":"GO:0001963","count":28}]},{"hash":"1238151460702626217","title":"Nuclear transport and cytoskeletal organization","description":"The top GO terms center on NLS-bearing protein import into the nucleus, microtubule polymerization, mitotic nuclear membrane reassembly, and ciliary basal body docking, with additional references to protein complex assembly and transcription regulation. This pattern suggests a cohesive theme of coordinating nuclear transport, cytoskeletal dynamics, and organelle positioning during cell division and ciliogenesis, with some broader regulatory roles.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006607","count":3},{"id":"GO:0046785","count":2},{"id":"GO:0007084","count":2},{"id":"GO:0045945","count":2},{"id":"GO:0097711","count":2}]},{"hash":"1193960099895214550","title":"Cell Cycle and Neural Development","description":"The most frequent GO terms are mitotic cell cycle, DNA replication, and cell cycle transitions (G1/S, G2/M), which strongly indicate core roles in cell division. Additional terms such as nervous system development, cell morphogenesis, and axon extension suggest a developmental aspect, particularly linked to neural development or morphogenesis. Together, these points support a cohesive theme of cell-cycle regulation intertwined with developmental processes, especially in neural contexts.","confidence":"High","size":28,"edges":9,"triangles":1,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":10},{"id":"GO:0006260","count":8},{"id":"GO:0071276","count":8},{"id":"GO:0006351","count":8},{"id":"GO:0000086","count":7}]},{"hash":"2297823271907532764","title":"Neural development and synaptic signaling","description":"The cluster is enriched for neural-related processes: CNS projection neuron axonogenesis, dopaminergic synaptic transmission, and regulation of neural patterning, along with components tied to vesicle trafficking and signaling that support neural communication (e.g., endosome transport and signaling regulation). While there are some non-neural terms present (e.g., NK T cell differentiation, cartilage condensation), the dominant theme centers on neural development and synaptic signaling. ","confidence":"Medium","size":28,"edges":290,"triangles":1598,"max_degree":27,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":28},{"id":"GO:0007124","count":28},{"id":"GO:1901621","count":28},{"id":"GO:1904637","count":28},{"id":"GO:0001963","count":28}]},{"hash":"1052017711908187511","title":"Neuronal signaling and ion homeostasis","description":"This cluster is enriched for components of neural signaling and membrane physiology: small GTPase signaling, cAMP response and PKA regulation, and ion transport that shapes resting membrane potential (Na+ import, K+ homeostasis). The presence of terms like cellular response to cAMP and response to antipsychotic drugs supports a neural-context functional theme, with transcription and some immune-related terms likely representing broader regulatory roles or background annotations. Overall, the common thread is signaling-driven regulation of neural excitability and ion balance.","confidence":"Medium","size":28,"edges":116,"triangles":187,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0046827","count":6},{"id":"GO:0007264","count":5},{"id":"GO:0098719","count":5},{"id":"GO:0046007","count":5}]},{"hash":"2252267158466821588","title":"Ribosome Biogenesis and Stress-Development Links","description":"Primarily enriched for maturation of rRNA (SSU/5.8S/LSU) indicating ribosome biogenesis; additional GO terms reflect cellular stress responses (cadmium, ER stress) and developmental processes (neural tube and forebrain development), which align with known links between ribosome biogenesis and development/stress phenotypes. The cluster likely groups ribosome assembly factors with stress- and development-related roles.","confidence":"Medium","size":28,"edges":378,"triangles":3276,"max_degree":27,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000462","count":6},{"id":"GO:0000466","count":5},{"id":"GO:0000463","count":5},{"id":"GO:0001843","count":4},{"id":"GO:0050830","count":4}]},{"hash":"56526080421680209","title":"Neuroimmune Signaling and Development","description":"The cluster includes neural development terms (axonogenesis, corpus callosum development) alongside innate immune and antiviral response terms (defense to Gram-positive bacteria, LPS signaling, interferon-beta production, dsRNA response), suggesting a set of genes bridging neural development with neuroimmune signaling. Confidence in a cohesive single function is moderate due to the mix of developmental and immune terms rather than a single dominant process.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0050830","count":4},{"id":"GO:0007409","count":4},{"id":"GO:0006351","count":4},{"id":"GO:1903351","count":3}]},{"hash":"1161184340357545590","title":"Developmental and Immune Signaling Proteins","description":"Based on the top GO terms, the proteins appear involved in developmental processes across several tissues (brain development, spinal cord development, skin development, lens fiber cell differentiation) and in immune signaling (NF-kappaB regulation, NOD2 signaling, defense against Gram-positive bacteria). Additional terms like protein homooligomerization and SCF-dependent ubiquitin-proteasomal degradation suggest regulation and turnover supporting signaling. Together these indicate a cluster of factors bridging development and immune response rather than a single, narrow function.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0070431","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0021510","count":2}]},{"hash":"1813339174675266647","title":"Unknown","description":"These 28 proteins map to a highly diverse set of GO terms, spanning neuronal development (axonogenesis, dopaminergic synaptic transmission), immune differentiation (NK T cell differentiation), endosomal transport, and stress/signal pathways. There is no single, coherent biological theme that ties the majority of terms together, so a specific functional label would be misleading; the cluster is best described as Unknown.","confidence":"","size":28,"edges":4,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0034198","count":28},{"id":"GO:2000641","count":26},{"id":"GO:0007124","count":26},{"id":"GO:1901621","count":26},{"id":"GO:1904637","count":26}]},{"hash":"697324985469050347","title":"Cell growth, morphogenesis, and signaling","description":"I named it \"Cell growth, morphogenesis, and signaling\" because the top GO terms cluster around cellular shape and developmental processes (cell morphogenesis, cartilage condensation, pseudohyphal growth) alongside proliferation and regulatory signaling (mitotic cell cycle; regulation of Hedgehog/SMO signaling; regulation of p53-mediated signaling). There are also related themes in vesicle trafficking (regulation of endosome transport) and signaling responses (ionomycin response, dopaminergic synaptic transmission). While the terms span diverse contexts, they collectively point to growth, morphological changes, and signal regulation rather than a single narrowly defined function, justifying this composite label. ","confidence":"Medium","size":28,"edges":10,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000902","count":28},{"id":"GO:0000278","count":28},{"id":"GO:2000641","count":27},{"id":"GO:0007124","count":27},{"id":"GO:1901621","count":27}]},{"hash":"1865143069079128994","title":"Ion transport and membrane potential regulation","description":"The cluster shows strong enrichment for ion transport and membrane potential processes: intracellular potassium ion homeostasis, sodium import across the plasma membrane, potassium ion transmembrane transport, membrane repolarization, stabilization and regulation of resting membrane potential, and signaling responses to cGMP and cAMP that modulate these channels, with a note on aerotaxis. This combination points to proteins coordinating ionic gradients and electrical properties of membranes.","confidence":"High","size":28,"edges":364,"triangles":2959,"max_degree":27,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030007","count":18},{"id":"GO:0098719","count":17},{"id":"GO:0071805","count":17},{"id":"GO:0071321","count":16},{"id":"GO:0010754","count":16}]},{"hash":"1362174846361366508","title":"Potassium ion transport and membrane potential regulation","description":"This cluster is dominated by GO terms for potassium ion transport, stabilization and regulation of membrane potential, and intracellular potassium homeostasis, with a cardiac atrial action potential reference. These themes point to a set of proteins that govern cellular excitability and ion gradients, with mechanosensory and transcription/development terms likely representing broader cellular contexts. ","confidence":"High","size":28,"edges":274,"triangles":1373,"max_degree":26,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":20},{"id":"GO:0006351","count":20},{"id":"GO:0019233","count":19},{"id":"GO:0007275","count":19},{"id":"GO:0071805","count":17}]},{"hash":"39208291922484977","title":"Plant stress signaling and ubiquitin regulation","description":"The cluster shows multiple plant-specific terms such as osmotic-stress response, cytokinin-activated signaling, and regulation of root meristem growth, indicating a plant stress signaling/development theme. The presence of ubiquitin-related terms (autoubiquitination, ERAD) suggests regulation of protein turnover, possibly linked to stress responses or host-virus interactions (viral process/intracellular transport of viral material). Together, these terms support a cohesive theme around plant stress signaling coupled with ubiquitin-mediated protein regulation, though the viral-related terms introduce some heterogeneity.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006970","count":3},{"id":"GO:0010082","count":3},{"id":"GO:0016032","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0030433","count":3}]},{"hash":"823128981472102833","title":"Muscle remodeling and transcriptional regulation","description":"Top GO terms include muscle-related processes such as positive regulation of satellite cell activation involved in skeletal muscle regeneration and cardiac myofibril assembly, suggesting a cluster enriched for muscle remodeling; additional terms point to transcriptional control (positive regulation of DNA binding, NLS-bearing protein import into nucleus) and kinase activity regulation, indicating broader regulatory roles. The presence of diverse processes like chitin-based cuticle development and urea homeostasis elsewhere suggests heterogeneity, but the strongest signals are muscle remodeling and transcriptional regulation, supporting this label.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014718","count":3},{"id":"GO:0033234","count":3},{"id":"GO:0043388","count":3},{"id":"GO:0055003","count":2},{"id":"GO:0097274","count":2}]},{"hash":"908470543957957304","title":"Unknown","description":"The terms span epigenetic regulation, innate immunity, plant development, germination, salt response, and transcription control across different kingdoms, with no single shared function uniting the proteins. With zero edges and dispersed themes, there is no coherent motif to name.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016575","count":3},{"id":"GO:0045087","count":2},{"id":"GO:0060348","count":2},{"id":"GO:0009736","count":2},{"id":"GO:0045793","count":2}]},{"hash":"1580633744018378291","title":"Transcription and ER-Golgi Vesicle Trafficking","description":"This cluster centers on gene expression and RNA processing, including DNA-templated transcription, mRNA splicing, and mRNA export, with additional signals of histone modification and stress response. It also features vesicle trafficking between the ER and Golgi (anterograde and retrograde transport) and growth-related signaling such as TORC1 and regulation of ubiquitin ligase activity. While developmental terms appear, the core enrichment points to transcription/RNA processing tied to vesicle trafficking and growth control.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0021510","count":4},{"id":"GO:0006890","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0035264","count":4}]},{"hash":"948388077852747103","title":"Neuronal synaptic plasticity and vesicle trafficking","description":"This cluster centers on neural signaling and plasticity: long-term synaptic potentiation, positive regulation of dendrite extension, and cellular responses to calcium, along with ER-to-Golgi vesicle transport and calcium-regulated lysosome exocytosis. While there are a few terms related to general lipid metabolism and RNA processing, the dominant themes point to synaptic function and membrane trafficking in neurons.","confidence":"Medium","size":28,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0060291","count":3},{"id":"GO:0009395","count":3},{"id":"GO:0006888","count":2},{"id":"GO:1990927","count":2},{"id":"GO:2000235","count":2}]},{"hash":"1769524339553347271","title":"DNA replication and transcription with proteasomal regulation","description":"This cluster is dominated by GO terms tied to nuclear processes: DNA replication, centrosome cycle, and DNA-templated transcription, suggesting a primary association with cell cycle and gene expression. The presence of positive regulation of proteasomal ubiquitin-dependent protein catabolic process hints at coordinated protein turnover during these processes. Additional terms like regulation of endosome transport and lipopolysaccharide response, pseudohyphal growth, and developmental signaling appear as secondary, possibly reflecting broader stress response or housekeeping roles across proteins. Overall, a core emphasis on nuclear functions with ancillary trafficking/response terms.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0007098","count":3},{"id":"GO:0008542","count":3},{"id":"GO:0071222","count":3},{"id":"GO:0006351","count":3}]},{"hash":"783119254199152716","title":"Ubiquitin-Dependent Proteolysis and ERAD","description":"The cluster is dominated by ubiquitin-related protein catabolic processes, including ubiquitin-dependent proteolysis, autoubiquitination, and K48- and K6-linked ubiquitination, highlighting the ubiquitin-proteasome system and ERAD as the core theme; a few terms touch on signaling and chromatin turnover, but these appear peripheral to the main degradation-focused function.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":15},{"id":"GO:0051865","count":14},{"id":"GO:0070936","count":13},{"id":"GO:0030433","count":13},{"id":"GO:1903265","count":12}]},{"hash":"160701594445705808","title":"Aromatic Compound Degradation and Detoxification","description":"These proteins share a theme of broad catabolic and detoxification activity, including aromatic compound degradation (beta-ketoadipate pathway, stilbene catabolic, chlorophyll and uracil catabolic processes), lipid and nucleotide catabolism, and oxidoreductase/P450\u2013mediated detoxification pathways. The absence of network edges does not preclude a cohesive functional set centered on breaking down diverse substrates and mitigating oxidative stress.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0017000","count":17},{"id":"GO:0055114","count":16},{"id":"GO:0098869","count":16},{"id":"GO:0015996","count":16},{"id":"GO:0042952","count":15}]},{"hash":"2069512575234667193","title":"Ras/cAMP signaling and transcription regulation","description":"This cluster is dominated by terms for small GTPase signaling (Ras) and cAMP-related regulation, including GO:0007264, GO:0046580, GO:0071320, and GO:2000480, plus DNA-templated transcription and nuclear export terms, suggesting signaling pathways that control gene expression. While ion transport terms (potassium/sodium) appear, they are less central to the core theme, indicating additional regulatory roles. Therefore the name reflects the central theme of Ras/cAMP signaling converging on transcription.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046580","count":4},{"id":"GO:0007264","count":4},{"id":"GO:0071805","count":4},{"id":"GO:0006351","count":4},{"id":"GO:2000480","count":3}]},{"hash":"659562511315413312","title":"Nuclear gene expression and chromatin regulation","description":"The dominant GO terms point to nuclear processes: DNA-templated transcription, mRNA splicing, ribosome biogenesis, and CENP-A chromatin assembly, along with mRNA export and ubiquitination\u2014together reflecting regulation of gene expression and chromatin state. Some terms (cell division, cytokine production, growth hormone response) suggest broader roles in growth and stress responses, but the core motif is nuclear gene expression and chromatin maintenance.","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:0060416","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0042254","count":4},{"id":"GO:2000728","count":3}]},{"hash":"859191234689361896","title":"Neural stress response and RNA processing","description":"The topology shows a convergence on stress-related regulation of gene expression (mRNA export, splicing) alongside ubiquitin-mediated regulation, cell-cycle control, and neural-associated processes (glial apoptosis, brain development), suggesting a neural-specific stress-response module that integrates RNA processing with protein homeostasis.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000728","count":3},{"id":"GO:1904668","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0061641","count":3},{"id":"GO:0002534","count":3}]},{"hash":"1151846016867780610","title":"DNA Damage Response and Inflammatory Signaling","description":"The cluster centers on stress response pathways: DNA damage sensing and p53-mediated apoptosis, cell-cycle regulation, and inflammatory signaling such as LPS response, TNF signaling, and NF-kB regulation. While a few terms like late viral transcription and mammary gland development are less related, the dominant GO terms point to connections between DNA-damage responses, cell-cycle control, and inflammation.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0042771","count":2},{"id":"GO:0071222","count":2},{"id":"GO:0033209","count":2}]},{"hash":"761804853585520399","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":4},{"id":"GO:2000134","count":4},{"id":"GO:0070940","count":4},{"id":"GO:1903740","count":4},{"id":"GO:0010867","count":4}]},{"hash":"2050911661079509090","title":"Sphingolipid metabolism and signaling","description":"The cluster shows a consistent motif around sphingolipid metabolism: sphingosine metabolic process, sphinganine-1-phosphate metabolic process, and regulation of sphingolipid mediated signaling pathway. Additional lipid-related terms like phospholipid catabolic process also align with a lipid-centric theme, while other annotations (neural differentiation, wound healing signaling, detoxification) may be peripheral or broader annotations. Thus, the core theme appears to be sphingolipid metabolism and signaling.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044257","count":2},{"id":"GO:0021523","count":2},{"id":"GO:1902068","count":2},{"id":"GO:0006668","count":2},{"id":"GO:0098869","count":2}]},{"hash":"2303612233294484031","title":"Membrane trafficking and morphogenesis","description":"The prominent GO terms point to vesicle trafficking and membrane remodeling (endosome-lysosome transport, endocytic recycling, membrane tubulation, lipid biosynthesis), while related terms reflect cytoskeletal remodeling during division and development (cleavage furrow formation, sporulation membrane formation, ECM disassembly). Developmental contexts like eye and osteoblast lineages suggest these processes are relevant across morphogenesis. Overall, the cluster seems to group proteins involved in membrane dynamics that support cell division and developmental remodeling.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008333","count":4},{"id":"GO:0000278","count":4},{"id":"GO:1990126","count":3},{"id":"GO:0097320","count":3},{"id":"GO:0022617","count":3}]},{"hash":"1754118449246229858","title":"Auxin signaling and adventitious root development","description":"The cluster is anchored by plant-specific auxin-related terms: auxin-activated signaling pathway, ER-to-cytosol auxin transport, and adventitious root development, suggesting proteins involved in auxin-mediated growth and root formation. Other terms like skin development and responses to polyphenols or metals may reflect broader stress or background annotations but do not override the primary auxin-root theme.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050960","count":2},{"id":"GO:0043588","count":2},{"id":"GO:1904643","count":2},{"id":"GO:0007155","count":2},{"id":"GO:0046689","count":2}]},{"hash":"2036431915675330305","title":"ER\u2013Golgi vesicle transport","description":"This cluster is dominated by GO terms for vesicle trafficking between the endoplasmic reticulum and Golgi (ER-to-Golgi and Golgi-to-ER), with additional related transport steps such as endosome-to-Golgi routing. The strong er-Golgi transport signal suggests the proteins mainly function in the secretory pathway and vesicle trafficking, despite a few peripheral developmental terms in the mix.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":6},{"id":"GO:0006890","count":2},{"id":"GO:0001501","count":2},{"id":"GO:0034498","count":2},{"id":"GO:0006507","count":1}]},{"hash":"2237591553591839284","title":"Fibrinolysis and ECM Regulation","description":"Top GO terms include fibrinolysis and regulation of plasminogen activation, plus positive regulation of extracellular matrix constituent secretion, all pointing to proteolytic remodeling of the extracellular matrix and blood clot-related processes. The presence of cardiovascular-related terms (regulation of angiotensin levels) supports a vascular remodeling theme. Some terms (insulin processing, Purkinje cell differentiation, deglutamylation) are more peripheral, suggesting the cluster may be functionally heterogeneous. Overall, a moderate coherence around proteolysis/ECM remodeling with some outliers.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010757","count":3},{"id":"GO:0009408","count":3},{"id":"GO:0002002","count":3},{"id":"GO:0003331","count":3},{"id":"GO:2000346","count":3}]},{"hash":"1296031211575535637","title":"Telomere and chromatin regulation","description":"This cluster shows several GO terms tied to chromatin and telomere biology, including nucleosome assembly, histone H2A deubiquitination, telomeric D-loop disassembly, and protein localization to telomeres, suggesting a chromatin/telomere maintenance theme despite sparse term support. Peripheral terms like snRNA transcription and osmotic stress appear incidental to the main signal.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061820","count":1},{"id":"GO:0009736","count":1},{"id":"GO:1901347","count":1},{"id":"GO:0072362","count":1},{"id":"GO:0006334","count":1}]},{"hash":"1120996829881560190","title":"RNA processing and post-transcriptional gene silencing","description":"This cluster is dominated by terms about RNA metabolism and post-transcriptional regulation: post-transcriptional gene silencing, miRNA-mediated gene silencing, mRNA destabilization, positive regulation of mRNA binding, and ribosomal small subunit export from the nucleus, which together point to RNA processing and gene regulation at the RNA level. A few terms like endosome transport or bone development are less aligned and may reflect broader or incidental associations. Overall, the RNA-centric terms provide the strongest unifying theme. ","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":2},{"id":"GO:0010992","count":2},{"id":"GO:0034499","count":2},{"id":"GO:0060348","count":2},{"id":"GO:2000637","count":2}]},{"hash":"1189398357972933400","title":"TLR-Mediated Innate Immune Signaling","description":"The cluster is dominated by GO terms for Toll-like receptor signaling pathways (MyD88-dependent and TLR2/3/4/10), lipopolysaccharide signaling, and the innate immune response, indicating proteins function together in TLR-driven pathogen sensing and cytokine signaling. A single bone development term exists but does not detract from the overall TLR/innate immunity theme.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0002755","count":4},{"id":"GO:0060348","count":3},{"id":"GO:0002730","count":3},{"id":"GO:0034142","count":3},{"id":"GO:0051770","count":3}]},{"hash":"652728384150467146","title":"DNA-Templated Transcription Regulation","description":"The cluster is best characterized by strong enrichment for GO terms related to DNA-templated transcription and its regulation, indicating a group of proteins involved in transcriptional control rather than metabolism or structural processes. A couple of outliers (sperm individualization, spindle orientation) are present but do not define the majority pattern.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0007291","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0055114","count":1},{"id":"GO:0006558","count":1}]},{"hash":"833130748631111531","title":"Rac-mediated cytoskeletal remodeling","description":"This cluster centers on actin-based structures and adhesion: positive regulation of substrate adhesion-dependent cell spreading, filopodium assembly, and positive regulation of stress fiber assembly, pointing to dynamic cytoskeletal organization. The Rac protein signal transduction term supports Rac GTPase\u2013driven control of protrusions and adhesion, suggesting a cohesive theme of cytoskeletal remodeling and cell movement. Some other terms (xenobiotic response, mitotic components) are less directly connected but may reflect broader signaling or cell-cycle contexts within the set.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900026","count":2},{"id":"GO:0010796","count":2},{"id":"GO:0031384","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0016601","count":2}]},{"hash":"350129936980057519","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":110,"triangles":157,"max_degree":17,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":17},{"id":"GO:0048026","count":17},{"id":"GO:0000398","count":13},{"id":"GO:0071031","count":13},{"id":"GO:0034475","count":12}]},{"hash":"1151696664780820011","title":"Neural Development and Signaling","description":"The cluster is dominated by GO terms related to neural development and neuronal communication, including CNS projection neuron axonogenesis, dopaminergic synaptic transmission, and neural tube patterning. Endosomal trafficking is also critical for neuron function, supporting vesicle transport in synapses. Some terms (cartilage condensation, NK T cell differentiation, certain stress/p53-related terms) are less clearly neuronal, suggesting some noise or multi-function annotations, but the core signal points to neural development and signaling as the primary theme.","confidence":"Medium","size":27,"edges":220,"triangles":722,"max_degree":21,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":27},{"id":"GO:0007124","count":27},{"id":"GO:1901621","count":27},{"id":"GO:1904637","count":27},{"id":"GO:0001963","count":27}]},{"hash":"73844761197407883","title":"Negative regulation of signaling and cellular organization","description":"The proteins in this cluster are enriched for GO terms that describe the suppression of multiple signaling pathways (negative regulation of cyclin-dependent kinase activity, ERK cascade, PI3K/AKT signaling, and T cell receptor signaling) as well as terms related to cytoskeletal and structural organization (focal adhesion assembly, postsynaptic density assembly, synaptic vesicle clustering) and kinetochore localization. This pattern suggests a core role as regulators that dampen signaling and coordinate cellular architecture; mRNA capping is less directly connected but may reflect transcriptional regulation. Therefore, a label capturing broad negative regulation of signaling and cellular organization best represents the cluster.","confidence":"Medium","size":27,"edges":195,"triangles":1080,"max_degree":20,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0034501","count":18},{"id":"GO:0045736","count":18},{"id":"GO:0050860","count":16},{"id":"GO:0000200","count":16},{"id":"GO:0070373","count":16}]},{"hash":"1738163238860903807","title":"Chromosome Segregation and Mitosis","description":"The cluster is enriched for mitotic cell cycle, chromosome condensation and separation, and DNA replication/transcription terms, indicating a core role in cell division and chromosome dynamics; some vesicle transport terms are present but do not define the main function.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000902","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0006886","count":3},{"id":"GO:0034499","count":3},{"id":"GO:0006260","count":2}]},{"hash":"223028656281307896","title":"Bacterial biosynthesis and antibiotic metabolism","description":"The proteins co-occur with GO terms spanning bacterial biosynthetic pathways (phylloquinone catabolism, colanic acid and O antigen biosynthesis, galactose and PHB biosynthesis) as well as antibiotic biosynthesis and response. This mix points to a theme of microbial metabolite production and cell-surface component assembly rather than a single, cohesive enzymatic pathway, especially given the lack of edges in the network. Some terms (e.g., androgen or C21-steroid metabolism) may reflect broad metabolic capacity or annotation noise, but the dominant signal is bacterial biosynthesis/metabolism.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":13},{"id":"GO:0042619","count":11},{"id":"GO:0006012","count":9},{"id":"GO:0017000","count":9},{"id":"GO:0008207","count":8}]},{"hash":"686812952159301997","title":"Endosome trafficking and neuronal signaling cluster","description":"The top GO terms point to a shared function in endosome transport (early to late endosomes) and neural processes, including dopaminergic synaptic transmission and CNS neuron axonogenesis, suggesting a module linking vesicular trafficking with neuronal signaling and development. A couple of terms (pseudohyphal growth, cartilage condensation) seem less directly related, likely reflecting broader developmental annotations, but do not override the central endosomal\u2013neural theme.","confidence":"Medium","size":27,"edges":266,"triangles":1353,"max_degree":25,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":27},{"id":"GO:0007124","count":27},{"id":"GO:1901621","count":27},{"id":"GO:1904637","count":27},{"id":"GO:0001963","count":27}]},{"hash":"1186282001627587190","title":"Neuronal development and signaling","description":"The top terms point to neural development and communication, including CNS projection neuron axonogenesis, dopaminergic synaptic transmission, and dorsal/ventral neural tube patterning, along with related endosomal transport and calcium signaling processes. While a few terms are less clearly connected (e.g., cartilage condensation, NK T cell differentiation), the dominant themes across the cluster are neuronal development and signaling, making this a representative label.","confidence":"Medium","size":27,"edges":56,"triangles":10,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":27},{"id":"GO:0007124","count":27},{"id":"GO:1901621","count":27},{"id":"GO:1904637","count":27},{"id":"GO:0001963","count":27}]},{"hash":"2294422085766174581","title":"Neuronal Growth and Morphogenesis Signaling","description":"The top GO terms cluster around neuronal development and morphology (hippocampus development, dendrite morphogenesis, axon extension) and signaling pathways (ephrin receptor signaling, ERK cascade) with cytoskeletal remodeling (focal adhesion, actin cytoskeleton reorganization). This combination points to proteins involved in neuron growth, connectivity, and associated cytoskeletal dynamics, despite a few peripheral immune-related terms. ","confidence":"High","size":27,"edges":4,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":7},{"id":"GO:0070374","count":6},{"id":"GO:0051893","count":6},{"id":"GO:0043366","count":6},{"id":"GO:0031532","count":6}]},{"hash":"1811870671288823560","title":"Oocyte meiosis and vesicle trafficking","description":"The top GO terms include oocyte maturation and meiotic spindle assembly, suggesting a meiotic role. At the same time, several terms describe vesicle transport pathways (anterograde/retrograde transport, Golgi-ER, endosome to melanosome), implying a coordinated trafficking function during meiosis or oocyte development. A few terms (antigen processing via MHC class Ib) are less related, but overall the cluster appears to reflect a module linking meiotic progression with intracellular vesicle trafficking.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044655","count":2},{"id":"GO:0040038","count":2},{"id":"GO:0001556","count":2},{"id":"GO:0090306","count":2},{"id":"GO:0006890","count":2}]},{"hash":"1883966719330957961","title":"Mitotic cell cycle progression and nuclear transport","description":"This cluster is enriched for mitosis- and cell cycle-related terms (G1/S and G2/M transitions, re-entry into mitosis, spindle pole separation) and kinetochore localization, indicating a cohesive role in mitotic progression. Additional associations with protein export from the nucleus and transcription suggest coordinated regulation of gene expression and nuclear transport during cell division, with supporting notes on protein turnover and DNA repair that fit mitotic control. Overall, the dominant theme is mitotic cell cycle regulation.","confidence":"High","size":27,"edges":323,"triangles":2307,"max_degree":26,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0034501","count":6},{"id":"GO:0032435","count":5},{"id":"GO:0010696","count":5},{"id":"GO:2001033","count":5}]},{"hash":"1691657774798111399","title":"Nuclear gene expression and ubiquitin regulation","description":"This cluster concentrates on nuclear processes that control gene expression\u2014transcription, splicing, and chromatin assembly\u2014and on ubiquitin-related regulation of protein turnover, including polyubiquitination and ERAD pathways. The presence of translation initiation terms may reflect coordination between nuclear transcript processing and cytoplasmic translation, particularly under heat-stress conditions affecting mRNA export. Overall, these proteins appear to govern gene expression and proteostasis.","confidence":"Medium","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0030433","count":3},{"id":"GO:0000209","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0002188","count":3}]},{"hash":"1829677223987707665","title":"Neural development and signaling","description":"The dominant GO terms point to nervous system development and neuronal signaling, notably central nervous system projection neuron axonogenesis and dopaminergic synaptic transmission. Additional terms involve endosomal transport and signal transduction regulation, which can support neuronal function, suggesting a cohesive theme around neural development and communication. Some terms are less central (e.g., pseudohyphal growth, cartilage condensation), but they don\u2019t override the neural-centric signal.","confidence":"Medium","size":27,"edges":36,"triangles":6,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":27},{"id":"GO:0007124","count":27},{"id":"GO:1901621","count":27},{"id":"GO:1904637","count":27},{"id":"GO:0001963","count":27}]},{"hash":"798444565980820124","title":"Mitotic Cell Cycle and COPII Vesicle Trafficking","description":"This cluster is enriched for mitosis-related terms (cell division, mitotic spindle assembly, mitotic cell cycle) and vesicle trafficking (COPII-coated vesicle budding, retrograde Golgi-ER transport), suggesting a group of proteins coordinating cell division with secretory transport, potentially during spermatogenesis or development. Other terms like defense response to protozoan and ameboid-type migration are less central but reflect broader cellular movement contexts.","confidence":"Medium","size":27,"edges":42,"triangles":15,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090114","count":4},{"id":"GO:0007286","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0090307","count":3},{"id":"GO:0000278","count":3}]},{"hash":"611748781452515571","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":9,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006986","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0071374","count":2},{"id":"GO:0090084","count":2},{"id":"GO:1901621","count":2}]},{"hash":"740488844179311286","title":"Cell signaling and vesicle trafficking","description":"This cluster combines proteins involved in multiple signaling pathways (Smoothened/Hedgehog; Wnt signalosome assembly) with processes tied to vesicle trafficking and membrane dynamics (phagosome maturation, degranulation in immune cells) and cytoskeleton-dependent movement (ameboidal migration, cell spreading). While a few terms are outliers (copper homeostasis, oligodendrocyte differentiation, cytokinetic furrow ingression), the dominant theme is coordinated signaling and vesicle-mediated processes that govern cell communication, movement, and secretion. ","confidence":"Medium","size":27,"edges":26,"triangles":6,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0007224","count":3},{"id":"GO:1903215","count":2},{"id":"GO:0001667","count":2},{"id":"GO:0006878","count":2},{"id":"GO:0043316","count":2}]},{"hash":"1330239598205293726","title":"Transcription and mitosis regulators","description":"Reason: The dominant GO terms are DNA-templated transcription and mitosis-related processes (G2/M transition, mitotic cell cycle, spindle pole body separation), with additional development-related terms. This points to a cluster of proteins that broadly regulate transcription and cell division, rather than a single signaling pathway.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0046626","count":5},{"id":"GO:0030900","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0000902","count":4}]},{"hash":"836133983762693593","title":"Mitochondrial dynamics and apoptosis regulation","description":"Based on the top GO terms, the cluster centers on mitochondrial processes\u2014genome maintenance (an obsolete term), apoptotic mitochondrial changes, and mitochondrial membrane fission\u2014with additional signals for necroptosis regulation and metabolic responses (fatty acids, adaptive thermogenesis) and even tissue-level processes (liver regeneration) and T cell activation. The strongest common thread is mitochondrial dynamics governing apoptosis and cell fate, with peripheral metabolic and immune associations likely reflecting broader mitochondrial functions rather than a single, uniform tissue context.","confidence":"Medium","size":27,"edges":13,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":3},{"id":"GO:0008637","count":3},{"id":"GO:0090149","count":3},{"id":"GO:0002291","count":2},{"id":"GO:0030212","count":2}]},{"hash":"940332675934836802","title":"mRNA Splicing and Translation Regulation","description":"The proteins are enriched for mRNA processing and splicing (via spliceosome, polyadenylation), mRNA modification and stability under stress, and translation control (miRNA-mediated silencing, eIF4F complex assembly), indicating a cohesive role in post-transcriptional regulation and translational control.","confidence":"High","size":27,"edges":8,"triangles":2,"max_degree":4,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1900363","count":4},{"id":"GO:0048025","count":4},{"id":"GO:0035278","count":4},{"id":"GO:0010610","count":4},{"id":"GO:0016556","count":4}]},{"hash":"1234557019935244742","title":"APC/C-driven mitotic progression","description":"This cluster centers on cell division and ubiquitin-mediated degradation, with GO terms spanning meiosis I, mitotic cell cycle, regulation of metaphase/anaphase transition, APC/C-dependent catabolic processes, and K11-linked ubiquitination, suggesting proteins that orchestrate mitotic/meiosis progression via targeted proteolysis.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007127","count":1},{"id":"GO:0042787","count":1},{"id":"GO:0000278","count":1},{"id":"GO:0030071","count":1},{"id":"GO:0070979","count":1}]},{"hash":"473228056885462744","title":"Ribosome Biogenesis and Translation Initiation","description":"This cluster is driven by translation- and ribosome-related functions: ribosome biogenesis, formation of the translation preinitiation complex, and translation reinitiation, indicating a core association with protein synthesis machinery and its assembly. Additional vesicle transport and developmental annotations are present but less central, suggesting some multifunctionality or annotation noise rather than a distinct secondary theme. ","confidence":"Medium","size":27,"edges":31,"triangles":12,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0021510","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0000747","count":2},{"id":"GO:0001731","count":2}]},{"hash":"2091645683866863668","title":"Embryonic Development and Transcription Regulation","description":"The top GO terms cluster around developmental processes (neural tube closure, forebrain development, skeletal system development, multicellular organism development) and transcriptional control (DNA-templated transcription), suggesting a cohesive set of proteins involved in embryogenesis and regulation of gene expression. Some terms like cadmium response and defense are present but appear ancillary to the dominant developmental/transcription theme.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071276","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0070208","count":3},{"id":"GO:0001843","count":3},{"id":"GO:0001501","count":3}]},{"hash":"249161344127319581","title":"Developmental transcription factors","description":"The cluster shows a strong enrichment for DNA-templated transcription and multiple development-related processes, including forebrain development, neural tube closure, skeletal system development, and multicellular organism development, suggesting a group of proteins that regulate gene expression during development. Other terms like cadmium response and defense are present but less central to the core theme.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0071276","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0046827","count":3},{"id":"GO:0001843","count":3}]},{"hash":"1448028450188142275","title":"Ciliary transport and microtubule-based motility","description":"The top terms cluster around movement and transport along microtubules and cilia, including intraciliary transport, spindle localization, minus-end-directed vesicle transport, and flagellated motility, suggesting a group of proteins involved in ciliary/flagellar motion and microtubule-based intracellular transport, with a developmental component (left/right symmetry, ventricle development). Stress granule assembly is present but less central to the core theme.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034063","count":3},{"id":"GO:0003341","count":2},{"id":"GO:0007018","count":2},{"id":"GO:0035721","count":2},{"id":"GO:0051293","count":2}]},{"hash":"1388598761205263597","title":"Innate immune signaling and cellular stress response","description":"This cluster centers on inflammatory and immune-regulatory GO terms (NF-kappaB signaling, interferon production regulation, NLRP3 inflammasome modulation) and stress-related processes (stress granule localization), suggesting a cohesive theme around innate immune signaling and cellular stress response. Some terms like skin development or muscle contraction are less directly related and introduce heterogeneity, so the label is a best-fit with moderate confidence.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043123","count":1},{"id":"GO:0043588","count":1},{"id":"GO:0030433","count":1},{"id":"GO:1901896","count":1},{"id":"GO:0006936","count":1}]},{"hash":"1017345394423151567","title":"Ribosome biogenesis and translation","description":"Most terms point to ribosome biogenesis, ribosome assembly, and translation, with additional cell-cycle terms reflecting growth-linked protein synthesis. This cohesive theme supports labeling the cluster as ribosome biogenesis and translation.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0000747","count":3},{"id":"GO:1901001","count":3},{"id":"GO:0090529","count":3},{"id":"GO:0042274","count":3}]},{"hash":"1547241907625985891","title":"Virus-responsive transcription and cell cycle regulation","description":"The top GO terms cluster around viral response (late viral transcription, response to X-ray, host-virus cell cycle perturbation) and transcriptional regulation (CDK activity, RNA Pol II CTD phosphorylation), with supporting signals from Wnt signaling and epithelial proliferation. This suggests a cohesive theme of transcription and cell-cycle control modulated during viral stress or infection, with broader developmental signaling context.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019086","count":12},{"id":"GO:0060749","count":12},{"id":"GO:0010696","count":12},{"id":"GO:0010165","count":12},{"id":"GO:0000411","count":12}]},{"hash":"2215710611191057713","title":"Ubiquitin-Driven Proteostasis and Cell Cycle","description":"The cluster is dominated by ubiquitination-related GO terms (polyubiquitination, K11- and K63-linked ubiquitination, ubiquitin-dependent protein catabolic process, ERAD) alongside cell cycle and proteostasis processes (mitotic cell cycle, cell division, unfolded protein response, DNA-templated transcription). This pattern points to a module of proteins coordinating protein quality control via ubiquitin tagging with regulation of cell cycle progression. A plant-specific term (abscisic acid biosynthesis) is present but less central, not altering the overall theme.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000209","count":7},{"id":"GO:0051301","count":6},{"id":"GO:0000278","count":5},{"id":"GO:0070535","count":5},{"id":"GO:0030433","count":5}]},{"hash":"782324946632144950","title":"Chromatin Remodeling and Telomere Regulation","description":"The GO terms converge on chromatin dynamics (chromatin remodeling, nucleosome assembly, G-quadruplex DNA formation) and telomere biology (telomeric D-loop disassembly, regulation of protein localization to telomere, telomere-associated transcription), suggesting a shared function in chromatin structure and telomere maintenance, with a few ancillary transcriptional/plant-signaling terms mixed in.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":3},{"id":"GO:0061820","count":2},{"id":"GO:0009736","count":2},{"id":"GO:1901347","count":2},{"id":"GO:0072362","count":2}]},{"hash":"2268451405029077268","title":"Developmental Regulation and Stem Cell Differentiation","description":"These GO terms collectively point to developmental processes across tissues (bone development, brain morphogenesis, ventricle development, mammary duct growth) and their control via stem cell differentiation. The presence of histone demethylation terms (even if labeled obsolete) and RITS complex localization suggests epigenetic regulation of development. Together, the cluster appears to capture proteins coordinating development with chromatin states and gene expression.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060348","count":2},{"id":"GO:0021555","count":1},{"id":"GO:0033169","count":1},{"id":"GO:0034630","count":1},{"id":"GO:0060763","count":1}]},{"hash":"1350695415509381355","title":"ER-stress\u2013linked anti-apoptotic regulation","description":"The cluster centers on negative regulation of apoptotic signaling in relation to endoplasmic reticulum stress, including ER-stress\u2013induced intrinsic and extrinsic pathways, Fas signaling, and hypoxia-related apoptosis. Additional terms about ER calcium homeostasis and ER-stress\u2013driven transcriptional responses support a theme of dampening cell death while coordinating calcium signaling and transcription under ER stress. The cerebellar development term appears incidental rather than core to the cluster\u2019s main function.","confidence":"High","size":27,"edges":14,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1902042","count":2},{"id":"GO:0032469","count":2},{"id":"GO:0051025","count":2},{"id":"GO:0060702","count":2},{"id":"GO:0021681","count":2}]},{"hash":"2196398579869666753","title":"Ubiquitin-regulated innate antiviral signaling","description":"This cluster centers on innate immune response and antiviral defense, with strong signals for ubiquitin-mediated protein turnover and regulation of cell death pathways (necroptosis, apoptosis) and TLR signaling, suggesting a cohesive role in ubiquitin-controlled innate antiviral signaling and cell fate.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045087","count":7},{"id":"GO:0051607","count":7},{"id":"GO:0000209","count":6},{"id":"GO:0034121","count":5},{"id":"GO:0042787","count":5}]},{"hash":"1944877728172826398","title":"Regulatory signaling and cell cycle control","description":"Based on the top GO terms, the cluster is enriched for regulators of signaling and phosphorylation (positive regulation of protein serine/threonine kinase activity, autophosphorylation, GTPase activity) and ubiquitin ligase activity, with additional links to cell cycle checkpoint regulation, chromatin assembly at centromeres (CENP-A), and RNA processing under stress. This pattern points to proteins that modulate signaling pathways and cell cycle progression, rather than a single specific process, supporting a broad label of regulatory signaling and cell cycle control.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071902","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0031954","count":5},{"id":"GO:2000728","count":4},{"id":"GO:1904668","count":4}]},{"hash":"213201343987645588","title":"Unknown","description":"The top GO terms span core nuclear processes (DNA-templated transcription and replication, telomerase assembly) plus a wide mix of signaling and stress responses (cytokinin, ethylene, interleukin-4, xenobiotic response, hypoxia) and even bacterial motility. This combination across kingdoms and functions lacks a single cohesive theme, so a specific, representative label cannot be confidently assigned.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006261","count":2},{"id":"GO:0009736","count":2},{"id":"GO:0033160","count":2},{"id":"GO:0035690","count":2}]},{"hash":"2031477430853442968","title":"Transcription and RNA Processing with Telomere Regulation","description":"Top GO terms show a clear emphasis on nuclear processes (DNA-templated transcription, mRNA processing) and genome maintenance (telomere maintenance/capping), with additional signals of spindle assembly and differentiation. This suggests a cluster centered on transcriptional regulation and genome stability, with some related differentiation cues.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0032088","count":3},{"id":"GO:0051225","count":3},{"id":"GO:0035994","count":3},{"id":"GO:0032212","count":3}]},{"hash":"1126277473722247248","title":"Cell Cycle and Kinase Signaling","description":"The cluster centers on mitotic cell cycle progression and regulation of proliferation, with multiple GO terms tied to kinase activity and phosphorylation (positive regulation of serine/threonine kinase activity, autophosphorylation), along with GTPase signaling, PI-mediated signaling, and protein interactions. While there are additional terms such as mRNA transport and sporulation-related membrane formation, the dominant theme is cell-cycle control and phosphorylation-driven signaling governing growth.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":6},{"id":"GO:0043547","count":6},{"id":"GO:0071456","count":5},{"id":"GO:0051028","count":5},{"id":"GO:0071902","count":5}]},{"hash":"478816173119995696","title":"Ubiquitin-Dependent Deubiquitination and Proteolysis","description":"The top GO terms are dominated by deubiquitination and ubiquitin\u2011dependent protein catabolic processes, indicating a core theme of ubiquitin signaling controlling protein turnover and chromatin state; other terms like transcription and CDK regulation likely reflect downstream regulatory effects.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000338","count":2},{"id":"GO:0045737","count":2},{"id":"GO:0097421","count":2},{"id":"GO:0034499","count":2}]},{"hash":"1586870085144762173","title":"Developmental Transcriptional Regulation and Stress Responses","description":"The top GO terms cluster around gene expression control (DNA-templated transcription, imprinting-related regulation), developmental processes (forebrain development, neural tube closure), cell cycle, and various stress responses (ER stress\u2013induced apoptosis, cadmium response, defense against bacteria) as well as ubiquitination. This suggests a cohesive theme of transcriptional control tied to developmental programs and cellular stress signaling rather than a single pathway.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000209","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0001843","count":4},{"id":"GO:0050830","count":4},{"id":"GO:0071276","count":4}]},{"hash":"1537335350483807756","title":"Glutamatergic signaling and endosomal trafficking","description":"Based on the top GO terms, the cluster is enriched for glutamatergic synaptic transmission and receptor recycling/endosome regulation, pointing to neuronal signaling coupled with vesicle trafficking. While there are additional terms spanning calcium channel regulation, Rho signaling, and transcription, the dominant theme centers on neuronal communication with endosomal trafficking, justifying this label with Medium confidence. ","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0060316","count":9},{"id":"GO:0035249","count":7},{"id":"GO:0001881","count":7},{"id":"GO:0051036","count":7},{"id":"GO:0034968","count":7}]},{"hash":"486006351568583116","title":"Gene expression and ribosome biogenesis","description":"The top GO terms show both transcription-related processes (transcription initiation-coupled chromatin remodeling, negative regulation of transcription by RNA polymerase II) and translation-related processes (cytoplasmic translation, ribosomal small subunit biogenesis, tRNA modification), suggesting a cluster centered on gene expression regulation and assembly/maintenance of the translation machinery. A couple of terms about sarcomere organization and septum assembly appear more structural and may reflect broader cellular roles. ","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0045214","count":2},{"id":"GO:0048096","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0002181","count":2}]},{"hash":"171543638939313338","title":"Unknown","description":"The top GO terms cover a wide range of unrelated processes (calcium signaling, GTPase regulation, cytokinesis, germ cell proliferation, tissue remodeling, kidney development, metabolism). There is no single dominant function or coherent pathway that ties these proteins together, and several terms are obsolete; thus a clear, representative cluster name cannot be assigned.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0097274","count":2},{"id":"GO:1905205","count":2},{"id":"GO:0072286","count":2},{"id":"GO:0051281","count":2}]},{"hash":"497357853049966919","title":"Neuronal cytoskeleton and microtubule dynamics","description":"This cluster\u2019s top GO terms converge on microtubule behavior and cytoskeletal organization, including cytoplasmic microtubule depolymerization, establishment/maintenance of microtubule polarity, spindle dynamics, and microtubule-dependent transport in neurons (anterograde transport of receptor complexes, neuron projection maintenance, cerebellar structure). While a plant term (chloroplast movement) appears, the overall theme is cytoskeletal dynamics and neuron structure maintenance, with signaling terms (Rap) potentially modulating these processes. ","confidence":"High","size":26,"edges":231,"triangles":1070,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0010938","count":11},{"id":"GO:0001560","count":11},{"id":"GO:0032487","count":11},{"id":"GO:0098971","count":11},{"id":"GO:0009904","count":11}]},{"hash":"194295103018451614","title":"Mitochondrial function and cell cycle regulation","description":"This cluster is dominated by mitochondrial-related terms (regulation of mitochondrial membrane permeability; protein import into the mitochondrial matrix) together with cell cycle control terms (negative regulation of G1/S transition, DNA replication, centrosome cycle), suggesting a cohesive theme of mitochondrial status influencing cell cycle progression. Additional terms related to signaling and trafficking are present but appear secondary to this core coupling between mitochondrial maintenance and division.","confidence":"High","size":26,"edges":4,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046902","count":6},{"id":"GO:2000134","count":6},{"id":"GO:0070940","count":6},{"id":"GO:1903740","count":6},{"id":"GO:0010867","count":6}]},{"hash":"1080828436235556224","title":"Cross-tissue developmental regulation","description":"The top GO terms cluster around developmental regulation and tissue-specific development across brain, heart, and kidney, plus general processes like transcriptional regulation and cell cycle; there isn't a single focused pathway, but the common theme is involvement in developmental regulation across multiple tissues rather than a specific function.","confidence":"Medium","size":26,"edges":16,"triangles":0,"max_degree":10,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0060316","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0060079","count":3},{"id":"GO:0035690","count":3},{"id":"GO:0000278","count":3}]},{"hash":"1557887018641404243","title":"Cytokinin signaling and chlorophyll biosynthesis regulation","description":"The strongest GO term is cytokinin-activated signaling pathway, with matching instances of negative regulation of chlorophyll biosynthetic process, pointing to a plant-specific module where cytokinin signaling modulates chlorophyll production. While several terms are obsolete, the core theme ties plant hormone signaling to chloroplast/chlorophyll regulation.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0009736","count":20},{"id":"GO:1902325","count":20},{"id":"GO:1903071","count":20},{"id":"GO:0046661","count":20},{"id":"GO:0051348","count":20}]},{"hash":"617680104246653319","title":"Developmental signaling and intracellular trafficking","description":"The GO terms emphasize signaling pathways (dopaminergic transmission, p53-mediated signaling, Hedgehog pathway regulation) and intracellular trafficking steps (protein export from nucleus, endosome transport), plus several development-related processes (pseudohyphal growth, cartilage condensation). Taken together, the cluster seems enriched for proteins involved in signal transduction coupled to intracellular transport and developmental processes, rather than a single narrow function.","confidence":"Medium","size":26,"edges":85,"triangles":85,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046827","count":23},{"id":"GO:0034198","count":23},{"id":"GO:2000641","count":22},{"id":"GO:0007124","count":22},{"id":"GO:1901621","count":22}]},{"hash":"278685709578392483","title":"Embryonic Development and Cell Cycle Signaling","description":"The top GO terms point strongly to vertebrate embryogenesis (neural tube closure, heart development, embryonic cranial skeleton morphogenesis) and foundational cell cycle processes (DNA replication, centrosome cycle). Additional signaling terms (interleukin-1 signaling, LPS response, nitric oxide response) suggest these proteins participate in broader developmental signaling and stress responses, but the core theme remains embryonic morphogenesis coupled with cell cycle regulation.","confidence":"Medium","size":26,"edges":26,"triangles":26,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009190","count":18},{"id":"GO:0070498","count":15},{"id":"GO:0001843","count":15},{"id":"GO:0046827","count":15},{"id":"GO:0006260","count":15}]},{"hash":"1512564503836946266","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":7,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0036494","count":3},{"id":"GO:0006626","count":3},{"id":"GO:0006986","count":3},{"id":"GO:0070389","count":3},{"id":"GO:0006855","count":3}]},{"hash":"1861205934031241299","title":"Neuronal development and signaling","description":"The set of frequent GO terms centers on neural development and neural communication, including CNS projection neuron axonogenesis, dorsal/ventral neural tube patterning, dopaminergic synaptic transmission, and endosome trafficking relevant to neuronal transport, alongside a calcium-related response and hedgehog pathway regulation in neural contexts. While a few terms (e.g., cartilage condensation, NK T cell differentiation, yeast pseudohyphal growth) are outliers, the dominant pattern points to neural development and signaling functions.","confidence":"Medium","size":26,"edges":72,"triangles":29,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":26},{"id":"GO:0007124","count":26},{"id":"GO:1901621","count":26},{"id":"GO:1904637","count":26},{"id":"GO:0001963","count":26}]},{"hash":"519231789021864504","title":"Mitochondrial energy production and ion transport","description":"This cluster is dominated by GO terms related to proton motive force-driven ATP synthesis in mitochondria, mitochondrial respiratory chain assembly, and various ion transport processes, suggesting a core theme of energy metabolism and membrane transport. There are some outlier terms (bacterial flagellum assembly/motility and cell adhesion) that may reflect annotation noise or mixed origins, which lowers overall confidence in a single cohesive function. ","confidence":"Low","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042776","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0033617","count":2},{"id":"GO:0006814","count":1},{"id":"GO:0042777","count":1}]},{"hash":"673992968605315408","title":"Nuclear snoRNP assembly and RNA modification","description":"The GO terms point to box H/ACA snoRNP assembly, snRNA pseudouridine synthesis, and snoRNA-guided rRNA pseudouridylation, along with telomerase RNA stabilization/localization to Cajal bodies and holoenzyme assembly, indicating a nucleus-based program of snoRNP and telomerase RNP maturation and RNA modification, with ribosome biogenesis as a connected process. Zinc transport terms appear ancillary.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090116","count":2},{"id":"GO:0090669","count":1},{"id":"GO:0000493","count":1},{"id":"GO:0031120","count":1},{"id":"GO:1904874","count":1}]},{"hash":"2094215206315621729","title":"Plant Telomere and Chromatin Regulation","description":"This cluster centers on nuclear genome maintenance and chromatin-related processes: telomere dynamics (telomeric D-loop disassembly, protein localization to telomere), nucleosome assembly and histone H2A deubiquitination, and G-quadruplex DNA formation, plus snRNA transcription. The presence of plant-specific contexts (cytokinin signaling, secondary cell wall biogenesis, osmotic stress response) suggests a plant-oriented nuclear regulatory module that ties chromatin/telomere biology to stress-responsive gene regulation. Overall, the common theme is plant telomere and chromatin regulation.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0061820","count":3},{"id":"GO:0009736","count":3},{"id":"GO:1901347","count":3},{"id":"GO:0072362","count":3},{"id":"GO:0006334","count":3}]},{"hash":"2289094435888558511","title":"Cyclic nucleotide signaling and transcription","description":"The Top Terms show a strong focus on cyclic nucleotide signaling (cAMP and cGMP pathways) with several terms for cellular responses to cAMP/cGMP and regulation of related kinases and guanylyl cyclase signaling, plus DNA-templated transcription. The presence of olfactory signaling (sensory perception of smell) and related transport/regulation hints suggests these proteins connect signaling events to transcriptional regulation. Overall, the cluster appears to group proteins involved in cyclic-nucleotide\u2013driven signaling that culminates in transcriptional responses, with a few broader/ambiguous terms accounting for annotation noise.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":20},{"id":"GO:0046827","count":18},{"id":"GO:0098719","count":18},{"id":"GO:0071320","count":18},{"id":"GO:0010754","count":18}]},{"hash":"2037897404190130130","title":"Unknown","description":"The top terms include several cilia-related processes (axoneme assembly, motile cilium assembly, cilium movement) but also chromatin remodeling and diverse immune/stress signaling (LPS response, TNF signaling, NF-kappaB regulation) and calcium signaling, indicating no single, cohesive function that ties all 26 proteins together. ","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035082","count":2},{"id":"GO:0043044","count":2},{"id":"GO:0042771","count":1},{"id":"GO:0071222","count":1},{"id":"GO:0033209","count":1}]},{"hash":"743472546223936662","title":"Nuclear gene expression and DNA replication","description":"The top GO terms are centered on nuclear processes: DNA-templated transcription, DNA replication, and mRNA processing, which together point to core gene expression and genome maintenance activities. Although there are some outlier terms related to development and signaling, the dominant theme is nuclear machinery for transcription and RNA processing, with DNA replication also represented. The cluster does not show tight interaction structure, so the label reflects a broad functional grouping rather than a single 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:0006260","count":3},{"id":"GO:0060324","count":3},{"id":"GO:0045727","count":3},{"id":"GO:0001890","count":3}]},{"hash":"573530047683380524","title":"Calcium-Dependent Signaling in Muscle and Immune Cells","description":"The terms cluster around calcium handling in muscle (regulation of sarcoplasmic reticulum calcium release, cardiac contraction regulation, hypertrophy) and immune signaling (CSF stimuli responses, T cell receptor signaling, interferon production). This suggests proteins involved in calcium-mediated signal transduction across muscle and immune contexts, with retinal cone development appearing as a less central, divergent term. ","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0086004","count":3},{"id":"GO:0097011","count":3},{"id":"GO:0010880","count":2},{"id":"GO:0036006","count":2},{"id":"GO:0046549","count":2}]},{"hash":"1050482745807086793","title":"Symbiont-driven host immune modulation","description":"This cluster is dominated by GO terms that describe how symbionts perturb or suppress host immune functions (symbiont-mediated perturbation of ubiquitin-like protein modification; symbiont-mediated suppression of host adaptive immune response; antigen processing and presentation via MHC class II; regulation of MHC II biosynthetic process). While a couple terms relate to plant barrier biosynthesis (cutin/suberin), the overarching signal is immune modulation by symbiotic organisms, making this a concise and representative label.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0039648","count":1},{"id":"GO:0010143","count":1},{"id":"GO:0002643","count":1},{"id":"GO:0039504","count":1},{"id":"GO:0010345","count":1}]},{"hash":"1657031754329199178","title":"Membrane trafficking and cytoskeletal remodeling","description":"The Top Terms point to endosomal transport (endosome to lysosome, endocytic recycling), membrane remodeling (plasma membrane tubulation, cleavage furrow formation), and signaling via phosphatidylinositol and GTPases, suggesting a cohesive role in vesicle trafficking and cytoskeletal dynamics during endocytosis, trafficking, and cytokinesis. Some terms like transcription and brain development may reflect multifunctional proteins rather than a dominant nuclear function in this cluster.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0000278","count":4},{"id":"GO:0008333","count":3},{"id":"GO:0048015","count":3},{"id":"GO:0006351","count":3}]},{"hash":"2180496426520711783","title":"Unknown","description":"The annotations span endocytosis, ERAD/glycoprotein processing, vacuolar proteolysis, transcription, and cell cycle-related processes like spindle assembly, which together show no single cohesive function for the cluster. The diversity makes it difficult to assign a concise, representative label with confidence.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006898","count":2},{"id":"GO:0051225","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0034638","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1570944759623636000","title":"RNA processing and ribosome biogenesis","description":"The cluster shows strong representation of RNA maturation and processing (mRNA splicing, rRNA maturation for 5.8S/SSU/LSU) and ribosome biogenesis (large subunit biogenesis), with links to transcription and TORC1 signaling, as well as ubiquitin-mediated protein regulation, indicating a theme of coordinated RNA processing and ribosome assembly with proteostasis control.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0031146","count":5},{"id":"GO:1904263","count":5},{"id":"GO:0000398","count":5},{"id":"GO:0000466","count":5}]},{"hash":"1273872158550381663","title":"Transcription Regulation and Cell Cycle Control","description":"The Top Terms are dominated by DNA-templated transcription, regulation of transcription, and CDK-related signaling (e.g., positive regulation of cyclin-dependent protein serine/threonine kinase activity) plus cell division, pointing to a cluster centered on transcriptional control linked to cell cycle progression. Growth hormone and nutrient responses add signaling context that can influence transcription and division, supporting this as a cohesive theme despite a few ancillary terms.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0060416","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0045737","count":2},{"id":"GO:0046726","count":2}]},{"hash":"402322916714363222","title":"Neural\u2013vascular\u2013immune signaling and development","description":"The proteins cluster is dominated by GO terms spanning neural development and synaptic function (corpus callosum development, positive regulation of synapse assembly, glutamatergic transmission), vascular signaling and angiogenesis (angiogenesis, VEGF receptor signaling, receptor serine/threonine kinase signaling), and immune signaling (innate immune response, T cell receptor signaling). This suggests a broad, integrated signaling theme across neural, vascular, and immune contexts, even though one term (pollen recognition) appears anomalous. Overall, the cluster seems to reflect interconnected developmental and signaling processes across tissues.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0022038","count":21},{"id":"GO:0048544","count":20},{"id":"GO:0051965","count":20},{"id":"GO:0014068","count":20},{"id":"GO:0001525","count":20}]},{"hash":"1825257740762472576","title":"Eye and Heart Organogenesis","description":"The cluster is enriched for multicellular development and organogenesis-related GO terms, with strong signals for eye/visual system development (lens development, visual perception) and cardiovascular development (heart development, angiogenesis). Transcriptional regulation and cell-cycle transition terms likely reflect developmental control, supporting a cohesive program of organ formation. A plant-specific term (abscisic acid signaling) may be noise, but does not undermine the central theme of eye and heart development. Overall, the label Eye and Heart Organogenesis captures the dominant functions of this cluster.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":8},{"id":"GO:0046827","count":7},{"id":"GO:0019233","count":7},{"id":"GO:0007601","count":7},{"id":"GO:0006351","count":7}]},{"hash":"212115163557906567","title":"Ciliogenesis and mitotic spindle organization","description":"This cluster combines cilium-related processes (intraciliary transport and cilium assembly) with mitotic machinery (spindle orientation and microtubule-based movement), plus vesicle trafficking and transcriptional regulation, suggesting coordination between ciliogenesis and cell division.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000132","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0007018","count":2}]},{"hash":"2302888143074539181","title":"Cilium/axoneme assembly and sperm motility","description":"The cluster shows strong representation of GO terms tied to cilium and axoneme function, including regulation of cilium movement, axon extension, sperm axoneme assembly, microtubule severing, and flagellated sperm motility. Also, tubulin post-translational modifications (polyglycylation, polyglutamylation) support a microtubule/ciliary role. A few terms like eating behavior appear incidental. Overall, the proteins likely participate in ciliary/flagellar structure and movement, especially in sperm, justifying this label.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042755","count":3},{"id":"GO:0003353","count":3},{"id":"GO:0030516","count":3},{"id":"GO:0018094","count":3},{"id":"GO:0018095","count":3}]},{"hash":"120365698912335550","title":"Ubiquitin-Proteasome Regulation and NF-\u03baB Signaling","description":"These proteins are enriched for ubiquitination and proteasome-related processes (autoubiquitination, K63-linked ubiquitination, ubiquitin-dependent protein catabolic processes) and are linked to NF-\u03baB and TNF signaling, plus proteostasis (aggresome assembly). The shared themes point to a group that modulates protein turnover and inflammatory signaling via ubiquitin pathways.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":6},{"id":"GO:1903265","count":5},{"id":"GO:0016049","count":5},{"id":"GO:0043123","count":4},{"id":"GO:1901253","count":4}]},{"hash":"776435255388467398","title":"Ubiquitin-Dependent Protein Degradation","description":"This cluster is dominated by GO terms for ubiquitination and proteasomal degradation\u2014autoubiquitination, ubiquitin-dependent protein catabolic process, and K48- and K6-linked ubiquitination\u2014suggesting the proteins largely function to tag substrates for degradation, including through ERAD. A few other terms (peroxisome import, histone turnover) appear but are less represented.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051865","count":12},{"id":"GO:0042787","count":12},{"id":"GO:0070936","count":11},{"id":"GO:0030433","count":10},{"id":"GO:0036205","count":8}]},{"hash":"1531293291002050122","title":"Autophagy and vacuolar targeting","description":"This cluster is dominated by autophagy-related GO terms, including cytoplasm-to-vacuole targeting (Cvt pathway), nucleophagy, glycophagy, and autophagy regulation in response to ER stress, plus related vesicle/ membrane targeting. The recurring theme is selective autophagy and trafficking of cellular components to the vacuole, indicating a cohesive autophagy-centric cluster.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032258","count":1},{"id":"GO:0043653","count":1},{"id":"GO:0034727","count":1},{"id":"GO:0006612","count":1},{"id":"GO:1902017","count":1}]},{"hash":"851458485822485981","title":"Kinase signaling and RNA processing regulators","description":"The top terms indicate regulation of kinase and GTPase activity, autophosphorylation, ubiquitin ligase activity, and RNA processing steps (mRNA splicing and export), plus centromeric chromatin assembly, suggesting a group of regulatory proteins that influence signaling and gene expression rather than a single coherent pathway.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":8},{"id":"GO:0051260","count":6},{"id":"GO:0007568","count":6},{"id":"GO:0071902","count":5},{"id":"GO:0031954","count":5}]},{"hash":"1163278371920725197","title":"Unknown","description":"The top GO terms are highly diverse, including cell adhesion, responses to various chemicals (curcumin, mercury, catechin), salivary gland development, circadian sleep/wake cycle, axon injury response, and regulation of endopeptidase activity or endothelial chemotaxis. There is no dominant shared function or process linking most proteins, and the cluster shows no internal edges (Edges: 0, Max Degree: 0), suggesting it does not represent a coherent functional module. Therefore, a concise Unknown label is appropriate. ","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007155","count":2},{"id":"GO:1904643","count":1},{"id":"GO:0046689","count":1},{"id":"GO:1902168","count":1},{"id":"GO:0010951","count":1}]},{"hash":"154920596610959000","title":"Chromatin modification and transcription regulation","description":"Based on the top GO terms, the cluster is enriched for DNA-templated transcription, histone methylation, RNA methylation and mRNA processing, which together reflect regulation of gene expression and chromatin state in the nucleus. The presence of terms related to cellular response to cadmium and mitotic cell cycle suggests coordination of transcription during stress and cell division. A few terms (lipid biosynthesis and microvillus assembly regulation) appear as outliers, but the strongest signal is nuclear gene-expression control.","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:0071276","count":2},{"id":"GO:0051568","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0034729","count":2}]},{"hash":"2078676603810850842","title":"Diverse Transmembrane Transporters","description":"The top GO terms all point to transmembrane transport across membranes for a variety of substrates (sugars, ions, vitamins, xenobiotics, nitrite/nitrate, phosphate), suggesting a cluster of membrane transporter proteins with broad substrate specificity rather than a single cargo.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015757","count":2},{"id":"GO:0035725","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0015707","count":2},{"id":"GO:0006004","count":2}]},{"hash":"302661308614412468","title":"RNA Polymerase Assembly and Transcription Regulation","description":"This cluster\u2019s top GO terms are dominated by RNA polymerase complex assembly (I, II, III) and regulation of transcription elongation by RNA polymerase II, indicating a core theme around transcription machinery. Secondary terms include tubulin complex assembly and protein folding, suggesting some involvement in structural or chaperone roles, but the predominant signal is assembly and regulation of transcription. A few items (face morphogenesis, oskar mRNA localization, telomerase RNA stabilization) are less directly related and may reflect broader or multifunctional annotations. Overall, the cluster appears centered on transcriptional machinery rather than a single cohesive phenotype.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990115","count":1},{"id":"GO:0007021","count":1},{"id":"GO:1990114","count":1},{"id":"GO:0032968","count":1},{"id":"GO:1990113","count":1}]},{"hash":"2299680122526840900","title":"Neural development and synaptic signaling","description":"This cluster is enriched for GO terms related to neuronal development and communication: axonogenesis of CNS projection neurons, dopaminergic synaptic transmission, and neural patterning signaling. While there are also terms tied to endosome transport and cell-cycle regulation, the strongest common theme among the top terms is neural development and signaling, justifying the name.","confidence":"Medium","size":25,"edges":234,"triangles":1162,"max_degree":24,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0034501","count":25},{"id":"GO:0045736","count":25},{"id":"GO:2000641","count":22},{"id":"GO:0007124","count":22},{"id":"GO:1901621","count":22}]},{"hash":"681932818964859973","title":"Neural development and signaling with cell-cycle control","description":"The top GO terms point to cerebellar development and neural differentiation (Bergmann glial differentiation, cerebellar cortex formation, axon regeneration) along with signaling pathways (insulin receptor signaling, T cell receptor signaling). There is also clear emphasis on cell-cycle regulation (negative regulation of CDK activity, negative regulation of cell proliferation) and endosome transport, suggesting these proteins participate in both neural development and broader growth/signaling processes that include cell-cycle control. Taken together, this cluster seems to represent a network coordinating neural development with growth signaling and cell-cycle regulation rather than a single narrowly defined function.","confidence":"Medium","size":25,"edges":300,"triangles":2300,"max_degree":24,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008286","count":25},{"id":"GO:0060020","count":25},{"id":"GO:0021697","count":25},{"id":"GO:0034501","count":25},{"id":"GO:0045736","count":25}]},{"hash":"1709564383026184850","title":"Nervous system development and dopaminergic signaling","description":"The cluster\u2019s top GO terms cluster around nervous system development and neuronal function, including sensory perception of pain, CNS projection neuron axonogenesis, and dopaminergic synaptic transmission, along with neural patterning and signal regulation. While a couple terms relate to other cell biology (endosome transport, pseudohyphal growth), the dominant theme is neural development and signaling.","confidence":"Medium","size":25,"edges":2,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0019233","count":9},{"id":"GO:0007275","count":9},{"id":"GO:2000641","count":8},{"id":"GO:0007124","count":8},{"id":"GO:1901621","count":8}]},{"hash":"988593531927051994","title":"Genome Integrity and Cell Cycle Regulation","description":"The top GO terms cluster around DNA replication, telomere maintenance, and DNA damage response (SOS response), together with regulation of cyclin-dependent kinase activity. These point to genome stability and coordinated cell cycle control during growth, even though other terms (development, ribosome biogenesis, signaling) appear, the cohesive theme is maintaining genome integrity and proper cell-cycle progression. ","confidence":"Medium","size":25,"edges":52,"triangles":49,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048701","count":6},{"id":"GO:0006260","count":6},{"id":"GO:0009432","count":4},{"id":"GO:0042273","count":4},{"id":"GO:0048026","count":4}]},{"hash":"1462374115484066948","title":"Dopaminergic signaling and neural development","description":"This cluster is dominated by neural-related terms: nervous system development and dopaminergic synaptic transmission, plus calcium signaling (ionomycin/response to calcium) and regulation of endosome transport, all pointing to neuronal communication and maturation. A few terms are less directly related (pseudohyphal growth, parathyroid hormone stimulus), but the overall theme centers on neural development and dopaminergic signaling. ","confidence":"Medium","size":25,"edges":137,"triangles":255,"max_degree":20,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071374","count":20},{"id":"GO:0007124","count":20},{"id":"GO:2000641","count":20},{"id":"GO:0000187","count":20},{"id":"GO:0007094","count":20}]},{"hash":"1854985258583933866","title":"Developmental signaling and transcription regulation","description":"This cluster centers on multicellular development, DNA-templated transcription, and neural signaling terms, with additional links to endosomal transport and Hedgehog-related pathway regulation, suggesting a cohesive role in coordinating development through transcriptional control and signaling, with trafficking supporting these processes.","confidence":"Medium","size":25,"edges":48,"triangles":14,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":16},{"id":"GO:0019233","count":16},{"id":"GO:0007275","count":16},{"id":"GO:0006351","count":16},{"id":"GO:0007118","count":14}]},{"hash":"2179863326048179849","title":"Neural development and signaling","description":"Based on GO terms including dopaminergic synaptic transmission, CNS projection neuron axonogenesis, and dorsal/ventral neural tube patterning, the cluster appears to be driven by neural development and neuronal signaling processes. While there are related terms to endosome transport and other pathways, the neural development signals are the most prominent and coherent across the term set.","confidence":"Medium","size":25,"edges":72,"triangles":36,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":25},{"id":"GO:0007124","count":25},{"id":"GO:1901621","count":25},{"id":"GO:1904637","count":25},{"id":"GO:0001963","count":25}]},{"hash":"322345815249209373","title":"Mitotic spindle dynamics and nuclear transport","description":"The terms include meiotic spindle elongation, mitotic nuclear membrane reassembly, NLS-bearing protein import, plus ciliary basal body docking and kinase signaling, pointing to a module around cell division, spindle organization, centrosome/ciliary functions, and related regulation.","confidence":"Medium","size":25,"edges":23,"triangles":1,"max_degree":22,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0051232","count":6},{"id":"GO:0007084","count":5},{"id":"GO:0045945","count":5},{"id":"GO:0097711","count":5},{"id":"GO:0001938","count":5}]},{"hash":"1492224280108349328","title":"Ubiquitination and Protein Degradation","description":"The cluster is dominated by GO terms centered on ubiquitination and ubiquitin-dependent proteolysis (autoubiquitination, K48- and K6-linked ubiquitination, ERAD), indicating a core link to the ubiquitin-proteasome system and protein turnover; additional terms touch on apoptosis regulation and signaling, which are often connected to ubiquitin-mediated pathways. This cohesive theme supports labeling the cluster as ubiquitination-driven protein degradation.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051865","count":12},{"id":"GO:0042787","count":12},{"id":"GO:0030433","count":11},{"id":"GO:0036205","count":11},{"id":"GO:1903265","count":11}]},{"hash":"1666342726259891648","title":"Membrane trafficking and cytokinesis","description":"The top GO terms cluster around membrane remodeling and division: endocytic recycling, plasma membrane tubulation, and cleavage furrow formation point to membrane trafficking and cytokinesis as the core theme. Phosphatidic acid biosynthesis supports membrane lipid dynamics. A couple of terms related to development are present but peripheral, so the dominant signal is membrane dynamics during cell division. Overall, this label appropriately captures the main function represented in the cluster with moderate confidence.","confidence":"Medium","size":25,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006370","count":2},{"id":"GO:1990126","count":2},{"id":"GO:0097320","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0022617","count":2}]},{"hash":"1753417881702428954","title":"Signaling and proteostasis under stress","description":"The cluster includes diverse signaling-related terms (Wnt planar cell polarity, T cell receptor signaling, Fc-epsilon receptor signaling) alongside protein quality-control processes (proteasome core complex assembly, endopeptidase activity regulation) and stress responses (mitochondrial autophagy, salt stress, regulation of cellular respiration). This suggests proteins that participate in signal transduction coupled with protein degradation/ turnover and autophagy during cellular stress. Confidence: Medium","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090116","count":1},{"id":"GO:0043457","count":1},{"id":"GO:0000422","count":1},{"id":"GO:0010259","count":1},{"id":"GO:0080129","count":1}]},{"hash":"2208097709945645604","title":"Synaptic Vesicle Docking and Neurotransmitter Release","description":"This cluster is dominated by terms tied to vesicle trafficking and synaptic function, including ER-to-Golgi and Golgi-to-vacuole transport, synaptic vesicle docking, and positive/ spontaneous neurotransmitter secretion and excitatory postsynaptic potential regulation. While some terms touch broader cellular processes (transcription regulation, microtubule-based movement), the core signals point to secretory pathway activities linked to synaptic vesicle docking and neurotransmitter release.","confidence":"High","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0006355","count":3},{"id":"GO:0030473","count":3},{"id":"GO:2000463","count":2},{"id":"GO:0010811","count":2}]},{"hash":"1738009264723082929","title":"Nuclear transcription regulation and mitotic control","description":"The cluster centers on nuclear processes: regulation of DNA-templated transcription, snoRNP assembly (RNA processing), and components involved in chromosome segregation and mitotic transitions (anaphase-promoting complex-dependent catabolic process, metaphase/anaphase transition). These together point to a theme of gene expression control in the nucleus coupled with cell-cycle/mitosis regulation. Some terms like innate immune response or photoreceptor localization appear less central but may reflect broader functional associations; however, the core signal is nuclear transcription and mitotic control.","confidence":"High","size":25,"edges":27,"triangles":50,"max_degree":7,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":11},{"id":"GO:0000492","count":11},{"id":"GO:0006463","count":10},{"id":"GO:0045087","count":10},{"id":"GO:1903546","count":10}]},{"hash":"1035122723124082388","title":"Ion Transport and Membrane Potential Regulation","description":"The top GO terms cluster around potassium and sodium ion transport, membrane potential stabilization and resting potential regulation, and signaling responses (cGMP/cAMP), with a mechanosensory touch term. This points to a cohesive group of ion channels/transporters that maintain membrane potential and respond to signaling and mechanical stimuli.","confidence":"High","size":25,"edges":298,"triangles":2255,"max_degree":24,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071805","count":25},{"id":"GO:0098914","count":25},{"id":"GO:0030322","count":25},{"id":"GO:0060075","count":25},{"id":"GO:0050976","count":25}]},{"hash":"398770233931151356","title":"Transcription Regulation and Splicing in Development","description":"The cluster\u2019s top terms center on regulation of DNA-templated transcription and spliceosome-mediated RNA processing, with developmental terms like syncytial blastoderm and eye-antennal disc development. A few other terms (Golgi transport, vitamin D receptor signaling) are less connected, but the dominant theme is transcription control and RNA processing during development.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006893","count":2},{"id":"GO:0070564","count":1},{"id":"GO:0016567","count":1}]},{"hash":"259520623673126983","title":"Plant osmotic stress response and chromatin/telomere dynamics","description":"The terms point to plant-specific nuclear regulation: osmotic stress response paired with chromatin-related processes (nucleosome assembly, G-quadruplex DNA), plus telomere dynamics (telomeric D-loop disassembly, telomere localization) and cytokinin signaling; the inclusion of secondary cell wall biogenesis further supports a plant context. This suggests a cluster centered on plant chromatin/telomere regulation under osmotic stress rather than a single cytosolic pathway.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0006970","count":4},{"id":"GO:0061820","count":3},{"id":"GO:0009736","count":3},{"id":"GO:1901347","count":3},{"id":"GO:0072362","count":3}]},{"hash":"462365109168553829","title":"Regulation of signaling and transcription","description":"Based on the top GO terms, these proteins appear to regulate multiple signaling pathways (dopamine signaling, dopamine response, Wnt signalosome assembly) and gene expression processes (regulation of DNA-templated transcription), with also hints of intracellular trafficking regulation. The diverse regulatory themes rather than a single pathway suggest a broad regulatory cluster rather than a specific biochemical function.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:1903215","count":2},{"id":"GO:1902499","count":2},{"id":"GO:1903351","count":2},{"id":"GO:1904887","count":2}]},{"hash":"116870080700445420","title":"Vesicle trafficking and membrane transport","description":"Most of the top GO terms cluster around vesicle budding, Golgi-to-transport, endosome-to-lysosome transport, exocytosis, and related membrane organization (plus related processes like cell polarity and spine development). Although there is a transcription-related term present, the dominant theme appears to be vesicle trafficking and membrane transport across different cell types, making this a coherent label for the cluster.","confidence":"Medium","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0009736","count":3},{"id":"GO:0045956","count":2},{"id":"GO:0090162","count":2},{"id":"GO:0070142","count":2}]},{"hash":"2058880731646041321","title":"Neural development and glutamatergic synaptic signaling","description":"The cluster is enriched for nervous system development and neural signaling: nervous system development, and notably synaptic transmission, glutamatergic. Additional terms like sensory perception of pain and DNA-templated transcription support neural functions, while sarcomere organization and skeletal muscle development hint at neuromuscular context. Some immune signaling term (B cell receptor signaling) is present but less central to the primary theme. Overall, the dominant pattern points to neural development and glutamatergic synaptic activity.","confidence":"Medium","size":25,"edges":241,"triangles":1251,"max_degree":24,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":8},{"id":"GO:0006351","count":8},{"id":"GO:0019233","count":7},{"id":"GO:0007275","count":7},{"id":"GO:0007519","count":5}]},{"hash":"702799853322065198","title":"Ubiquitin-mediated inflammatory signaling","description":"The GO terms point to ubiquitination processes (autoubiquitination, polyubiquitination, ubiquitin-dependent protein catabolic process) combined with inflammatory signaling pathways (TNF signaling, TLR regulation, JNK cascade, I\u03baB phosphorylation) and transcriptional regulation. This suggests a coherent theme of ubiquitin-dependent control of immune signaling and gene expression.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033151","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0034121","count":3},{"id":"GO:0033209","count":3},{"id":"GO:0036205","count":3}]},{"hash":"1576882411275872894","title":"Ubiquitin-dependent immune signaling and apoptosis","description":"These GO terms cluster around both innate and adaptive immune responses (innate and adaptive immune response, negative regulation of T cell proliferation), TNF-mediated signaling, and processes governing cell death (apoptotic and necroptotic regulation). The presence of ubiquitin-related processes (ubiquitin-dependent protein catabolic process, autoubiquitination) suggests that ubiquitin-mediated regulation is a central organizing principle for this cluster's immune signaling and programmed cell death functions.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:0046007","count":3},{"id":"GO:0046328","count":3},{"id":"GO:0042787","count":3},{"id":"GO:0006915","count":3}]},{"hash":"1190849388640482546","title":"GPCR-cAMP Signaling in Neuronal Excitability","description":"The cluster\u2019s top GO terms center on GPCR-related signaling and cAMP pathways, including negative regulation of PKA activity, cellular response to cAMP, and receptor signaling regulation, alongside sensory and neural excitability processes (olfactory perception, membrane potential regulation, sodium transport). The inclusion of antipsychotic/clozapine response further ties this to neural signaling and GPCR pharmacology. While some terms (e.g., cardiac proliferation) hint broader signaling roles, the dominant theme appears to be GPCR-cAMP\u2013mediated signaling in neural and sensory contexts.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000480","count":2},{"id":"GO:0098719","count":2},{"id":"GO:0071320","count":2},{"id":"GO:0097332","count":2},{"id":"GO:0046827","count":2}]},{"hash":"463736398235882028","title":"Cell cycle regulation and transcription","description":"Based on the top GO terms, the cluster is enriched for DNA-templated transcription, DNA replication, cell division, and regulation of G1/S transition, indicating a core connection to cell cycle control and transcriptional machinery. While other terms like endosome transport, xenobiotic response, forebrain development, and angiogenesis appear, they are less central to the dominant theme of cell cycle and transcriptional regulation.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0048227","count":3},{"id":"GO:0000027","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0051301","count":2}]},{"hash":"1094663942439586054","title":"Gene Expression and Protein Trafficking","description":"The core terms cluster around gene expression, with DNA-templated transcription and translation initiation/reinitiation, plus ER-to-Golgi vesicle transport and nuclear export. This points to coordinated control of transcription and translation and subsequent protein trafficking/processing, with proteasomal turnover reinforcing regulatory dynamics. Some developmental and signaling terms appear, but the dominant theme is gene expression and protein trafficking.","confidence":"Medium","size":25,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0001731","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0006888","count":3}]},{"hash":"889686250522606397","title":"Ion transport and membrane potential regulation","description":"Based on frequent GO terms for potassium and sodium ion transport, stabilization and regulation of membrane potential, and cellular responses related to cGMP/cAMP signaling, plus a mechanosensory touch component, the cluster appears to center on ion channels and regulators controlling ionic homeostasis and membrane excitability. This combination supports a label focusing on ion transport and membrane potential regulation.","confidence":"High","size":25,"edges":247,"triangles":1293,"max_degree":24,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071805","count":19},{"id":"GO:0098914","count":19},{"id":"GO:0030322","count":19},{"id":"GO:0060075","count":19},{"id":"GO:0050976","count":19}]},{"hash":"1996216542960153193","title":"Sodium/Potassium Ion Transport and Membrane Potential","description":"This cluster is dominated by GO terms for sodium and potassium ion transport across the plasma membrane, intracellular potassium homeostasis, and membrane potential stabilization, including cardiac-related repolarization. These consistently point to ion channels/transporters and regulators of membrane excitability, with supporting signals from cGMP/cAMP pathways, while transcription-associated terms appear less central. Overall, the core theme is ion transport and maintenance of membrane potential.","confidence":"High","size":25,"edges":25,"triangles":1,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0098719","count":16},{"id":"GO:0046827","count":16},{"id":"GO:0071805","count":16},{"id":"GO:0006351","count":16},{"id":"GO:0030007","count":16}]},{"hash":"442987359451144505","title":"ER quality control and ubiquitin-mediated degradation","description":"The dominant GO terms describe ER-to-Golgi transport, ER lumen retention, ubiquitin-dependent degradation (ERAD and related ubiquitination), and related protein catabolic processes. Although a few terms touch on signaling pathways (Wnt, TNF) or lymphocyte recombination, the central theme across the cluster is ER-associated protein handling and ubiquitin-driven degradation, suggesting a cohesive group focused on ER quality control and proteolysis.","confidence":"High","size":25,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0006621","count":2},{"id":"GO:0046621","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0038018","count":2}]},{"hash":"684969606585234479","title":"Steroid hormone signaling in male reproductive development","description":"The cluster's top terms center on male sex differentiation, prostate gland development, and steroid hormone receptor complex assembly, pointing to steroid-driven reproductive development in males. Some unrelated or obsolete terms appear, suggesting annotation noise, but the core signal supports steroid signaling in reproduction.","confidence":"Medium","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0046661","count":12},{"id":"GO:0071357","count":12},{"id":"GO:0006463","count":12},{"id":"GO:0030850","count":12},{"id":"GO:0009736","count":11}]},{"hash":"1389939592448524225","title":"Sperm axoneme and microtubule assembly","description":"The top GO terms cluster around cytoskeletal organization and structures essential for sperm flagella, including tubulin complex assembly, cortical microtubule organization, and sperm individualization. This points to a cohesive theme of microtubule-based assembly and axoneme formation in sperm, suggesting the proteins together participate in spermatogenesis-related flagellar/cytoskeletal processes. Some other terms (interferon-beta production, hearing-related sensory detection) appear only peripherally, but the core signal supports a microtubule/axoneme\u2013focused function.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0099132","count":1},{"id":"GO:0042777","count":1},{"id":"GO:0007288","count":1},{"id":"GO:0032608","count":1},{"id":"GO:0050910","count":1}]},{"hash":"1925167549705881379","title":"Unknown","description":"The terms cover telomere maintenance, cadmium response, cell cycle (G2/M), abscisic acid signaling, heart and Schwann cell development, visual perception, Wnt signaling, telomere capping, and cyclic nucleotide biosynthesis\u2014too diverse to anchor a single cohesive function. There\u2019s no clear shared pathway or process linking these proteins, so a specific label isn\u2019t justifiable. ","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0000086","count":2},{"id":"GO:0009738","count":2},{"id":"GO:0007507","count":2}]},{"hash":"254177905853849860","title":"Neuronal Synaptic Transmission and Receptor Recycling","description":"The cluster shows a clear tilt toward neuronal signaling, with enrichment for glutamatergic and dopaminergic synaptic transmission, plus receptor recycling and endosome size regulation, pointing to proteins involved in synaptic communication and vesicle trafficking; some transcription-related terms appear as secondary annotations, but the dominant theme is synaptic signaling and trafficking.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0035249","count":5},{"id":"GO:0034968","count":3},{"id":"GO:0001881","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0051036","count":3}]},{"hash":"1428762016107972179","title":"Regulatory Signaling and Gene Expression","description":"The terms point to a mix of signaling-related processes (GPCR signaling, regulation of protein kinase activity) and gene expression control (DNA-templated transcription, mRNA transport), with supporting themes of ubiquitination and broader cellular responses (hypoxia, mechanical stimulus, axonogenesis). This suggests a cluster centered on signaling cascades that regulate transcription and cellular responses, rather than a single, tight pathway.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0007409","count":2},{"id":"GO:0071260","count":2}]},{"hash":"448457296411537501","title":"Unknown","description":"The GO terms span transcription, metabolism, signaling, development, and immunity (e.g., DNA-templated transcription, glucose metabolism, response to cocaine, placenta development, chemotaxis, glutamatergic synaptic transmission, and defense to Gram-positive bacteria) with no clear single function tying the cluster together; plus no interactions among proteins. This suggests a non-cohesive grouping rather than a defined pathway.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":13},{"id":"GO:0006006","count":12},{"id":"GO:0033160","count":11},{"id":"GO:0042220","count":11},{"id":"GO:0045793","count":11}]},{"hash":"341291973590590556","title":"Fatty acid oxidation and energy metabolism","description":"This cluster centers on fatty acid catabolism, including long- and medium-chain beta-oxidation, carnitine biosynthesis, and related energy pathways, with links to gluconeogenesis, glycogen biosynthesis, and starvation response. The cardiac muscle differentiation term suggests metabolic activity in muscle tissue, reinforcing an overall energy metabolism theme driven by fatty acid oxidation.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0006111","count":3},{"id":"GO:0042758","count":3},{"id":"GO:0045329","count":3},{"id":"GO:0033539","count":3}]},{"hash":"1343226031951564820","title":"Neurotransmitter regulation and stress responses","description":"The cluster shows enrichment for neurotransmitter-related processes, including dopamine metabolism and serotonin secretion regulation, along with responses to various stressors and xenobiotics (lipopolysaccharide, corticosterone, ethanol). Although bone development and related pathways appear among the terms, the dominant signal centers on neuromodulation and broad stimulus-response roles, suggesting proteins involved in neurotransmitter dynamics under stress conditions. This supports a cohesive, if broad, functional theme, hence a medium confidence level.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060348","count":4},{"id":"GO:0032496","count":2},{"id":"GO:0014063","count":2},{"id":"GO:0051412","count":2},{"id":"GO:0043046","count":2}]},{"hash":"312161411392444273","title":"Unknown","description":"The terms are too diverse (cilia-related processes coexist with brain development, nitrogen transport, plant root branching, and yeast pseudohyphal growth) to form a coherent, shared function for this cluster; no single theme ties the proteins together with confidence.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090116","count":2},{"id":"GO:0035082","count":1},{"id":"GO:0007420","count":1},{"id":"GO:0033326","count":1},{"id":"GO:0032053","count":1}]},{"hash":"1140137643363491487","title":"Organelle-specific autophagy (plant)","description":"The cluster is dominated by GO terms about autophagy and turnover of organelles (mitochondria, peroxisomes, nucleus with nucleophagy, autophagosome assembly), plus related processes like leaf senescence and stress-responsive regulation. This combination points to a coherent theme of organelle quality control via autophagy in plants, with nucleophagy and organelle-specific autophagy as central features.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":2},{"id":"GO:0032147","count":1},{"id":"GO:0034727","count":1},{"id":"GO:0030242","count":1},{"id":"GO:0044805","count":1}]},{"hash":"56735214069599773","title":"Membrane remodeling and lipid signaling","description":"Top GO terms cluster around membrane- and lipid-related processes: phosphatidylinositol-mediated signaling, phosphatidic acid biosynthesis, endocytic recycling, plasma membrane tubulation, and cleavage furrow formation. This pattern points to membrane dynamics and signaling rather than a single tissue-specific function. While there are development terms like eye development and osteoblast fate commitment present, these likely reflect broader roles or annotation cross-talk, with the core theme being dynamic membranes and lipid signaling.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048015","count":3},{"id":"GO:1990126","count":2},{"id":"GO:0097320","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0022617","count":2}]},{"hash":"294974953915502159","title":"ER stress response and COPII vesicle trafficking","description":"The top terms cluster around endoplasmic reticulum functions: localization to ER, ER unfolded protein response, COPII-coated vesicle budding, and calcium homeostasis, pointing to an ER-centered module for protein folding stress and ER-to-Golgi trafficking. Some virus-host interaction terms are present but do not define the core theme.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044828","count":1},{"id":"GO:0044829","count":1},{"id":"GO:0060304","count":1},{"id":"GO:0070972","count":1},{"id":"GO:0090114","count":1}]},{"hash":"1645369786626329930","title":"Hormone Signaling and Stress Response","description":"This cluster centers on hormone signaling pathways (cytokinin, steroid/nuclear receptor\u2013mediated glucocorticoid signaling) and stress/immunity responses (innate immune response, unfolded protein response, metal ion response), suggesting a cohesive theme of ligand-driven signaling and stress adaptation, though there is some diversity including cell cycle processes.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0009736","count":18},{"id":"GO:0006463","count":17},{"id":"GO:2000324","count":17},{"id":"GO:0045087","count":17},{"id":"GO:0031400","count":17}]},{"hash":"482408437236397283","title":"ER Stress and Unfolded Protein Response","description":"The top GO terms cluster around ER-associated processes\u2014protein localization to the ER, ER/UFR signaling, COPII vesicle budding, and calcium homeostasis\u2014pointing to a coordinated ER stress response and secretory pathway activity, with some virus-related context noted but not essential to the core theme.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044828","count":2},{"id":"GO:0044829","count":2},{"id":"GO:0060304","count":2},{"id":"GO:0070972","count":2},{"id":"GO:0090114","count":2}]},{"hash":"1042330965998309817","title":"Lipid and small-molecule catabolism","description":"The Top Terms cluster around various catabolic processes, especially lipid breakdown (triglycerides, monoacylglycerols, phosphatidylserine) and degradation of small molecules (uracil, beta-ketoadipate, stilbene), with an additional note on regulation of endocannabinoid signaling. This suggests a broad metabolic theme centered on catabolism of lipids and other small substrates, rather than a single cohesive pathway, which fits a heterogeneous set of proteins. There are no observed edges, implying the proteins may participate in multiple, distinct catabolic routes rather than a tight functional module.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0019433","count":10},{"id":"GO:0052651","count":10},{"id":"GO:2000124","count":10},{"id":"GO:0006660","count":10},{"id":"GO:0017000","count":9}]},{"hash":"1435065510612937131","title":"Neural development and morphogenesis","description":"The top GO terms are dominated by developmental processes: cell morphogenesis, bone development, corpus callosum development, and neural tube closure, which point to a cohesive theme of neural development and tissue morphogenesis. While there are additional terms related to transcription, the mitotic cell cycle, and some immune signaling, these do not outweigh the developmental signal. The immune-related terms may reflect multifunctional proteins but do not define the cluster\u2019s primary function.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000902","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0060348","count":3}]},{"hash":"2187076850275319887","title":"Neuronal Cytoskeleton Dynamics and Trafficking","description":"The cluster centers on cytoskeleton remodeling and signaling relevant to neuronal development: filopodium assembly, microtubule-based movement, Rho pathway regulation, and dendrite/spinal cord development, plus endosomal transport. While there are some RNA processing and ubiquitin-related terms, the dominant theme is actin/microtubule dynamics and trafficking in neurons.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046847","count":3},{"id":"GO:0021510","count":2},{"id":"GO:0007018","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0016197","count":2}]},{"hash":"2275938894566228628","title":"Cellular stress response and protein homeostasis","description":"The top GO terms suggest a broad theme around how cells manage stress: heat-stress\u2013related mRNA export, mRNA splicing, and cell cycle regulation; together with protein ubiquitination/oligomerization and chromatin assembly, plus inflammatory signaling and glial apoptosis, implying a cluster focused on coordinating gene expression and protein quality control under stress rather than a single specific pathway.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:2000728","count":2},{"id":"GO:1904668","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0061641","count":2}]},{"hash":"827643329026123001","title":"Endosome-Golgi Transport and COPII Cargo Loading","description":"The top GO terms emphasize intracellular protein transport, including plasma membrane to endosome transfer, recycling endosome to Golgi, retrograde transport to Golgi, COPII-coated vesicle cargo loading, and Rab/Rap signaling. This set suggests a cohesive class of proteins functioning in vesicle trafficking between endosomes and the Golgi apparatus, with regulation by Rab and Rap signaling pathways.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032483","count":2},{"id":"GO:0048227","count":1},{"id":"GO:0071955","count":1},{"id":"GO:0006886","count":1},{"id":"GO:0035526","count":1}]},{"hash":"136626195701193013","title":"Transcriptional regulation and signaling regulators","description":"The top terms point to regulation of DNA-templated transcription and chromatin modification, alongside diverse signaling and trafficking roles (Rho signaling, calcium-channel regulation, receptor recycling, endosome size) and even synaptic transmission. This suggests a cluster of regulatory proteins that influence gene expression and intracellular signaling/trafficking rather than a single enzymatic function, though the mix is broad. Therefore, a label focusing on transcriptional regulation combined with signaling/trafficking makes the most concise, representative sense for the group.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":4},{"id":"GO:0035023","count":4},{"id":"GO:0060316","count":4},{"id":"GO:0034968","count":3},{"id":"GO:0001881","count":3}]},{"hash":"573887941375953142","title":"Male Germline Spermatogenesis and Meiosis","description":"This cluster is dominated by GO terms tied to male germline development and meiotic processes: male germ-line cyst formation, chromosome segregation during male meiosis, G1/S transition in the cell cycle, spermatocyte division, and male meiosis cytokinesis. These together point to a cohesive theme of spermatogenesis and meiotic progression in the male germline. A few unrelated terms (neuronal differentiation, autophagy regulation, behavioral responses, viral processes) are likely noise or pleiotropic annotations and do not undermine the primary germline-meiosis signal.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048136","count":1},{"id":"GO:0007060","count":1},{"id":"GO:0000082","count":1},{"id":"GO:0016032","count":1},{"id":"GO:0048137","count":1}]},{"hash":"2066625314075820021","title":"Innate immune signaling and antiviral defense","description":"The top terms center on NF-kappaB pathway regulation, inflammasome control, antiviral defense, and modulation of LPS signaling, indicating a cluster of proteins involved in innate immune signaling and host defense against viruses, with possible roles in trafficking of signaling components (protein localization to microtubules).","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043123","count":2},{"id":"GO:0046597","count":2},{"id":"GO:1900226","count":2},{"id":"GO:0032897","count":2},{"id":"GO:0043569","count":2}]},{"hash":"1518944534686580156","title":"Regulated signaling and receptor trafficking","description":"The top GO terms point to regulation-related processes across signaling and trafficking, including regulation of Rho-mediated signal transduction, receptor recycling, and regulation of endosome size, with some notes on transcription regulation and synaptic signaling. This suggests the proteins collectively participate in controlling signaling output via membrane trafficking and cytoskeletal dynamics, rather than a single specific activity. Confidence is medium due to some obsolete terms and mixed functions.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060316","count":3},{"id":"GO:0034968","count":2},{"id":"GO:0001881","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0051036","count":2}]},{"hash":"1787344324354252855","title":"Glutamatergic synaptic trafficking and receptor recycling","description":"The top terms cluster around glutamatergic synaptic transmission, receptor recycling, and endosome size regulation, indicating a focus on maintaining glutamatergic synapses via endosomal trafficking and receptor turnover. Weighing in are other, less cohesive terms like transcription regulation and neurodevelopment, but the dominant signal supports synaptic maintenance through endosomal processes.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0035249","count":17},{"id":"GO:0001881","count":17},{"id":"GO:0051036","count":17},{"id":"GO:0060316","count":17},{"id":"GO:0034968","count":17}]},{"hash":"6550219541584273","title":"Developmental regulation and synaptic signaling","description":"This cluster centers on neuronal signaling functions, including excitatory postsynaptic potentials and regulation of synaptic vesicle exocytosis, suggesting roles in synaptic transmission. Coupled with terms for transcription regulation and broad development (blastocyst development, ossification), it points to developmental regulation with a strong emphasis on neural communication. The mixed terms also include cellular trafficking and calcium signaling hints, which fit into synaptic function in developing cells. ","confidence":"Medium","size":24,"edges":21,"triangles":7,"max_degree":6,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0035690","count":5},{"id":"GO:0060316","count":4},{"id":"GO:0006355","count":4},{"id":"GO:2001246","count":3},{"id":"GO:0043931","count":3}]},{"hash":"1546355990522313170","title":"Cardiac calcium signaling and contraction","description":"The top GO terms point to calcium handling and contractile machinery in the heart (calcium release regulation, cardiac myofibril assembly, and positive regulation of heart contraction), suggesting a cohesive theme of calcium-dependent cardiac function. Some nephron development terms appear as noise, but the core cluster seems centered on cardiac calcium signaling and contraction.","confidence":"High","size":24,"edges":31,"triangles":8,"max_degree":23,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0055003","count":8},{"id":"GO:0072286","count":8},{"id":"GO:0051281","count":8},{"id":"GO:0042994","count":8},{"id":"GO:0042554","count":8}]},{"hash":"2163867913452919334","title":"Neuronal development and signaling","description":"Most of the top GO terms cluster around neural development and neuronal signaling: axonogenesis of CNS projection neurons, dopaminergic synaptic transmission, and dorsal/ventral neural tube patterning, with related signaling pathway regulation. There are also broader cellular signaling and trafficking terms (endosome transport, calcium response, p53-mediated signaling) that could support neural functions. A few terms (cartilage condensation, NK T cell differentiation, pseudohyphal growth) appear less connected, suggesting some annotation noise. Overall, the cluster seems best described by neural development and signaling.","confidence":"Medium","size":24,"edges":259,"triangles":1678,"max_degree":23,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":24},{"id":"GO:0007124","count":24},{"id":"GO:1901621","count":24},{"id":"GO:1904637","count":24},{"id":"GO:0001963","count":24}]},{"hash":"435292737762108242","title":"Regulated signaling and receptor trafficking","description":"These proteins cluster around control of signaling pathways (Rho and Ras), membrane receptor recycling and endosome dynamics, with links to synaptic glutamatergic transmission and transcriptional regulation, and even acrosome reaction. The common thread is coordinated signal transduction coupled to membrane trafficking and downstream gene regulation, spanning neuronal and secretory contexts. While some terms are specialized or obsolete, the overarching theme is regulated signaling intertwined with vesicle trafficking.","confidence":"Medium","size":24,"edges":29,"triangles":8,"max_degree":15,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0035023","count":14},{"id":"GO:0035249","count":9},{"id":"GO:0034968","count":8},{"id":"GO:0001881","count":8},{"id":"GO:0006355","count":8}]},{"hash":"1720583313165350818","title":"Actin Cytoskeleton Remodeling and Kinase Signaling","description":"This cluster centers on actin dynamics, including actin filament bundle assembly and Arp2/3-mediated nucleation, plus regulation of GTPase activity and protein phosphorylation. Ubiquitination signals suggest turnover control, tying cytoskeletal remodeling to signaling cascades. Development terms for skeletal muscle fiber and substantia nigra hint at roles in muscle and neural development where actin remodeling is critical.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":3},{"id":"GO:0051017","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0042994","count":2},{"id":"GO:0071902","count":2}]},{"hash":"13229943310315952","title":"Cell Growth and Division Signaling","description":"The cluster includes mitotic nuclear membrane reassembly, nuclear import, ciliary basal body docking, TORC1 signaling, and regulation of kinase activity, alongside links to endothelial proliferation and apoptotic morphogenesis. Taken together, these terms point to coordinated control of cell growth, division, and signaling pathways, rather than a single narrowly defined function.","confidence":"Medium","size":24,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007084","count":4},{"id":"GO:0045945","count":4},{"id":"GO:0097711","count":4},{"id":"GO:0001938","count":4},{"id":"GO:2001241","count":4}]},{"hash":"2028176165029010082","title":"Neural, muscular, and sensory development with synaptic signaling","description":"The top GO terms point to broad developmental programs across nervous system (axonogenesis, Schwann cell development, visual perception, synaptic plasticity) and muscle/heart formation (myoblast fusion, heart development), plus general mitotic and cell-cycle processes. Together they suggest coordinated development of neural, muscular, and sensory systems with synaptic activity, rather than a single specific complex. Confidence: Medium","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000086","count":17},{"id":"GO:0060079","count":17},{"id":"GO:0007520","count":17},{"id":"GO:0007409","count":17},{"id":"GO:0009738","count":17}]},{"hash":"1317671754567056446","title":"Phytochrome-Mediated Light Signaling and Transcription","description":"Top GO terms strongly point to phytochrome-like photoreceptors (tetrapyrrole/chromophore linkage, red/far-red phototransduction) and transcriptional regulation, with cross-talk to ethylene and cytokinin signaling, suggesting a cluster of light-sensing proteins that regulate gene expression in plants.","confidence":"High","size":24,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000160","count":23},{"id":"GO:0006351","count":23},{"id":"GO:0009584","count":22},{"id":"GO:0018298","count":22},{"id":"GO:0017006","count":22}]},{"hash":"560853882230911329","title":"Unknown","description":"The top GO terms span diverse and unrelated processes (cell size regulation, placenta development, glucose metabolism, transcription, chemotaxis, endosome transport, pseudohyphal growth, neural patterning) and there is no evident shared function or interaction pattern linking the proteins, so a cohesive, specific label cannot be drawn. ","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045793","count":22},{"id":"GO:0001890","count":22},{"id":"GO:0006006","count":22},{"id":"GO:0033160","count":22},{"id":"GO:0042220","count":22}]},{"hash":"1802274785338373716","title":"Stress-Responsive Trafficking and Development","description":"The top GO terms suggest a blend of intracellular transport regulation (Golgi-to-plasma membrane, early-to-late endosome transport), transcription (DNA-templated), and developmental signaling, alongside stress-related responses (toxic substances, ionomycin) and growth programs (pseudohyphal growth, multicellular development, Hedgehog-related signaling). This points to a cohesive theme where proteins coordinate trafficking and transcriptional responses in the context of stress and developmental processes, rather than a single isolated function.","confidence":"Medium","size":24,"edges":77,"triangles":59,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009636","count":7},{"id":"GO:0046827","count":7},{"id":"GO:0019233","count":7},{"id":"GO:0007275","count":7},{"id":"GO:0042997","count":7}]},{"hash":"513631130579632213","title":"Ion transport and cyclic nucleotide signaling in sensory pathways","description":"Proteins in this cluster show strong enrichment for potassium and sodium ion transport across membranes, and for signaling pathways involving cGMP and cAMP (including regulation of guanylyl cyclase). The inclusion of sensory perception of pain and aerotaxis suggests a role in sensory signal transduction and motility-driven responses, pointing to a common theme of membrane ion transport linked to cyclic nucleotide signaling underlying sensory and cellular signaling processes.","confidence":"Medium","size":24,"edges":15,"triangles":2,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071805","count":11},{"id":"GO:0019233","count":10},{"id":"GO:0007275","count":10},{"id":"GO:0098719","count":10},{"id":"GO:0071321","count":10}]},{"hash":"387218571759770544","title":"Transcriptional Regulation and Neuronal Development","description":"The GO terms show strong enrichment for DNA-templated transcription and its regulation, along with brain and spinal cord development and hypoxia detection, suggesting a core role in transcriptional control during neural development. The presence of rRNA maturation, DNA repair, chromatid cohesion, and histone methylation terms indicates accompanying genome-maintenance processes often linked to developmental regulation and chromatin state. Overall, the cluster seems centered on transcriptional control in neural development, with related genome maintenance activities.","confidence":"Medium","size":24,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006355","count":3},{"id":"GO:0070483","count":3},{"id":"GO:0035544","count":2},{"id":"GO:0021510","count":2}]},{"hash":"14137408224738052","title":"Ribosome Biogenesis and Translation Initiation","description":"This cluster is dominated by GO terms related to ribosome biogenesis and translation: maturation of 5.8S and LSU rRNA, formation of the translation preinitiation complex, and RNA guanine-N7 methylation, plus associated regulation of GTPase activity and SCF-ubiquitin\u2013proteasome\u2013dependent protein turnover that can tie into ribosome assembly quality control. Some terms (retina development, defense against Gram-positive bacteria, IL-6/NF-kappaB regulation) are less coherent with the core theme, suggesting some functional noise, but the main signal points to ribosome biogenesis and translation regulation.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032715","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0060041","count":2},{"id":"GO:0000466","count":2}]},{"hash":"1991933401052742699","title":"Unknown","description":"The Top Terms are highly diverse, spanning telomere-related and chromatin processes (nucleosome assembly, G-quadruplex DNA, histone deubiquitination) as well as signaling and stress responses (cytokinin signaling, osmotic stress, cell wall biogenesis). With no edges or clear cohesive function linking these terms, there isn\u2019t a single interpretable theme to label the cluster confidently.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061820","count":1},{"id":"GO:0009736","count":1},{"id":"GO:1901347","count":1},{"id":"GO:0072362","count":1},{"id":"GO:0006334","count":1}]},{"hash":"1373257212305085522","title":"Peroxisomal protein import and ubiquitin-proteasome turnover","description":"The top GO terms cluster around peroxisomal matrix protein import and receptor recycling, indicating a focus on peroxisome targeting machinery. Coupled with multiple ubiquitin-related pathways (SCF-dependent ubiquitination, K48-linked ubiquitination, autoubiquitination, and proteasomal degradation), the dominant theme appears to be ubiquitin-mediated regulation of peroxisomal proteins and general protein turnover. Some viral and DNA repair terms may reflect broader ubiquitin signaling connections, but the core represents peroxisome import linked to proteasomal degradation.","confidence":"Medium","size":24,"edges":97,"triangles":256,"max_degree":14,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0016558","count":13},{"id":"GO:0030433","count":13},{"id":"GO:0051301","count":12},{"id":"GO:0016562","count":12},{"id":"GO:0070987","count":12}]},{"hash":"1241349184709070512","title":"ER-Golgi proteostasis and antigen processing","description":"This cluster centers on protein handling in the secretory pathway and ubiquitin-dependent degradation: ER-Golgi vesicle transport, ERAD/ubiquitin-proteasome activity, and SCF-mediated proteolysis. The presence of translation-related terms and cilium assembly suggests broader cellular housekeeping, but the recurrent immune-associated terms (defense response to Gram-positive bacteria and dendritic cell cytokine regulation) point to a link with antigen processing and immune signaling through proteostasis. Overall, the shared theme appears to be protein quality control in the ER-Golgi axis coupled with immune processing pathways.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050830","count":4},{"id":"GO:0006890","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0001731","count":3}]},{"hash":"2259563613139677259","title":"Translation Initiation and Ribosome Biogenesis","description":"Most terms center on translation initiation, reinitiation, and ribosome biogenesis, pointing to proteins involved in protein synthesis and ribosome assembly. A few terms (brain development, transcription) are broader annotations and less central but do not override the main theme. Thus, Translation Initiation and Ribosome Biogenesis is a concise, representative label.","confidence":"Medium","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0038028","count":2},{"id":"GO:0071276","count":2}]},{"hash":"1690826693096258556","title":"Ribosome Biogenesis and RNA Transcription","description":"Most enriched terms point to ribosome biogenesis and export of the large ribosomal subunit from the nucleus, indicating a module related to ribosome assembly. Additional signals come from RNA transcription processes (RNA-templated transcription, tRNA transcription by RNA polymerase III, and RNA polymerase II\u2013related activity), suggesting a broader RNA production/processing role in the same nuclear context. Some terms are obsolete or appear as noise, and a single outlier relates to hematopoietic stem cell homeostasis, which likely reflects annotation noise rather than a core shared function. ","confidence":"Medium","size":24,"edges":15,"triangles":0,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:2000616","count":2},{"id":"GO:0008284","count":2},{"id":"GO:0051573","count":2},{"id":"GO:0000055","count":2}]},{"hash":"26052115325325884","title":"Ion transport and membrane potential regulation (K+/Na+)","description":"The top GO terms cluster around maintaining and restoring membrane potential (resting potential regulation, membrane stabilization, and cardiac repolarization) and involve potassium and sodium ion transport/homeostasis, pointing to ion-channel\u2013mediated control of cellular excitability. Additional signaling terms (cAMP/cGMP responses) likely reflect modulation rather than core function, reinforcing a cohesive theme of ion transport shaping membrane potential.","confidence":"High","size":24,"edges":212,"triangles":973,"max_degree":23,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060075","count":21},{"id":"GO:0098914","count":21},{"id":"GO:0030322","count":21},{"id":"GO:0050976","count":21},{"id":"GO:0071805","count":21}]},{"hash":"553292480241787088","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0006296","count":2},{"id":"GO:0046621","count":2},{"id":"GO:0070911","count":2},{"id":"GO:0016567","count":2}]},{"hash":"1366414865612665857","title":"Developmental transcription regulation and RNA methylation","description":"Top GO terms indicate developmental processes (brain, retina, forebrain, male gonad development) and transcriptional control (RNA polymerase II activity and negative regulation), with RNA guanine-N7 methylation also represented. This suggests a cluster of proteins involved in developmental gene regulation and RNA modification rather than a single pathway. The absence of edges does not negate a shared functional theme among these terms.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0036265","count":3},{"id":"GO:0000122","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0060041","count":2}]},{"hash":"56469103418114993","title":"Chromatin regulation and translation","description":"These proteins cluster around gene-expression control, spanning chromatin-level regulation (histone methylation) and transcription, through ribosome maturation and translation, to mRNA export and ubiquitin-related regulation. The common theme is regulation of gene expression from chromatin state to protein synthesis, with some stress/defense signaling context.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0034729","count":3},{"id":"GO:0051568","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0000463","count":3}]},{"hash":"331426504327348340","title":"Nuclear stress response and ubiquitin signaling","description":"The top terms cluster around regulation of nuclear processes under stress and during cell cycle progression, including heat-stress\u2013related mRNA export and splicing, chromatin assembly (CENP-A), and checkpoint control. They are complemented by ubiquitin-related processes (polyubiquitination and E3 ligase activity), suggesting a theme of protein turnover and chromatin/ gene-expression regulation in response to stress and cell-cycle cues. Some inflammatory and signaling terms appear as less central outliers. ","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007584","count":2},{"id":"GO:2000728","count":1},{"id":"GO:1904668","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0061641","count":1}]},{"hash":"1765706932536785641","title":"Cell-Cycle Regulation and Nuclear Transcription","description":"Top GO terms point to cell-cycle control (G1/S and G2/M transitions), mitotic spindle regulation, CDK activity, and DNA-templated transcription, with related nuclear processes such as protein export, reflecting coordinated epithelial proliferation.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0046827","count":3},{"id":"GO:0010696","count":2},{"id":"GO:0033598","count":2},{"id":"GO:0045737","count":2}]},{"hash":"1068389145334347832","title":"Aromatic compound degradation","description":"GO terms are dominated by catabolic processes targeting aromatic and related xenobiotic substrates (beta-ketoadipate pathway, stilbene and 3-phenylpropionate catabolism, uracil catabolic process), plus a general response to toxic substances. This points to a shared function in breaking down aromatic compounds rather than synthesis; the antibiotic biosynthetic term is less consistent with the main theme.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009636","count":8},{"id":"GO:0055114","count":8},{"id":"GO:0017000","count":8},{"id":"GO:0042952","count":7},{"id":"GO:0046272","count":7}]},{"hash":"1244395924280712205","title":"Neural stress response and development","description":"The GO terms point to brain development and glial apoptotic processes, coupled with inflammatory signaling and stress-related RNA processing and ubiquitination pathways, suggesting a cluster tied to neural development with stress-response mechanisms rather than a single, narrow function.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000728","count":2},{"id":"GO:1904668","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0061641","count":2},{"id":"GO:0002534","count":2}]},{"hash":"2025787730786747673","title":"Sphingolipid and Ceramide Biosynthesis","description":"The GO terms are dominated by sphingolipid and ceramide biosynthetic processes (sphingomyelin biosynthesis, ceramide biosynthesis, ceramide phosphoethanolamine biosynthesis) and regulation of ceramide synthesis, indicating a cohesive cluster centered on sphingolipid metabolism. Related signaling terms (apoptotic signaling, TNF signaling, responses to LPS) reflect ceramide\u2019s role in stress and immune signaling, reinforcing the lipid-derivative signaling theme despite some broader terms. Overall, the pattern points to a dedicated lipid metabolism and ceramide-mediated signaling cluster.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006686","count":2},{"id":"GO:0046513","count":2},{"id":"GO:0046335","count":2},{"id":"GO:0060305","count":2},{"id":"GO:1905373","count":2}]},{"hash":"748511455943295732","title":"Neural development and synaptic signaling","description":"The proteins show enrichment for nervous system development, negative regulation of synaptic plasticity, visual perception, and glutamatergic synaptic transmission, pointing to a core theme of neuronal development and synaptic function. A few terms (apoptotic process, protein ubiquitination) are present but less central to the cluster\u2019s\u4e3b theme.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":2},{"id":"GO:0031914","count":2},{"id":"GO:0007519","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0033138","count":2}]},{"hash":"88041521800483507","title":"Neural gene expression and chromatin regulation under stress","description":"This cluster aggregates proteins involved in neural development and stress-responsive regulation of RNA processing and chromatin structure (mRNA export, splicing, CENP-A chromatin assembly), with supporting roles for ubiquitination and cell-cycle control, plus neural-specific processes like glial apoptosis and brain development. The combination suggests a coordinated neural response where transcriptional/post-transcriptional regulation, chromatin dynamics, and proteostasis interplay during stress and development.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000728","count":2},{"id":"GO:1904668","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0061641","count":2},{"id":"GO:0002534","count":2}]},{"hash":"1511878518237259808","title":"Meiosis and Germ Cell DNA Repair","description":"This cluster is dominated by GO terms tied to meiotic recombination and DNA repair in germ cells, including DSB repair, repair of cross-links, NHEJ, meiotic gene conversion, and cell-cycle regulation, all characteristic of meiotic genome maintenance. A few terms like oxidative phosphorylation and IgA isotype switching appear but are likely secondary annotations; overall the proteins appear to participate in meiotic processes and germ-cell development.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006119","count":3},{"id":"GO:0007281","count":3},{"id":"GO:0061500","count":3},{"id":"GO:0006311","count":3},{"id":"GO:0006302","count":3}]},{"hash":"2176348818804552088","title":"Planar polarity and tissue morphogenesis","description":"The top GO terms cluster around developmental processes: head morphogenesis, neural tube patterning, eye pigmentation, imaginal disc wing hair orientation, planar polarity establishment, and PCP-related protein localization, with Wnt signaling regulation also fitting this context. Although a few terms like angiotensin maturation and short-term memory are less directly connected, the dominant theme is coordinated tissue morphogenesis guided by planar polarity cues. Therefore, the label Planar polarity and tissue morphogenesis captures the core function of this cluster.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002003","count":3},{"id":"GO:0030177","count":3},{"id":"GO:0048069","count":3},{"id":"GO:0007614","count":3},{"id":"GO:0060323","count":3}]},{"hash":"353917714954566690","title":"Telomere-associated chromatin remodeling","description":"The top GO terms cluster around telomere biology and chromatin dynamics: telomeric D-loop disassembly, nucleosome assembly, chromatin remodeling, G-quadruplex DNA formation, and histone H2A deubiquitination\u2014all pointing to chromatin regulation at telomeres. While there are some plant-specific terms (cytokinin signaling, secondary cell wall biogenesis), the dominant theme is chromatin structure and telomere maintenance, suggesting these proteins function together in telomere-associated chromatin remodeling.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0061820","count":4},{"id":"GO:0043044","count":4},{"id":"GO:0009736","count":3},{"id":"GO:1901347","count":3},{"id":"GO:0072362","count":3}]},{"hash":"1972795714693108812","title":"Muscle-energy metabolism and NMJ regulation","description":"This cluster is enriched for mitochondrial membrane potential regulation, insulin response, lipid metabolism (lipid droplets, adipose development), and neuromuscular processes including NMJ regulation, with additional signals related to peroxisome inheritance and BMP pathway modulation, suggesting a theme of coordinated energy metabolism and neuromuscular signaling in muscle/adipose contexts.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051881","count":7},{"id":"GO:0032869","count":4},{"id":"GO:0045033","count":4},{"id":"GO:0050905","count":4},{"id":"GO:0034389","count":4}]},{"hash":"144203037171180910","title":"Neural development and mitosis","description":"This cluster centers on neurodevelopmental processes (forebrain development, neural tube closure) and core cell-cycle activities (cell division, mitotic cell cycle, spindle orientation), suggesting a link between neuronal development and regulated mitosis. While there are a few stress or immune-related terms present, the strongest and most frequent signals are developmental and cell-division related, making this a coherent theme for the cluster.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0001843","count":2},{"id":"GO:0050830","count":2}]},{"hash":"358735751950700683","title":"Hypoxia-Related Signaling and Cell-Cycle Regulation","description":"The top GO terms cluster around cellular response to hypoxia, regulation of protein phosphorylation (including kinase activity and autophosphorylation), and mitotic cell cycle processes, with additional hints from mRNA transport and chromatin-associated activities. This pattern suggests a broad stress-induced signaling module that impacts phosphorylation networks and cell-cycle control, rather than a single, tightly defined pathway. Given the dispersed terms and lack of interaction data, the label is plausible but not definitive.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071456","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0071902","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0000278","count":2}]},{"hash":"74641927733541683","title":"Transcription Regulation and Endosome Trafficking","description":"Genes in this cluster point to chromatin-level control of gene expression (histone methylation and transcription regulation) alongside endosomal trafficking activities (receptor recycling and regulation of endosome size), with a neuronal context suggested by glutamatergic synaptic transmission. This combination suggests a functional grouping where transcriptional regulation is linked to membrane trafficking in neurons, rather than a single linear pathway.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0034968","count":5},{"id":"GO:0001881","count":5},{"id":"GO:0006355","count":5},{"id":"GO:0051036","count":5},{"id":"GO:0035023","count":5}]},{"hash":"1023508808033454896","title":"Chemokine Production and Cytoskeletal Dynamics","description":"The top GO terms show clear signals of chemokine production regulation (MIP-1\u03b1 and CCL5), pointing to immune signaling. Other terms emphasize cytoskeletal and cell organization processes (actin bundle assembly, spindle assembly, membrane localization, polarity), suggesting a cluster that links immune signaling with cytoskeletal dynamics and cell structure. Confidence: Medium","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071642","count":4},{"id":"GO:1901594","count":4},{"id":"GO:0086070","count":4},{"id":"GO:0071651","count":4},{"id":"GO:0090162","count":4}]},{"hash":"917867385915205827","title":"Epigenetic transcription regulation and chromatin modification","description":"This cluster centers on gene expression control through chromatin state and transcription machinery, dominated by DNA-templated transcription and histone modification terms. The co-occurrence of histone methylation/deacetylation and mRNA processing supports an epigenetic regulation theme, with additional hints of protein oligomerization and cell proliferation roles.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0051568","count":4},{"id":"GO:0006397","count":4},{"id":"GO:0051260","count":3},{"id":"GO:0051301","count":3}]},{"hash":"2003119252919581466","title":"DNA replication and genome maintenance","description":"The top GO terms are dominated by DNA replication and genome maintenance processes\u2014such as removal of RNA primers, Okazaki fragment processing, replication checkpoint signaling, telomere maintenance, and mitochondrial DNA repair\u2014suggesting this cluster comprises proteins involved in replication and safeguarding genome integrity.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000733","count":1},{"id":"GO:0000184","count":1},{"id":"GO:1902990","count":1},{"id":"GO:0043137","count":1},{"id":"GO:0033567","count":1}]},{"hash":"1173947305710394532","title":"Cardiac Sarcomere Organization and Signaling","description":"The top GO terms point to heart muscle structure and function, including sarcomere organization, cardiac muscle cell proliferation, membrane potential regulation, sodium ion import, and cAMP signaling pathways. While there are a couple of terms related to antipsychotic drug responses, the strongest, most coherent theme across the cluster is cardiac muscle architecture and its associated signaling. This justifies a label focused on cardiac sarcomere organization and signaling.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045214","count":3},{"id":"GO:2000480","count":2},{"id":"GO:0098719","count":2},{"id":"GO:0071320","count":2},{"id":"GO:0097332","count":2}]},{"hash":"622020370239342968","title":"Synaptic vesicle maturation and neurotransmitter release","description":"These proteins strongly link to neuronal synaptic function: synaptic vesicle maturation, presynaptic dense core vesicle exocytosis, and neurotransmitter secretion dominate the top GO terms, pointing to a cluster of proteins involved in vesicle trafficking and release at synapses. Brain development is also reflected, supporting a neuronal-context role, while lysosome localization and transcription term hints are likely peripheral. ","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016188","count":2},{"id":"GO:0007269","count":2},{"id":"GO:0099525","count":2},{"id":"GO:0051291","count":2},{"id":"GO:0007420","count":2}]},{"hash":"190755086834842121","title":"Actin-based protrusions and membrane trafficking","description":"This cluster shows strong signals for actin-driven structures (filopodium and microspike assembly) together with endomembrane system organization, Golgi regulation, pinocytosis, and PI5P metabolism, indicating coordinated cytoskeletal remodeling with membrane trafficking processes.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0007183","count":1},{"id":"GO:0010256","count":1},{"id":"GO:1904562","count":1},{"id":"GO:0030035","count":1}]},{"hash":"1879621672236005486","title":"Genome maintenance and ER stress","description":"The cluster highlights genome maintenance features (DNA repair: single-strand break repair; DNA ligation in recombination; attachment of DSBs to the nuclear envelope) alongside ER stress signaling (unfolded protein response) and cell-cycle regulation (CDK activity). The viral-host interaction terms and vasculogenesis appear less central and may reflect broader or cross-tutting processes. Overall, a cohesive theme around genome integrity and proteostasis/cell-cycle coordination fits best.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990683","count":2},{"id":"GO:0045737","count":2},{"id":"GO:0030968","count":2},{"id":"GO:0044828","count":2},{"id":"GO:0044829","count":2}]},{"hash":"2155314365089462799","title":"Eye and retina development with ciliary signaling","description":"The top GO terms converge on eye/retina ontologies (embryonic camera-type eye development, retina development, photoreceptor cell maintenance) and ciliary functions (receptor localization to non-motile cilium), with additional neural patterning and head morphogenesis terms that fit a broader ocular/neural developmental program. This suggests proteins in this cluster are involved in eye/retina formation and related ciliary signaling pathways.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061548","count":1},{"id":"GO:0097500","count":1},{"id":"GO:1901621","count":1},{"id":"GO:0045494","count":1},{"id":"GO:0021914","count":1}]},{"hash":"1901106809254381444","title":"Negative Regulation of Signaling Pathways and Synaptic Organization","description":"The cluster is enriched for GO terms involving negative regulation of multiple signaling cascades (MAPK/ERK, PI3K/AKT, TCR signaling) and processes related to synaptic structure (postsynaptic density assembly, synaptic vesicle clustering) as well as cytoskeletal/cell-adhesion regulation, suggesting proteins that broadly suppress or modulate signaling and synaptic/cytoskeletal organization rather than a single pathway.","confidence":"Medium","size":23,"edges":253,"triangles":1771,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0034501","count":21},{"id":"GO:0045736","count":21},{"id":"GO:0050860","count":21},{"id":"GO:0000200","count":21},{"id":"GO:0070373","count":21}]},{"hash":"1501172079034233561","title":"Stress-Responsive Transcription and Redox Regulation","description":"The top GO terms cluster around transcriptional control (DNA-templated transcription), stress responses (endoplasmic reticulum stress), and redox maintenance (oxidant detoxification, redox homeostasis), with additional signals related to insulin response and growth. This suggests a coordinated program where transcription is modulated under metabolic and cellular stress conditions, integrating NF-kappaB signaling regulation and metabolic cues. Overall, the proteins likely participate in managing cellular stress while linking metabolic signals to transcriptional outputs. ","confidence":"Medium","size":23,"edges":30,"triangles":9,"max_degree":22,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043124","count":6},{"id":"GO:0032869","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0098869","count":5},{"id":"GO:0045454","count":5}]},{"hash":"1064722404623940390","title":"Actin Cytoskeleton Dynamics and Organelle Inheritance","description":"The set of GO terms centers on actin-based structures (cortical patches, contractile rings, sarcomere organization) and inheritance processes (mitochondria, vacuoles), with additional cell polarity context. This points to a cohesive theme of cytoskeletal organization driving organelle inheritance and cell shape, hence the chosen label.","confidence":"High","size":23,"edges":18,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0071963","count":3},{"id":"GO:0061587","count":3},{"id":"GO:0000147","count":2},{"id":"GO:1903475","count":2},{"id":"GO:0000011","count":2}]},{"hash":"561339220368432820","title":"Neuronal Development and Endosomal Trafficking","description":"This cluster blends neural development signals (cerebellar cortex development, dopaminergic synaptic transmission, neural tube patterning) with intracellular trafficking processes (regulation of endosome transport) and autophagy/xenophagy, suggesting a core theme where endosomal and autophagic pathways influence neural development and signaling. Some terms (pseudohyphal growth, cartilage condensation) reflect broader developmental contexts and may involve shared regulatory components rather than a single tissue-specific function.","confidence":"Medium","size":23,"edges":82,"triangles":65,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":23},{"id":"GO:0007124","count":23},{"id":"GO:1901621","count":23},{"id":"GO:1904637","count":23},{"id":"GO:0001963","count":23}]},{"hash":"943342160412709689","title":"Developmental signaling and cell fate specification","description":"The cluster shows enrichment for developmental cell fate terms (endodermal and glial fate determination), maintenance of organ identity, and growth/EMT-related signaling (Wnt pathway\u2013linked EMT regulation, mesenchymal proliferation, anisotropic growth), suggesting a cohesive role in embryonic development and tissue patterning rather than a single molecular function.","confidence":"High","size":23,"edges":253,"triangles":1771,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0006607","count":7},{"id":"GO:0043547","count":7},{"id":"GO:0060916","count":6},{"id":"GO:0044334","count":6},{"id":"GO:0007403","count":6}]},{"hash":"1415208344686257801","title":"Meiosis and Chromosome Condensation","description":"The top GO terms cluster around meiosis-specific chromosome behavior and structure, including chromosome condensation and separation, synaptonemal complex assembly, and regulation of meiotic DSB formation, along with related gametogenesis processes like microsporogenesis and plant-specific organelle organization. This suggests a function in meiotic chromosome organization during gamete formation, rather than general mitotic division. ","confidence":"High","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0030466","count":4},{"id":"GO:0051307","count":4},{"id":"GO:0007076","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0043007","count":4}]},{"hash":"705575943692206465","title":"Unknown","description":"The GO terms are scattered across regulatory processes (kinetochore assembly, chromatin binding, protein modification) and various developmental contexts (labyrinthine and spongiotrophoblast layers, erythrocyte differentiation) with no coherent shared function. There are no edges among the proteins, suggesting little direct interaction within the cluster, so a single representative function cannot be confidently assigned.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090234","count":1},{"id":"GO:0060711","count":1},{"id":"GO:0016926","count":1},{"id":"GO:1904333","count":1},{"id":"GO:0035562","count":1}]},{"hash":"736298748525176306","title":"Mitotic regulation and developmental morphogenesis","description":"The cluster shows signals for cell cycle control (G1/S transition, re-entry into mitosis) alongside broad morphogenesis-related processes (axonogenesis, synapse assembly, cell morphogenesis, mammary gland duct branching) and transcription. This pattern suggests proteins involved in coordinating cell division with developmental/neuronal differentiation and tissue morphogenesis, rather than a single pathway. ","confidence":"Medium","size":23,"edges":185,"triangles":727,"max_degree":22,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000082","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0000320","count":2},{"id":"GO:0046827","count":2},{"id":"GO:0007409","count":2}]},{"hash":"1695080495112750825","title":"Regulation of apoptosis, development, and ubiquitination","description":"This cluster centers on regulatory processes across multiple layers: apoptotic signaling, multicellular development, ubiquitin-mediated protein regulation, cell cycle checkpoints, and RNA processing/chromatin dynamics. The GO terms point to a broad regulatory network that coordinates stress responses with development and protein turnover, rather than a single linear pathway.","confidence":"Medium","size":23,"edges":7,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2001235","count":2},{"id":"GO:0007275","count":2},{"id":"GO:2000728","count":1},{"id":"GO:1904668","count":1},{"id":"GO:0050773","count":1}]},{"hash":"442729465490853542","title":"Unknown","description":"The top GO terms span cardiac muscle function, muscle regulation, and cytoskeletal processes, but also kidney development and neural memory regulation, with no single cohesive theme tying all proteins together. This mix makes a concise, representative label unreliable.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051281","count":6},{"id":"GO:0051764","count":5},{"id":"GO:0055003","count":5},{"id":"GO:0010459","count":5},{"id":"GO:0007616","count":5}]},{"hash":"1204885282414721014","title":"Prostate development and steroid signaling","description":"The dominant GO terms are male sex differentiation, prostate gland development, and steroid hormone receptor complex assembly, pointing to a coherent theme of steroid-regulated male reproductive development. Peripheral terms such as regulation of gluconeogenesis, ubiquitination, and unfolded protein response exist but do not contradict this main theme.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0046661","count":8},{"id":"GO:0006463","count":8},{"id":"GO:0090526","count":8},{"id":"GO:0030850","count":8},{"id":"GO:1903071","count":7}]},{"hash":"2086499715116016383","title":"Dopaminergic Neuron Signaling and Axonogenesis","description":"This cluster centers on neuronal processes, with prominent terms for dopaminergic synaptic transmission and CNS projection neuron axonogenesis, indicating a theme of neuronal signaling and axon development. Endosomal transport and broad signal transduction terms provide supporting cellular machinery; a few outlier terms appear due to annotation noise.","confidence":"Medium","size":23,"edges":89,"triangles":129,"max_degree":19,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":22},{"id":"GO:0007124","count":22},{"id":"GO:1901621","count":22},{"id":"GO:1904637","count":22},{"id":"GO:0001963","count":22}]},{"hash":"1669265555226360839","title":"GTPase-Regulated Vesicle Trafficking","description":"Enriched terms point to vesicle trafficking and GTPase signaling, notably COPII-coated vesicle budding and both positive and negative regulation of GTPase activity, which couple to TORC1 signaling and growth-related processes such as the cell cycle and mitosis. This suggests a cohesive theme around small GTPase\u2013driven trafficking and growth control, with some developmental terms reflecting broader signaling roles.","confidence":"High","size":23,"edges":8,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007420","count":4},{"id":"GO:0045453","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0090114","count":3},{"id":"GO:0034260","count":3}]},{"hash":"604726987210605795","title":"Ubiquitin-Dependent Proteostasis and Antiviral Defense","description":"The cluster is dominated by ubiquitin-related processes (protein autoubiquitination, ubiquitin-dependent ERAD, ubiquitin-dependent protein catabolic process) and immune/virostatic responses (innate immune response, defense against virus, TNF signaling). Aggresome assembly also points to ubiquitin-driven protein quality control. Taken together, these proteins likely coordinate proteostasis via ubiquitin pathways with antiviral/immune signaling.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":7},{"id":"GO:0030433","count":7},{"id":"GO:1903265","count":6},{"id":"GO:1901253","count":5},{"id":"GO:1903762","count":5}]},{"hash":"648384927178289918","title":"Mitochondrial metabolism and nutrient transport","description":"The terms cluster around mitochondrial nutrient handling and energy metabolism, such as iron import into mitochondrion, NAD transmembrane transport, and adaptive thermogenesis, with additional signals of nutrient sensing (amino acid starvation, fatty acid response) and stress adaptation. A few terms (e.g., cytokinin signaling) are less aligned but do not override the dominant mitochondrial metabolism theme.","confidence":"High","size":23,"edges":23,"triangles":4,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0034198","count":12},{"id":"GO:0097421","count":10},{"id":"GO:0009736","count":7},{"id":"GO:1990845","count":7},{"id":"GO:0060546","count":7}]},{"hash":"305722483220504505","title":"DNA damage response and stress signaling","description":"This cluster centers on cellular stress responses and DNA damage-related regulation. Several prominent GO terms point to stress responses (to arsenite, cadmium, nitroglycerin, gamma radiation) and to regulation of DNA double-strand break repair via nonhomologous end joining, complemented by transcriptional control (DNA-templated transcription) and chromatin modification (histone demethylation). A few terms about peroxisomal protein import and ubiquitin-dependent ERAD reflect broader cellular quality-control and stress-related processes, making the theme broadly \u201cstress response with DNA repair/transcription regulation.\u201d ","confidence":"Medium","size":23,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:1903936","count":3},{"id":"GO:2001033","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0030433","count":3}]},{"hash":"310725101736496123","title":"Neuronal development and transcription","description":"In this cluster, multiple top GO terms point to neuronal biology and gene regulation, notably CNS neuron development and dendrite morphogenesis, along with DNA-templated transcription. The presence of an amphetamine response further supports a CNS-related function. Outliers like lactation and lipid metabolism terms likely reflect annotation noise or multi-functional proteins. Overall, the core signal is neuronal differentiation and transcriptional control, justifying the label.","confidence":"High","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0001975","count":3},{"id":"GO:0021954","count":3},{"id":"GO:0048813","count":3},{"id":"GO:0007595","count":3}]},{"hash":"1530954750249080157","title":"Deubiquitinase-Driven Signaling Regulators","description":"This cluster is dominated by GO terms relating to deubiquitination (monoubiquitinated protein deubiquitination; H2A K63-linked deubiquitination; K11-linked deubiquitination) and signaling pathways (NF-kappaB, TGF-beta/SMAD). The pattern suggests proteins that regulate signaling by removing ubiquitin, affecting transcriptional and developmental signaling. Some terms (heart development, meristem identity, photosystem) may reflect broader or context-specific roles of ubiquitin-mediated regulation. Overall, the data point to a cohesive theme of deubiquitinase-associated modulation of signaling networks, hence the label.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0007507","count":4},{"id":"GO:0035520","count":4},{"id":"GO:0070537","count":4},{"id":"GO:0035871","count":4},{"id":"GO:0042347","count":3}]},{"hash":"491462197513063480","title":"Calcium-driven vesicle trafficking and neuronal remodeling","description":"The GO terms cluster around calcium signaling (cellular response to calcium, calcium ion\u2013regulated lysosome exocytosis), vesicle trafficking (intracellular protein transport, lysosome exocytosis), and neuronal growth (positive regulation of dendrite extension). Membrane synthesis (phosphatidylethanolamine biosynthesis) supports vesicle/membrane dynamics, consistent with a calcium-dependent trafficking and neuronal remodeling theme. Some terms relate to neural/glial regulation, but the dominant signal is calcium\u2011linked trafficking and neuronal morphology.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006886","count":2},{"id":"GO:1990927","count":1},{"id":"GO:2000235","count":1},{"id":"GO:0034351","count":1},{"id":"GO:0002692","count":1}]},{"hash":"628494502043956830","title":"MAPK Signaling and Immune Response","description":"The enriched GO terms center on MAPK pathway cascades (p38 and ERK) and cellular responses to immune-related stimuli such as GM-CSF and PMA, pointing to MAPK-driven signaling in immune contexts. Transcriptional regulation terms alongside these cascades suggest coordinated gene expression changes. A cornea development term is present but the dominant theme is MAPK signaling linked to immune or inflammatory responses.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000288","count":2},{"id":"GO:0038066","count":2},{"id":"GO:0070371","count":2},{"id":"GO:0097011","count":2},{"id":"GO:1904628","count":2}]},{"hash":"1734692575839949533","title":"Chromatin remodeling and mitosis","description":"The top GO terms center on chromatin remodeling, transcription, and mitotic processes (chromosome condensation, spindle assembly), indicating a primary theme of nuclear gene regulation and chromosome dynamics during cell division. A few terms relate to broader nuclear differentiation or membrane trafficking, but they are less represented, so the dominant signal is chromatin and mitosis.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":2},{"id":"GO:0007289","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0043044","count":2},{"id":"GO:0006366","count":2}]},{"hash":"1582678991993318097","title":"Brain development and neuronal metabolism","description":"The top GO terms point to brain development (substantia nigra and cerebellum development) with additional neuron-related functions such as intracellular chloride ion homeostasis and creatine/phosphocreatine metabolism, suggesting a cluster tied to neural development and neuronal energy maintenance. While ribosome biogenesis and rRNA processing appear, the strongest signal centers on neural development and metabolism.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021762","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0006364","count":1},{"id":"GO:0042273","count":1},{"id":"GO:0000280","count":1}]},{"hash":"1644394068073139065","title":"Ribosome biogenesis and translation","description":"The top terms are dominated by translation and ribosome biogenesis/assembly processes (translation; ribosome biogenesis; ribosomal subunit biogenesis; cytoplasmic translation; export of the large subunit), indicating these proteins function together in ribosome production and protein synthesis. A few immune-related terms appear but are much less represented and do not define the cluster.","confidence":"High","size":23,"edges":44,"triangles":37,"max_degree":15,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":17},{"id":"GO:0042254","count":9},{"id":"GO:0042273","count":4},{"id":"GO:0002181","count":4},{"id":"GO:0000055","count":4}]},{"hash":"59523648961759706","title":"Neuron development with mitochondrial and transcription regulation","description":"The cluster centers on neuron development while also showing strong signals for mitochondrial functions (membrane permeability regulation, matrix protein import) and transcriptional control (negative regulation of RNA polymerase II). This combination suggests neural development shaped by mitochondrial activity and gene expression regulation, justifying a label that highlights these interconnected themes.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0061086","count":3},{"id":"GO:0048666","count":3},{"id":"GO:0046902","count":3},{"id":"GO:2000134","count":3}]},{"hash":"884221807682262528","title":"Mitotic spindle and ER-Golgi transport","description":"The cluster shows strong representation of mitosis-related terms (cell division, mitotic spindle assembly, mitotic cell cycle) alongside ER-Golgi trafficking (COPII-coated vesicle budding, ER-to-Golgi and Golgi-to-ER transport). This suggests proteins involved in both cell division machinery and the secretory pathway, potentially coordinating growth and proliferation in developing tissues (brain development, multicellular organism growth). The combination indicates a cohesive theme around cellular proliferation with vesicle trafficking.","confidence":"Medium","size":23,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090114","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0000278","count":2}]},{"hash":"1320257457854759415","title":"Transcription Regulation and cAMP Signaling","description":"The dominant GO terms point to transcriptional control in the nucleus (DNA-templated transcription, export from the nucleus), while several terms implicate cAMP pathways and membrane excitability (cAMP response, regulation of membrane potential, PKA activity), plus developmental processes like neural tube closure and cardiac muscle proliferation. This pattern suggests a cluster of proteins that link gene expression regulation to cAMP-dependent signaling and related cellular excitability, rather than a single, narrow function.","confidence":"Medium","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0001843","count":4},{"id":"GO:2000480","count":3},{"id":"GO:0098719","count":3}]},{"hash":"1054839809754171142","title":"Membrane Transporters for Ions and Metabolites","description":"The top GO terms are dominated by various transmembrane transport activities across different substrates (nitrate, nitrite, arabinose, vitamins, xenobiotics, sodium, potassium, etc.), pointing to a cohesive group of membrane transporter proteins rather than a single pathway. Some terms like mitotic cell cycle appear, but the strongest signal is broad membrane transport function for ions and metabolites. The lack of edges does not undermine the functional coherence of a transporter-focused cluster.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0035725","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0042891","count":2}]},{"hash":"1979611909204543290","title":"Mechanosensory signaling and neuronal excitability","description":"This cluster shows strong enrichment for sensory perception of pain and detection of mechanical stimuli (touch), plus potassium ion transport and membrane potential regulation, pointing to a shared function in mechanosensory signaling and control of cellular excitability (neural or cardiac). Some unrelated terms like transcription/export may be general cellular processes, but the core theme aligns with mechanosensation and ion homeostasis. ","confidence":"Medium","size":23,"edges":19,"triangles":2,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019233","count":19},{"id":"GO:0007275","count":19},{"id":"GO:0050976","count":17},{"id":"GO:0071805","count":17},{"id":"GO:0098914","count":17}]},{"hash":"1198590948812677068","title":"Unknown","description":"The cluster's terms span chromatin/DNA processes (nucleosome assembly, snRNA transcription, G-quadruplex formation, telomeric D-loop disassembly) and separate processes like vesicle docking, potassium ion transport, and plant signaling, with no clear unifying function. Therefore no coherent label; Unknown with None.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006334","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0043524","count":2},{"id":"GO:0006904","count":2},{"id":"GO:0061820","count":1}]},{"hash":"2285935172794713248","title":"Ubiquitin-Dependent Protein Degradation","description":"The cluster is clearly enriched for ubiquitin-related proteolysis terms, including ubiquitin-dependent protein catabolic process, autoubiquitination, and K48-linked ubiquitination, indicating a shared role in marking proteins for degradation. While a few other processes (e.g., peroxisomal import, histone catabolism, and growth regulation) appear, the predominant signal is ubiquitin-mediated protein turnover, suggesting this cluster centers on proteolytic regulation via ubiquitination.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042787","count":12},{"id":"GO:0051865","count":11},{"id":"GO:0070936","count":9},{"id":"GO:0030433","count":8},{"id":"GO:0046621","count":6}]},{"hash":"1194861086553792895","title":"Unknown","description":"The top terms cover a jumbled mix of transcriptional regulation, signaling, stress responses, and even bacterial motility and telomere assembly, with no single coherent function linking the cluster. This diversity suggests no clear shared function to name the cluster beyond Unknown.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":15},{"id":"GO:0009736","count":14},{"id":"GO:0006355","count":14},{"id":"GO:0071353","count":13},{"id":"GO:0006261","count":12}]},{"hash":"432930674848231602","title":"Chromatin remodeling and telomere maintenance","description":"The cluster's GO terms cluster around chromatin-related processes (nucleosome assembly, histone H2A deubiquitination, transcription regulation) and telomere biology (telomeric D-loop disassembly, telomere localization), with supporting themes in DNA structures (G-quadruplex) and snRNA transcription. This points to a cohesive role in chromatin organization and telomere maintenance, with transcriptional regulation as a broader linked function.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009736","count":11},{"id":"GO:0006355","count":7},{"id":"GO:0061820","count":7},{"id":"GO:1901347","count":7},{"id":"GO:0072362","count":7}]},{"hash":"238172341614432735","title":"Unknown","description":"The top GO terms span plant hormone signaling (cytokinin, ethylene), immune signaling (interleukin-4), xenobiotic response, and diverse nuclear processes (DNA replication, DNA topology, telomerase assembly), plus a bacterial motility term and hypoxia detection. This broad mix suggests no single cohesive biological function or pathway characterizes the cluster, and may reflect annotation noise or multi-function proteins rather than a unified cluster function.","confidence":"","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009736","count":6},{"id":"GO:0035690","count":4},{"id":"GO:0071353","count":4},{"id":"GO:0006261","count":3},{"id":"GO:0033160","count":3}]},{"hash":"1474201554560867627","title":"Phospho-signaling and cell cycle regulation","description":"Based on the top GO terms, this cluster centers on phosphorylation-driven signaling and regulation of growth: positive regulation of serine/threonine kinase activity, protein autophosphorylation, and GTPase activity regulation point to kinase- and switch-mediated signaling; mitotic cell cycle and positive regulation of cell proliferation indicate cell cycle control. Ubiquitination and mRNA transport fit within broader post-translational and RNA regulatory layers that modulate signaling outputs. A heart-specific term (regulation of SA node cell action potential) may reflect incidental annotation rather than a core theme.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007205","count":4},{"id":"GO:0071456","count":3},{"id":"GO:0051028","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0071902","count":3}]},{"hash":"1968572195224277387","title":"Transcriptional Regulation and Developmental Signaling","description":"A compact label reflecting the strong presence of transcription-related GO terms (negative regulation of transcription by RNA polymerase II; DNA-templated transcription) together with signaling and developmental processes (responses to hydrogen peroxide, IL-4, TGF-beta, Wnt regulation, chondrocyte differentiation in endochondral bone morphogenesis, and maintenance of cell polarity). This suggests a cluster of proteins that primarily govern transcriptional control with roles in developmental signaling and stress responses.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0070301","count":2},{"id":"GO:0071353","count":2},{"id":"GO:0071560","count":2}]},{"hash":"238909994517966393","title":"Seminiferous tubule development and histone acetylation","description":"The cluster centers on seminiferous tubule development and histone acetylation as recurring GO terms, suggesting a theme of testis-related chromatin regulation; while other terms touch on transcription regulation and stress responses, the strongest signals point to chromatin modification in a reproductive context.","confidence":"Medium","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0072520","count":2},{"id":"GO:0043982","count":2},{"id":"GO:0043966","count":2},{"id":"GO:0043981","count":2},{"id":"GO:0071447","count":1}]},{"hash":"448062106984183824","title":"Innate Immune Signaling and Chemokine Production","description":"These proteins show enrichment for NOD2 signaling, NF-\u03baB regulation, and chemokine production (e.g., MIP-1\u03b1/CCL3, CCL5), pointing to a theme of innate immune sensing and inflammatory signaling. While a few terms relate to cell cycle or polarity, the dominant GO terms center on bacterial recognition and inflammatory mediator production, supporting a cohesive functional theme for this cluster. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070431","count":3},{"id":"GO:0032088","count":3},{"id":"GO:0007049","count":3},{"id":"GO:0071642","count":2},{"id":"GO:1901594","count":2}]},{"hash":"939723653963957595","title":"Ubiquitin-Dependent Proteolysis and TNF Signaling","description":"The cluster is heavily enriched for ubiquitin-related processes (autoubiquitination and ubiquitin-dependent protein catabolic process), indicating a core role in protein degradation regulation. It also includes TNF-mediated signaling, NF-\u03baB-related regulation (I-kappaB phosphorylation), and JNK cascade modulation, pointing to inflammatory signaling functions. V(D)J recombination and histone catabolic processes further support immune regulation and chromatin remodeling. Overall, the proteins likely function together around ubiquitin-proteasome control and TNF/NF-\u03baB/JNK\u2013type signaling in immune contexts.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":14},{"id":"GO:0042787","count":12},{"id":"GO:1901253","count":12},{"id":"GO:1903762","count":12},{"id":"GO:1903265","count":11}]},{"hash":"1630979907449979013","title":"Unknown","description":"The GO terms include fibrinolysis and plasminogen activation, ECM-related secretion, insulin processing, neural differentiation, and deglutamylation, reflecting diverse, seemingly unrelated functions. With no edges or triangles and no clear shared pathway, there isn\u2019t a cohesive theme tying these proteins together. Confidence: None","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010757","count":1},{"id":"GO:0009408","count":1},{"id":"GO:0002002","count":1},{"id":"GO:0003331","count":1},{"id":"GO:2000346","count":1}]},{"hash":"590042671218721823","title":"Chromatin dynamics and cell cycle regulation","description":"The top terms cluster around chromatin assembly (CENP-A), DNA-templated transcription, and cell division, with supporting roles for proteasome regulatory particle assembly and poly-ADP-ribosylation, suggesting a nuclear program coordinating chromatin structure with transcription and cell-cycle progression. Some sensory-related terms seem incidental rather than core to the cluster.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0070682","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0006351","count":3},{"id":"GO:1901594","count":3}]},{"hash":"1789467900084173014","title":"ER Protein Folding and Redox Balance","description":"These terms cluster around protein maturation in the endoplasmic reticulum, including folding, deglycosylation, and prolyl hydroxylation, along with redox-related maintenance (oxidant detoxification and redox homeostasis). The rhodopsin biosynthetic process fits as a secretory pathway protein maturation example, while other terms (some obsolete or broad like viral process) are less specific. Overall, the cluster points to ER-associated protein processing and redox balance under stress.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006517","count":2},{"id":"GO:0016063","count":2},{"id":"GO:1903206","count":1},{"id":"GO:0034975","count":1},{"id":"GO:0055114","count":1}]},{"hash":"266769683838423157","title":"Endosome-Golgi Retrograde Transport","description":"Dominated by intracellular transport terms, especially endosome-to-Golgi and recycling endosome-to-Golgi routes, plus COPII cargo loading and Rab/Rap signaling, indicating a cohesive endomembrane trafficking module linking endosomes and the Golgi and ER-Golgi interface.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0034499","count":4},{"id":"GO:0048227","count":3},{"id":"GO:0071955","count":3},{"id":"GO:0006886","count":3},{"id":"GO:0035526","count":3}]},{"hash":"1242095918670421216","title":"Neuronal signaling and antipsychotic drug responses","description":"The cluster\u2019s GO terms center on neuronal signaling and excitability: regulation of membrane potential, sodium ion import, and cellular responses to cAMP, along with sensory perception of smell and responses to antipsychotic drugs (e.g., clozapine). This pattern suggests a coherent theme around neural signaling, olfactory pathways, and pharmacologic response to antipsychotics, despite a few more general terms.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":3},{"id":"GO:2000480","count":2},{"id":"GO:0098719","count":2},{"id":"GO:0071320","count":2},{"id":"GO:0097332","count":2}]},{"hash":"2212603160030720818","title":"APC/C-Mediated Cell Cycle Regulators","description":"Based on the strongest GO signals (mitotic cell cycle, cell division, and anaphase-promoting complex-dependent catabolic process), the proteins are best described as regulators of mitosis controlled by the APC/C ubiquitin ligase. Some terms are plant- or obsolete-linked (cadmium response, cytokinin signaling, chlorophyll regulation), but the core theme is APC/C-mediated cell cycle control.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0030433","count":2},{"id":"GO:2001162","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0051301","count":2}]},{"hash":"2096552786726472671","title":"Viral transcription and host transcription regulation","description":"This cluster centers on transcriptional control, highlighted by terms for DNA-templated transcription, viral transcription, and regulators of RNA polymerase II activity and cyclin-dependent kinases. The inclusion of host cell cycle and DNA damage response terms (response to X-ray, spindle pole body separation, CDK activity) suggests a set of proteins that coordinate transcription with cell cycle progression, and potentially virus\u2013host interactions. Some mammary gland development terms appear as tissue-specific annotations rather than core function.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":11},{"id":"GO:0019086","count":8},{"id":"GO:0060749","count":8},{"id":"GO:0010696","count":8},{"id":"GO:0010165","count":8}]},{"hash":"2176292771547877415","title":"Mitotic spindle regulation and cell division","description":"The top GO terms are dominated by cell cycle and mitosis-related processes: cell division, DNA-templated transcription, establishment of mitotic spindle orientation, and regulation of spindle pole separation, all pointing to mitotic control. While a few terms touch on viral transcription and mammary gland development, the strongest coherent signal is mitosis/spindle regulation, suggesting proteins in this cluster are involved in mitotic spindle assembly and cell division control.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0000132","count":2},{"id":"GO:0019086","count":1},{"id":"GO:0060749","count":1}]},{"hash":"1442007708267057719","title":"Chromatin remodeling and transcription regulation","description":"The top GO terms are dominated by chromatin remodeling and transcription-control processes (chromatin remodeling; regulation of transcription start-site selection and transcription termination; histone modification and DNA methylation regulation). Although a few terms touch on olfactory development or signaling, the overall pattern points to nuclear gene expression control via chromatin dynamics and transcription machinery. This cohesive theme justifies a Chromatin remodeling and transcription regulation label.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":2},{"id":"GO:0010880","count":1},{"id":"GO:0001178","count":1},{"id":"GO:0021553","count":1},{"id":"GO:2001229","count":1}]},{"hash":"739308957177659865","title":"Muscle and nervous system development","description":"The top GO terms cluster around muscle and neural development (sarcomere organization; skeletal muscle tissue development; neural tube development; nervous system development; swimming as a phenotype). Other terms appear unrelated (plant metabolism, tRNA modification, chromosome segregation, germinal center formation), suggesting either annotation noise or a mix of functions, but the dominant signal ties to muscle and neural development.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045214","count":2},{"id":"GO:0021915","count":2},{"id":"GO:0045762","count":2},{"id":"GO:0007399","count":1},{"id":"GO:0007519","count":1}]},{"hash":"668019810826927838","title":"Ubiquitin-Dependent Degradation and Deubiquitination","description":"Top GO terms indicate ubiquitin-dependent protein catabolic processes and multiple deubiquitination activities (K48, K63, K11) plus histone deubiquitination, with a minor link to mitochondrial fission. This suggests a cohesive cluster centered on ubiquitin turnover and removal by deubiquitinases, i.e., a deubiquitination/ubiquitin-regulated degradation module.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006511","count":3},{"id":"GO:0035520","count":3},{"id":"GO:0035616","count":3},{"id":"GO:0071108","count":3},{"id":"GO:0042787","count":3}]},{"hash":"690164877419382468","title":"Endosome-to-Golgi trafficking and PI signaling","description":"The cluster shows a clear enrichment for endosome-to-Golgi transport terms (early and late) and phosphatidylinositol-mediated signaling, suggesting a core function in vesicular trafficking and its regulation. While other terms (bone development, DNA replication/transcription, and ribosome biogenesis) point to broader cellular roles, the strongest common theme among the top terms is intracellular membrane trafficking linked to PI signaling. Confidence: Medium","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034498","count":2},{"id":"GO:0034499","count":2},{"id":"GO:0048015","count":2},{"id":"GO:0060348","count":2},{"id":"GO:0006261","count":2}]},{"hash":"322364940860136582","title":"RNA Polymerase Complex Assembly and Transcription Regulation","description":"The top terms point strongly to the assembly of RNA polymerase I, II, and III complexes and including positive regulation of transcription elongation by RNA polymerase II, indicating a core theme of transcription machinery assembly and transcription control. Additional terms like snoRNP assembly and actin nucleation suggest broader protein complexes involved in cellular assembly, but the dominant signal remains transcription-related. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990115","count":1},{"id":"GO:0007021","count":1},{"id":"GO:1990114","count":1},{"id":"GO:0032968","count":1},{"id":"GO:1990113","count":1}]},{"hash":"103865033195982833","title":"Cytoskeletal remodeling and mechanosensing","description":"This cluster is dominated by GO terms related to actin-based cytoskeleton dynamics and responses to mechanical cues, including filopodium assembly, Rac signaling, substrate adhesion-dependent cell spreading, and mechanotransduction, pointing to a cohesive theme of cytoskeletal remodeling and sensing the mechanical environment. While there are also terms like DNA-templated transcription and spindle assembly present, they appear less central to the cluster\u2019s main function.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0035556","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0006508","count":2}]},{"hash":"1814491129162865204","title":"Cell polarity and cytoskeleton dynamics","description":"The top GO terms cluster around architecture and organization of the cell: establishment of epithelial cell polarity, actin filament bundle assembly, spindle assembly, and maintenance/localization of proteins at membranes or chromosomes. While there are also immune signaling-related terms (cytokine and chemokine production) and a cardiac communication term, the strongest signal is toward cytoskeletal remodeling, polarity establishment, and subcellular localization, suggesting a cohesive theme of cellular structure and organization with signaling ties.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071642","count":2},{"id":"GO:1901594","count":2},{"id":"GO:0086070","count":2},{"id":"GO:0071651","count":2},{"id":"GO:0090162","count":2}]},{"hash":"471185588606121747","title":"Signaling Regulation and Protein Turnover","description":"Based on the GO terms, this cluster centers on regulation of multiple signaling pathways (Ras, Rho) and receptor trafficking (receptor recycling, endosome size), combined with ubiquitin-dependent protein catabolic processes and transcription regulation. The presence of synaptic transmission terms and sarcomere organization suggests some affiliation with neuronal/muscle signaling contexts, but the unifying theme appears to be how signaling is modulated together with protein turnover and trafficking. Therefore, a concise label is \u201cSignaling Regulation and Protein Turnover.\u201d","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046580","count":2},{"id":"GO:0045214","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0034968","count":1},{"id":"GO:0001881","count":1}]},{"hash":"1182151110034217259","title":"Glutamatergic signaling and receptor trafficking","description":"This cluster prominently features terms linked to glutamatergic synaptic transmission, receptor recycling, and endosome regulation, along with Rho-mediated signaling and kinase activity\u2014pointing to neuronal membrane trafficking and synaptic signaling as the core theme. While a subset of terms touches on transcriptional regulation and mRNA transport, the strongest shared function appears to be synaptic signaling and receptor cycling in neurons.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0060316","count":4},{"id":"GO:0034968","count":3},{"id":"GO:0001881","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0051036","count":3}]},{"hash":"363288368339859141","title":"Calcium signaling regulation","description":"The cluster\u2019s top GO terms center on calcium handling and signaling, including regulation of ryanodine-sensitive calcium-release channel activity, cellular response to calcium ion, and regulation of store-operated calcium channel activity. These points suggest a cohesive theme around calcium signaling, even though a few other terms are unrelated or reflect broader cellular processes. Overall, calcium signaling modulation best summarizes the prevalent pattern in this set.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060316","count":3},{"id":"GO:0097274","count":2},{"id":"GO:1905205","count":2},{"id":"GO:0072286","count":2},{"id":"GO:0032465","count":2}]},{"hash":"209263098771252027","title":"Neuronal signaling and endocytic trafficking","description":"The top terms indicate a cluster centered on neural development and function, including axonogenesis and dopaminergic synaptic transmission, alongside endosomal transport regulation, pointing to a module where neural signaling is closely tied to endocytic trafficking. While some terms are unrelated (e.g., cartilage condensation, NK T cell differentiation), the dominant theme is neuronal development and synaptic signaling with membrane trafficking. ","confidence":"Medium","size":22,"edges":221,"triangles":1355,"max_degree":21,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":22},{"id":"GO:0007124","count":22},{"id":"GO:1901621","count":22},{"id":"GO:1904637","count":22},{"id":"GO:0001963","count":22}]},{"hash":"331640888702981313","title":"Transmembrane nutrient and ion transport","description":"This cluster centers on transmembrane transport activities across membranes, with signals for xenobiotic and vitamin transport, sodium ion transport, and sugar (glucose, galactose, fructose) transport, along with osmotic stress response. While a few terms are obsolete or metabolic, the dominant theme is moving small molecules and ions across membranes, and coping with osmotic conditions, indicating a coherent transport-focused group.","confidence":"High","size":22,"edges":69,"triangles":49,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":17},{"id":"GO:0035461","count":17},{"id":"GO:0042891","count":15},{"id":"GO:0035725","count":10},{"id":"GO:0052106","count":9}]},{"hash":"526920834298757972","title":"Microtubule cytoskeleton and neuronal transport","description":"The GO terms cluster around microtubule dynamics, polarity, and transport, including spindle/kinetochore interactions, microtubule depolymerization, neuron projection maintenance, and anterograde dendritic transport. The presence of neuron-specific terms (neuron projection maintenance, Purkinje cell layer organization) alongside general cytoskeletal and division-related terms suggests a shared function in microtubule-based structure and trafficking across neuronal and dividing cells.","confidence":"High","size":22,"edges":203,"triangles":1192,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0010938","count":7},{"id":"GO:0000743","count":7},{"id":"GO:0001560","count":7},{"id":"GO:0032487","count":7},{"id":"GO:0098971","count":7}]},{"hash":"1620926385508130007","title":"Antioxidant detoxification and inflammation regulation","description":"The cluster is enriched for oxidative stress-related processes such as cellular oxidant detoxification and glutathione metabolic pathways, along with multiple terms describing downregulation of inflammatory signaling (e.g., IL-1\u03b2 production, neutrophil aggregation, acute inflammatory response) and redox-related terms like response to ascorbic acid and nitric oxide storage, suggesting a coordinated role in antioxidant defense and inflammation control.","confidence":"High","size":22,"edges":228,"triangles":1483,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":21},{"id":"GO:0033591","count":20},{"id":"GO:0035732","count":20},{"id":"GO:0032691","count":20},{"id":"GO:0042994","count":20}]},{"hash":"851146324209593259","title":"Calcium signaling and nuclear transport regulation","description":"The cluster is dominated by GO terms related to calcium signaling (positive regulation of voltage-gated calcium channel activity; positive regulation of release of sequestered calcium ion into cytosol) and nuclear/transcriptional control (NLS-bearing protein import into nucleus; cytoplasmic sequestration of transcription factor), suggesting a cohesive role in Ca2+-dependent signaling that interfaces with transcriptional regulation. Some developmental or obsolete terms appear as noise but do not override the calcium\u2013nuclear transport theme.","confidence":"Medium","size":22,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1901387","count":3},{"id":"GO:0055003","count":2},{"id":"GO:0097274","count":2},{"id":"GO:0008365","count":2},{"id":"GO:1905205","count":2}]},{"hash":"1443549610254898069","title":"Unknown","description":"The top GO terms cover a wide range of distinct biological areas (kinetochore localization and cell cycle regulation, endosome transport, fungal growth, hedgehog-like signaling, calcium response, dopaminergic synaptic transmission, p53-mediated signaling, NK T cell differentiation, and neuronal axonogenesis), with little overlap suggesting a single cohesive function. This diversity makes it difficult to assign a precise, representative label to the cluster. ","confidence":"","size":22,"edges":183,"triangles":800,"max_degree":21,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0034501","count":22},{"id":"GO:0045736","count":22},{"id":"GO:2000641","count":19},{"id":"GO:0007124","count":19},{"id":"GO:1901621","count":19}]},{"hash":"1085809936529160055","title":"Regulators of Ser/Thr Kinase and GTPase Signaling","description":"The top GO terms point to modulation of phosphorylation and GTPase activity (positive regulation of serine/threonine kinase activity, autophosphorylation, and GTPase activity), suggesting these proteins collectively regulate signaling cascades. While some kidney development (metanephric) and neuronal plasticity (synaptic potentiation) terms appear, the strongest unified theme centers on phosphorylation-driven signaling control, with ancillary terms reflecting broader regulatory roles. Overall, the cluster seems to capture regulators of phosphorylation signaling rather than a single, cohesive pathway.","confidence":"Medium","size":22,"edges":17,"triangles":0,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071902","count":10},{"id":"GO:0043547","count":10},{"id":"GO:0031954","count":10},{"id":"GO:0072286","count":8},{"id":"GO:0072205","count":8}]},{"hash":"473626492047595518","title":"Nuclear ribosome biogenesis and RNA processing","description":"The cluster\u2019s top GO terms cluster around ribosome biogenesis (ribosome assembly, ribosomal subunit biogenesis), rRNA maturation, and export steps (nuclear export of ribosomal subunits and mRNA), as well as translation. Additional terms involve RNA processing and regulation of splicing via ncRNAs, suggesting a cohesive nucleus-centric RNA metabolism program coordinating ribosome production with RNA processing and export. These connections support a central theme of ribosome assembly coupled with RNA handling in the nucleus.","confidence":"High","size":22,"edges":172,"triangles":645,"max_degree":20,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0000462","count":4},{"id":"GO:0000055","count":3},{"id":"GO:0006406","count":3},{"id":"GO:0048025","count":3}]},{"hash":"1510737712019059893","title":"Neuronal Development and Signaling","description":"The top GO terms cluster around neural development and neuronal signaling, including CNS projection neuron axonogenesis, dopaminergic synaptic transmission, and regulation of various signaling pathways (e.g., Smoothened in neural patterning, p53-mediated signaling). Endosomal transport regulation also fits with receptor trafficking that modulates neuronal signaling. A few terms (pseudohyphal growth, NK T cell differentiation) are less directly aligned, but the dominant theme is signaling and neural development, supporting this label with Medium confidence. ","confidence":"Medium","size":22,"edges":96,"triangles":131,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":22},{"id":"GO:0007124","count":22},{"id":"GO:1901621","count":22},{"id":"GO:1904637","count":22},{"id":"GO:0001963","count":22}]},{"hash":"1771140008700364164","title":"TGF-\u03b2/BMP Signaling Repression","description":"This cluster shows strong representation for negative regulation of TGF-\u03b2 receptor signaling and BMP signaling, plus related controls like SMAD complex assembly regulation and dephosphorylation, suggesting a core theme of dampening TGF-\u03b2/BMP pathway activity. Some terms may reflect species-specific biology or annotation noise (e.g., photosystem-related terms), but the dominant signal points to regulation of TGF-\u03b2/BMP signaling.","confidence":"Medium","size":22,"edges":193,"triangles":963,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":22},{"id":"GO:0042347","count":21},{"id":"GO:0071560","count":21},{"id":"GO:0080005","count":21},{"id":"GO:0061191","count":21}]},{"hash":"748158512681536508","title":"Sperm development and chromatin remodeling","description":"The top GO terms include sperm-specific processes (sperm axoneme assembly, sperm individualization) and epigenetic marks (histone ubiquitination, cytosine methylation), pointing to chromatin remodeling during spermatogenesis. The remaining terms (some metabolic and immune-related) appear as outliers rather than core features of the cluster.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070535","count":2},{"id":"GO:0090116","count":2},{"id":"GO:0007288","count":2},{"id":"GO:0032608","count":2},{"id":"GO:0050910","count":2}]},{"hash":"1596911845296620425","title":"Developmental and Cell Cycle Regulation","description":"This cluster includes GO terms tied to the mitotic cell cycle and broad developmental processes (multicellular organism development, forebrain development, fat cell differentiation), along with transcriptional control (DNA-templated transcription) and genome maintenance (telomere maintenance/capping). The combination suggests a coordinated regulatory program that links cell division with development across tissues, rather than a single, specific pathway; tissue-related hints (heart, muscle stretch) reinforce a general developmental regulatory theme.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0045444","count":4},{"id":"GO:0032212","count":4},{"id":"GO:1904355","count":4},{"id":"GO:0035994","count":4}]},{"hash":"561348983803436829","title":"Neural Development and Sensory System Formation","description":"This cluster centers on developmental and neural processes, highlighted by neural tube closure, forebrain development, and visual perception, with supporting terms on multicellular organism and skeletal system development. The mitotic cell cycle term aligns with tissue growth in development, while the cadmium response and Gram-positive defense terms may reflect ancillary or pleiotropic proteins present. Overall, the dominant theme points to neural development and sensory system formation.","confidence":"Medium","size":22,"edges":146,"triangles":468,"max_degree":21,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046827","count":19},{"id":"GO:0000278","count":12},{"id":"GO:0001843","count":11},{"id":"GO:0071276","count":11},{"id":"GO:0001501","count":11}]},{"hash":"1655532862238782323","title":"Neural Development and Synaptic Signaling","description":"This cluster is enriched for neural-related GO terms, including visual perception, dopaminergic synaptic transmission, CNS projection neuron axonogenesis, and neural tube patterning, suggesting a coherent theme around neural development and neuronal communication. While a few terms touch on broader cellular processes (endosome trafficking, cell cycle, calcium signaling), the dominant pattern centers on neuronal differentiation and signaling pathways, which supports the label.","confidence":"Medium","size":22,"edges":48,"triangles":47,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":21},{"id":"GO:0000278","count":21},{"id":"GO:2000641","count":18},{"id":"GO:0007124","count":18},{"id":"GO:1901621","count":18}]},{"hash":"865376351104271295","title":"Cell Proliferation and ER-Golgi Vesicle Trafficking","description":"This cluster centers on mitosis and cell cycle progression (cell division, mitotic spindle assembly, mitotic cell cycle) together with secretory pathway activity (COPII budding, ER-to-Golgi transport). Other growth-related terms (ribosome biogenesis, multicellular organism growth, brain development) align with proliferation and development, but the dominant theme is cell division coupled with ER-Golgi trafficking.","confidence":"High","size":22,"edges":144,"triangles":405,"max_degree":20,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":9},{"id":"GO:0090114","count":8},{"id":"GO:0090307","count":8},{"id":"GO:0000278","count":8},{"id":"GO:0006890","count":8}]},{"hash":"793072973926728280","title":"Nervous system and sensory organ development","description":"The top GO terms center on neural/sensory development: visual perception, retinal bipolar neuron differentiation, and facial nucleus development, suggesting proteins in this cluster largely function in nervous system and sensory organ formation. A heart development term appears but is less dominant, and other terms about mRNA regulation or viral/plant responses likely reflect incidental annotations rather than core function. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0060040","count":2},{"id":"GO:0031954","count":2}]},{"hash":"1202112598257216048","title":"Stress-Response Regulators","description":"The cluster's GO terms point to regulatory roles across a range of processes (RNA processing/export under heat stress, ubiquitin ligase activity, cell cycle regulation, chromatin assembly, signaling pathways, inflammatory cytokine production, and neural/glial development). Because no single pathway dominates and most terms denote regulation rather than a specific function, the common theme is regulation of stress responses and signaling. Thus the label is appropriate, with Moderate confidence given the breadth of functions.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000728","count":1},{"id":"GO:1904668","count":1},{"id":"GO:0050773","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0061641","count":1}]},{"hash":"1435012180408343902","title":"Unknown","description":"The GO terms span endosomal transport, yeast pseudohyphal growth, neural patterning signaling, calcium response, dopaminergic synaptic transmission, p53-mediated signaling, NK T cell differentiation, CNS neuron axonogenesis, aging-related stress response, and cartilage condensation. This broad mix shows no single cohesive function or pathway linking the proteins, so the cluster cannot be reliably labeled with a specific biological theme.","confidence":"","size":22,"edges":25,"triangles":6,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":22},{"id":"GO:0007124","count":22},{"id":"GO:1901621","count":22},{"id":"GO:1904637","count":22},{"id":"GO:0001963","count":22}]},{"hash":"1463694856659450449","title":"Developmental transcriptional regulators","description":"The top GO terms are dominated by DNA-templated transcription and development-related processes (multicellular organism development, forebrain development, neural tube closure, skeletal muscle differentiation), suggesting proteins that regulate gene expression during development, especially neurodevelopment and organogenesis. Some peripheral terms (cadmium response, defense to Gram-positive bacteria) may reflect broader stress responses, but the core theme is developmental transcriptional control.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0001843","count":4},{"id":"GO:0046827","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0006349","count":4}]},{"hash":"146714333622619859","title":"Post-transcriptional regulation and immune signaling","description":"The cluster includes GO terms related to mRNA processing and stability (polyadenylation, stability, translation initiation), along with chromatin remodeling and immune-related processes (dendritic cell cytokine production, B cell proliferation). While there are miscellaneous host-pathogen and plant defense terms, the dominant theme centers on gene expression control at post-transcriptional and immune-regulatory levels, justifying this label.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":2},{"id":"GO:0044829","count":2},{"id":"GO:0034052","count":2},{"id":"GO:0043488","count":2},{"id":"GO:1903679","count":2}]},{"hash":"1531587813108148354","title":"Unknown","description":"The top terms span several distinct themes, including developmental processes (heart morphogenesis, osteoblast differentiation, vitellogenesis) and various cellular regulation processes (endocytic recycling, sumoylation, membrane potential regulation, and DNA damage responses). There is no single coherent function tying all terms together, so a specific, representative label cannot be confidently assigned. Therefore, Unknown.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003007","count":2},{"id":"GO:1990126","count":2},{"id":"GO:0001649","count":2},{"id":"GO:0033235","count":1},{"id":"GO:1902231","count":1}]},{"hash":"1700206694999221267","title":"cAMP-Dependent Signaling and Membrane Potential Regulation","description":"Most represented terms center on cellular response to cAMP, negative regulation of PKA activity, and regulation of membrane potential, linking second-messenger signaling to ion transport (sodium import) and neuronal responsiveness (including antipsychotic drug response). While transcription and ER-Golgi trafficking terms appear, the dominant theme ties cAMP-mediated signaling to membrane excitability and related neuronal signaling pathways, suggesting this label captures the core function of the cluster.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0006888","count":4},{"id":"GO:2000480","count":3},{"id":"GO:0098719","count":3},{"id":"GO:0071320","count":3}]},{"hash":"1888049495136985574","title":"Stress-responsive transcription and chromatin regulation","description":"The cluster centers on cellular stress responses to metals/toxins (arsenite, cadmium) and links to transcriptional control and chromatin modification (DNA-templated transcription, RNA methylation, histone demethylation). It also touches on cell-cycle and cytoskeletal processes (mitotic cycle, microtubule severing) and signaling via GTPases, suggesting a coordinated response that links stress signaling with transcriptional/chromatin regulation and cell division.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903936","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0051013","count":2},{"id":"GO:0036265","count":2}]},{"hash":"1212996870274969711","title":"Neural development and signaling with metabolic pathways","description":"The dominant terms describe nervous system development, neural tube closure, and glutamatergic synaptic transmission, all pointing to neuronal differentiation and communication. ERK signaling further links to developmental regulation, while cholesterol biosynthesis suggests membrane and signaling lipid needs of developing neurons. A few terms (immune stimuli, skeletal muscle development, mitotic cell cycle) are present but less central, so the neural development/signaling theme best explains the cluster.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":6},{"id":"GO:0035249","count":5},{"id":"GO:0007399","count":5},{"id":"GO:0006695","count":5},{"id":"GO:0070371","count":5}]},{"hash":"2295917193618696618","title":"Neural development with RNA processing and ubiquitin regulation","description":"The terms cluster around brain development and glial contexts, with strong signals for RNA processing (splicing, mRNA export under heat stress) and ubiquitin-protein regulation, plus chromatin/cell-cycle elements and inflammatory signals, suggesting a neural development cluster governed by post-transcriptional and proteolytic regulation under stress.","confidence":"Medium","size":22,"edges":22,"triangles":0,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007420","count":7},{"id":"GO:2000728","count":6},{"id":"GO:1904668","count":6},{"id":"GO:0000398","count":6},{"id":"GO:0061641","count":6}]},{"hash":"2288115256015575674","title":"Mitochondrial membrane regulation and matrix import","description":"The cluster's top GO terms are dominated by mitochondrial functions, especially regulation of mitochondrial membrane permeability and protein import into the mitochondrial matrix, which together point to a mitochondrial-centric role for the proteins. While there are also terms related to cell-cycle regulation, lipid metabolism, and ubiquitination as secondary signals, the mitochondrial terms are the strongest in this set. Confidence: High","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":13},{"id":"GO:2000134","count":13},{"id":"GO:0070940","count":13},{"id":"GO:1903740","count":13},{"id":"GO:0010867","count":13}]},{"hash":"1539156860070388536","title":"Viral assembly and host stress response","description":"The top GO terms cluster around virion assembly, viral capsid assembly, and viral release, indicating a viral life-cycle theme. Added terms point to host chaperone-mediated protein folding, unfolded protein response, mitochondrial protein import, and cell cycle processes, suggesting these proteins are involved in viral interactions with host stress and cell-cycle pathways. Overall, the cluster appears to reflect viral particle assembly processes intertwined with host stress response mechanisms.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045041","count":2},{"id":"GO:0019068","count":2},{"id":"GO:0019069","count":2},{"id":"GO:0019076","count":2},{"id":"GO:0051301","count":2}]},{"hash":"1056313802262962071","title":"Nuclear organization and protein localization","description":"This cluster includes GO terms focused on nuclear processes, especially Cajal body organization (GO:0030576) and maintenance of protein location in the nucleus (GO:0051457), suggesting a core theme of nuclear organization and intracellular protein trafficking, with other terms representing peripheral or diverse cellular functions.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008284","count":2},{"id":"GO:1990966","count":1},{"id":"GO:0005975","count":1},{"id":"GO:0051457","count":1},{"id":"GO:0036099","count":1}]},{"hash":"1702907088550640924","title":"Ubiquitin-Dependent Protein Degradation","description":"The cluster is strongly enriched for ubiquitin-mediated proteolysis, including ubiquitin-dependent protein catabolic processes, autoubiquitination, and K48-linked ubiquitination, plus ERAD and related turnover of proteins such as histones and signaling components (e.g., Wnt receptor turnover, TNF signaling). This suggests a cohesive theme around regulated protein degradation via the ubiquitin\u2013proteasome system.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":15},{"id":"GO:0051865","count":14},{"id":"GO:0070936","count":13},{"id":"GO:0046621","count":12},{"id":"GO:0038018","count":12}]},{"hash":"1430885691118126468","title":"Membrane trafficking and cell division","description":"The top GO terms cluster around endocytic recycling, endosome-to-Golgi transport, plasma membrane remodeling (tubulation), cleavage furrow formation, and phosphatidic acid biosynthesis. Together these suggest a shared theme of membrane dynamics and trafficking underlying cytokinesis and membrane remodeling, with some developmental terms hinting at context-specific roles. While some terms are developmental, the dominant signal points to membrane trafficking/remodeling during cell division. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1990126","count":3},{"id":"GO:0097320","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0022617","count":3},{"id":"GO:0036089","count":3}]},{"hash":"2121989726055470655","title":"Neuronal signaling and transcription regulation","description":"The top GO terms point to regulation of signaling pathways (Ras, cAMP/PKA, guanylyl cyclase), transcriptional control (DNA-templated transcription, NF-kappaB-related activity), and neural-related responses (mechanical stimulus, antipsychotic drug response), suggesting a cohesive theme of neural signal transduction linked to transcriptional regulation.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046580","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0032088","count":2},{"id":"GO:0071260","count":2},{"id":"GO:2000480","count":2}]},{"hash":"2042298575834285253","title":"Plant Chromatin and Telomere Regulation","description":"This cluster centers on nuclear/chromatin biology: nucleosome assembly, histone deubiquitination, snRNA transcription, G-quadruplex DNA formation, and telomere maintenance/disassembly signals. The presence of plant-specific terms such as cytokinin signaling and regulation of cell wall biogenesis, along with osmotic stress response, suggests a plant-focused cluster linking chromatin/telomere regulation with stress and developmental signaling.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0006334","count":13},{"id":"GO:0061820","count":10},{"id":"GO:0009736","count":10},{"id":"GO:1901347","count":10},{"id":"GO:0072362","count":10}]},{"hash":"1790407195034041772","title":"Unknown","description":"No shared GO terms or network connections are evident: edges 0, triangles 0, and no top terms. With 22 proteins and only 4 re-added by ReCIPE (degree 0.75) but no interaction pattern, there is no coherent functional theme to label. Confidently cannot assign a meaningful cluster label.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"193307843707867586","title":"Unknown","description":"The top GO terms span signaling (neurotrophic/hormone responses, autophosphorylation), stress and death responses (anoxia, necroptosis), cytoskeletal dynamics (myosin II disassembly), cell adhesion, and ion homeostasis, with no single coherent function tying the cluster together. This broad and diverse mix makes a specific, reliable label difficult to justify.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990416","count":1},{"id":"GO:0010961","count":1},{"id":"GO:0031952","count":1},{"id":"GO:0071454","count":1},{"id":"GO:1990637","count":1}]},{"hash":"1024179081948505310","title":"Nuclear transcription and chromatin regulation","description":"These proteins cluster around nuclear gene expression control, featuring chromatin assembly/modification (CENP-A, histone methylation), DNA-templated transcription, RNA processing (splicing, mRNA export), and ribosomal RNA processing. The shared theme is regulation of chromatin state and RNA metabolism in the nucleus, with some cell-cycle regulation signals.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000447","count":3},{"id":"GO:0070317","count":3},{"id":"GO:0034729","count":3},{"id":"GO:0051568","count":3},{"id":"GO:0006351","count":3}]},{"hash":"2071375989473598567","title":"Light sensing and chromophore linkage","description":"The cluster\u2019s top GO terms cluster around photoreception and pigment/chromophore chemistry (response to very low fluence red light stimulus, detection of visible light, protein-chromophore linkage, protein-tetrapyrrole linkage), suggesting a shared function in light sensing. A few outlier terms (hypoxia detection, ethylene signaling, PTS, cardiac regulation) may reflect annotations or multifunctionality rather than a unifying theme. Overall, photoreception appears to be the core signal.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010203","count":1},{"id":"GO:0010613","count":1},{"id":"GO:0030823","count":1},{"id":"GO:0070483","count":1},{"id":"GO:0010105","count":1}]},{"hash":"811127614382531698","title":"Transcription Regulation and Endosomal Trafficking","description":"The cluster shows enrichment for chromatin modification and transcription regulation (histone methylation, transcription control) together with membrane trafficking (receptor recycling, endosome size) and signaling pathways (Rho signaling, NF-kappaB, synaptic transmission). This pattern suggests a module coordinating signaling events with gene expression via trafficking and chromatin regulation, rather than a single, discrete pathway.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0034968","count":6},{"id":"GO:0001881","count":6},{"id":"GO:0006355","count":6},{"id":"GO:0051036","count":6},{"id":"GO:0035023","count":6}]},{"hash":"624693158626595805","title":"Nuclear Regulation and Telomere Maintenance","description":"This cluster centers on nuclear processes, with terms for DNA-templated transcription, protein ubiquitination, and telomere maintenance/capping, suggesting regulation of gene expression and genome integrity; additional terms point to cell cycle, development, and signaling, reflecting a broader regulatory context rather than a single pathway.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2001275","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0051534","count":2}]},{"hash":"1138377117546144736","title":"Post-transcriptional mRNA processing and regulation","description":"The proteins are linked to multiple post-transcriptional processes\u2014mRNA splicing and polyadenylation, mRNA stability, modification, translation initiation, and ncRNA/miRNA-mediated silencing\u2014indicating a cohesive cluster governing post-transcriptional gene expression control.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":2},{"id":"GO:0048025","count":2},{"id":"GO:0035278","count":2},{"id":"GO:0010610","count":2},{"id":"GO:0016556","count":2}]},{"hash":"1849071405946453146","title":"Innate Immune Response and ER-Golgi Trafficking","description":"Top terms cluster around innate immune defense (innate immune response; defense against Gram-positive bacterium; defense against virus) with supporting hints of ER-to-Golgi transport and ER-associated processes, suggesting proteins involved in immune defense that rely on secretory trafficking. Some outliers (bone development, pigmentation, cell cycle) may reflect multifunctionality or annotation noise, but the core signal is immune defense linked to secretory pathways.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0060348","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0043547","count":2}]},{"hash":"583199087446334763","title":"MAPK/JAK-STAT inhibition and mitotic regulation","description":"The top terms point to dephosphorylation and suppression of signaling pathways (peptidyl-threonine/tyrosine dephosphorylation; negative regulation of ERK/MAPK and T cell receptor signaling; JAK-STAT pathway suppression) together with cell cycle/mitosis components (kinetochore localization; mitotic cytokinesis checkpoints; actomyosin ring maturation). This suggests a cohesive role for phosphatases in downregulating signaling while coordinating mitotic processes, hence the chosen label.","confidence":"Medium","size":21,"edges":118,"triangles":395,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035970","count":15},{"id":"GO:0070373","count":13},{"id":"GO:0050860","count":13},{"id":"GO:0000200","count":13},{"id":"GO:0034501","count":12}]},{"hash":"2159782867112062178","title":"Neuronal signaling and endosome trafficking","description":"This cluster is enriched for dopaminergic synaptic transmission, CNS projection neuron axonogenesis, and broader neuronal development, alongside regulation of endosome transport and related signaling pathways. The co-occurrence of endosomal trafficking regulation with neural signaling and axonogenesis suggests proteins that coordinate vesicle trafficking with neuronal communication. While a few terms (pseudohyphal growth, NK T cell differentiation) are less directly related, the dominant theme points to neuronal signaling and vesicle trafficking.","confidence":"Medium","size":21,"edges":201,"triangles":1175,"max_degree":20,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":21},{"id":"GO:0007124","count":21},{"id":"GO:1901621","count":21},{"id":"GO:1904637","count":21},{"id":"GO:0001963","count":21}]},{"hash":"1578919489201166816","title":"Synaptic Transmission and Plasticity","description":"The top GO terms are dominated by neural signaling activities: neurotransmitter secretion, regulation of synaptic vesicle exocytosis, long-term potentiation, cellular response to calcium, and phosphatidylinositol-mediated signaling. This points to a role in synaptic transmission and plasticity. A few terms (chlorophyll biosynthetic process, gluconeogenesis, ABA signaling, VEGF receptor-2 signaling) are more divergent and may reflect cross-species annotations or multifunctional proteins, but the core theme remains neural signaling.","confidence":"Medium","size":21,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006094","count":4},{"id":"GO:0071277","count":3},{"id":"GO:0007269","count":3},{"id":"GO:0036324","count":3},{"id":"GO:0009738","count":3}]},{"hash":"307734887976529278","title":"Xenobiotic and immune stress responses","description":"This cluster is enriched for terms related to responding to external chemicals and immune signaling (response to cocaine, cellular response to xenobiotic stimulus, interleukin-4 response, regulation of complement cytotoxicity) as well as related stress-response processes like protein folding. While there are some developmental terms (placenta development) and telomerase assembly hints, the shared theme across the majority of terms points to cellular adaptation to xenobiotic/immune challenges.","confidence":"Medium","size":21,"edges":48,"triangles":62,"max_degree":12,"top_function":"protein folding","top_go_terms":[{"id":"GO:0033160","count":8},{"id":"GO:0042220","count":8},{"id":"GO:0045793","count":8},{"id":"GO:0001890","count":8},{"id":"GO:0035690","count":7}]},{"hash":"229151838559647861","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0007317","count":1},{"id":"GO:0039563","count":1}]},{"hash":"1332265664252026747","title":"Telomere maintenance, DNA replication, and repair","description":"The cluster is dominated by GO terms for telomere maintenance via telomerase, telomerase activity regulation, DNA replication, and DNA damage response/repair (including meiotic DSB processing and radiation response), along with cell-cycle transitions. This cohesive pattern points to genome stability and telomere maintenance as the core function.","confidence":"High","size":21,"edges":143,"triangles":564,"max_degree":20,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0032212","count":10},{"id":"GO:0042220","count":10},{"id":"GO:0051973","count":10},{"id":"GO:0000082","count":10},{"id":"GO:0006260","count":10}]},{"hash":"621483159717248237","title":"Unknown","description":"The GO terms span endosomal trafficking, neural development and signaling, immune differentiation, calcium signaling, and developmental cartilage processes, with no single coherent function tying all terms together. This suggests the cluster does not map to one clear biological theme, so a consistent, representative label cannot be determined.","confidence":"","size":21,"edges":127,"triangles":363,"max_degree":18,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":21},{"id":"GO:0007124","count":21},{"id":"GO:1901621","count":21},{"id":"GO:1904637","count":21},{"id":"GO:0001963","count":21}]},{"hash":"981296536467844579","title":"Signaling and Trafficking Regulation","description":"These proteins appear to cluster around regulation of signaling pathways (e.g., p53-mediated signaling, cyclin-dependent kinase activity, Smoothened signaling) and intracellular trafficking (endosome transport, kinetochore localization). The presence of neural development terms (dopaminergic synaptic transmission, CNS projection neuron axonogenesis) and immune differentiation (NK T cell differentiation) suggests a broader theme: coordinated control of signaling and trafficking across diverse cellular contexts, including neurons, immune cells, and cell cycle processes.","confidence":"Medium","size":21,"edges":111,"triangles":214,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0034501","count":21},{"id":"GO:0045736","count":21},{"id":"GO:2000641","count":20},{"id":"GO:0007124","count":20},{"id":"GO:1901621","count":20}]},{"hash":"909590923307646735","title":"Vertebrate embryonic development and transcriptional regulation","description":"This cluster is dominated by terms linked to developmental processes (neural tube closure, skeletal system development, multicellular organism development) and fundamental transcription/replication activities (DNA-templated transcription, DNA replication, nuclear export regulation), suggesting a cohesive theme of embryonic gene regulation and morphogenesis in vertebrates. Some stress-response terms (lipopolysaccharide, cadmium) appear but do not define the primary function of the cluster.","confidence":"Medium","size":21,"edges":101,"triangles":282,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":11},{"id":"GO:0006351","count":10},{"id":"GO:0006260","count":9},{"id":"GO:0071222","count":9},{"id":"GO:0048701","count":9}]},{"hash":"1483529804401575542","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":11,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":3},{"id":"GO:0060416","count":3},{"id":"GO:0006207","count":3},{"id":"GO:0045471","count":3},{"id":"GO:0044205","count":3}]},{"hash":"1691821654817818438","title":"Cytoskeletal dynamics and meiotic spindle assembly","description":"Many top GO terms cluster around cytoskeletal organization and spindle dynamics: actomyosin contractile ring assembly, myofibril assembly, regulation of cell shape, centrosome localization, meiotic spindle localization, homologous chromosome movement in meiosis, and ER polarization. While a few items touch signaling or specialized contexts (histamine response, female gamete generation), the dominant theme is cytoskeletal remodeling guiding cell division and polarity, especially meiosis. Therefore the label Cytoskeletal dynamics and meiotic spindle assembly fits well.","confidence":"High","size":21,"edges":35,"triangles":28,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0055003","count":2},{"id":"GO:0060292","count":2},{"id":"GO:0007292","count":2},{"id":"GO:0071519","count":2},{"id":"GO:0008360","count":2}]},{"hash":"1446172528082418641","title":"Nuclear gene expression and cell cycle cluster","description":"The top GO terms show strong representation for DNA-templated transcription, DNA replication, and cell division, indicating a core nuclear program of gene expression and cell cycle progression. mRNA splicing also appears, supporting RNA processing within the nucleus. While some vesicle trafficking and neuronal signaling terms are present, these appear less central, likely reflecting multifunctional proteins. Overall, the cluster is best described by nuclear gene expression and cell cycle processes.","confidence":"Medium","size":21,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0006260","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0042220","count":3}]},{"hash":"1522159617127287801","title":"Placental Development and Cell Migration Regulation","description":"These proteins show a pattern centered on placental development, with negative regulation of cell proliferation and negative regulation of canonical Wnt signaling, suggesting controlled growth. They also emphasize cell migration and focal adhesion remodeling, along with apoptosis regulation, and general metabolic and transcriptional processes. Collectively, the cluster seems to function in placental tissue remodeling and growth control through migration and signaling dynamics.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0008285","count":11},{"id":"GO:0090090","count":11},{"id":"GO:0016477","count":11},{"id":"GO:0051893","count":11},{"id":"GO:0043065","count":11}]},{"hash":"1277172109793152293","title":"Vesicle trafficking and exocytosis in brain and immune cells","description":"This cluster centers on processes like regulation of synaptic vesicle exocytosis, protein/transmembrane transport, and related brain and immune cell activities (including T cell degranulation). The recurring emphasis on vesicle movement and membrane-associated secretion suggests a common theme of regulated exocytosis and trafficking across neural and immune contexts, despite some obsolete terms present. ","confidence":"Medium","size":21,"edges":167,"triangles":711,"max_degree":20,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010796","count":18},{"id":"GO:0031384","count":18},{"id":"GO:2000300","count":18},{"id":"GO:0007420","count":17},{"id":"GO:0000060","count":17}]},{"hash":"701415001569638126","title":"Nuclear transport, mitosis, and ciliogenesis","description":"The top GO terms cluster around import of NLS-bearing proteins into the nucleus and mitotic nuclear membrane reassembly, suggesting involvement in nuclear envelope dynamics and cell division. The ciliary basal body\u2013plasma membrane docking term indicates coordination of centrosome/cilium assembly with the plasma membrane. Additional terms hint at transcription regulation by RNA Pol III and protein complex assembly, which fit with nucleus/cytoskeleton\u2013associated processes. Some terms such as TORC1 signaling and apoptotic regulation reflect broader growth and stress responses that can intersect with these core processes, but the dominant themes are nuclear transport, mitosis, and ciliogenesis.","confidence":"Medium","size":21,"edges":117,"triangles":305,"max_degree":17,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0006607","count":7},{"id":"GO:0007084","count":6},{"id":"GO:0097711","count":6},{"id":"GO:0045945","count":6},{"id":"GO:0006461","count":6}]},{"hash":"984546545652327959","title":"Endosomal trafficking and neuronal autophagy","description":"The strongest shared theme is regulation of endosomal transport and autophagy-related processes (endosome maturation, xenophagy). Several terms also point to neural development and function (cerebellar cortex development, dopaminergic synaptic transmission, neural tube patterning), suggesting the proteins operate in neural contexts where endosomal trafficking and autophagy intersect with signaling. A minor term about pseudohyphal growth is likely from conserved trafficking components across species, but the dominant signal supports endosomal transport and neuronal autophagy.","confidence":"Medium","size":21,"edges":29,"triangles":4,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":21},{"id":"GO:0007124","count":21},{"id":"GO:1901621","count":21},{"id":"GO:1904637","count":21},{"id":"GO:0001963","count":21}]},{"hash":"1284719172319462953","title":"Synaptic vesicle trafficking and exosome secretion","description":"The cluster is dominated by neuronal vesicle trafficking and exosome-related GO terms: exosomal secretion, regulation of synaptic vesicle exocytosis/endocytosis, multivesicular body assembly, endosome-to-lysosome transport, and protein localization to endosomes, with brain development also represented. This points to a coherent theme of synaptic vesicle handling and extracellular vesicle release in neurons, though a few terms (tight junction assembly, mitotic cell cycle) may reflect broader trafficking components or incidental associations.","confidence":"Medium","size":21,"edges":4,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1990182","count":6},{"id":"GO:2000300","count":6},{"id":"GO:0036258","count":5},{"id":"GO:0060079","count":5},{"id":"GO:0008333","count":5}]},{"hash":"1304296657545481065","title":"Unknown","description":"The terms span plant hormone response (abscisic acid) through metabolic and growth-related processes (lipid homeostasis, fat differentiation, nutrient-responsive transcription), circadian rhythm, development, and wound healing. This broad and heterogeneous mix lacks a single cohesive function that would define a concise cluster label, so an Unknown label with no confidence is appropriate.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009737","count":4},{"id":"GO:0034198","count":4},{"id":"GO:1990418","count":3},{"id":"GO:0035470","count":3},{"id":"GO:0061614","count":3}]},{"hash":"169699833317274589","title":"ER-Golgi vesicle trafficking during mitosis","description":"This cluster is dominated by GO terms for ER-Golgi transport (COPII budding, ER-to-Golgi and retrograde transport) and cell division/mitosis (mitotic spindle assembly, mitotic cell cycle, cell proliferation, organism growth). The overlap suggests proteins involved in vesicle trafficking integrated with cell cycle progression, which can be especially relevant in developmental contexts like brain development, supporting a cohesive theme of vesicle transport coordinating mitosis and growth.","confidence":"High","size":21,"edges":36,"triangles":34,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090114","count":10},{"id":"GO:0051301","count":10},{"id":"GO:0090307","count":10},{"id":"GO:0000278","count":10},{"id":"GO:0006890","count":10}]},{"hash":"233993398981941787","title":"Regulatory signaling and cytoskeleton dynamics","description":"Top GO terms indicate a mix of signaling regulation (positive regulation of GTPase activity, ERK cascade, TORC1 signaling, peptidyl-serine phosphorylation), protein modification (ubiquitination), cytoskeletal remodeling (stress fiber assembly), and vesicle trafficking (COPII-coated vesicle budding). The combination suggests proteins involved in modulating signaling and structural/trafficking processes rather than a single pathway. Some tissue-specific terms (retina development, sensory perception of touch) may reflect broader developmental roles rather than core cluster activity.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0016567","count":2},{"id":"GO:0043149","count":2},{"id":"GO:0033138","count":2},{"id":"GO:0050975","count":2}]},{"hash":"1555489654962223100","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000447","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0000472","count":3},{"id":"GO:2000637","count":2}]},{"hash":"2224314986177363217","title":"Lipid Metabolism and Adipose Development","description":"This cluster centers on triglyceride and fatty-acid biosynthesis and storage (triglyceride and diacylglycerol synthesis, intracellular triglyceride homeostasis, fatty-acid metabolism) and fat-pad development, with additional signals of lipid absorption and lipoprotein clearance, reflecting a cohesive lipid metabolism/adipose tissue biology theme. Energy-related terms (ATP synthesis) complement the lipid processes, consistent with metabolic activity in adipose tissues.","confidence":"High","size":21,"edges":59,"triangles":99,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0019432","count":5},{"id":"GO:0015986","count":3},{"id":"GO:0099132","count":3},{"id":"GO:0050892","count":3},{"id":"GO:0035336","count":3}]},{"hash":"604145279859166285","title":"Transcription Regulation & Chromatin Modification","description":"This cluster is dominated by nuclear processes: DNA-templated transcription and its regulation, plus histone methylation signals (H3-K4/K79), suggesting chromatin-state control of gene expression. Additional terms for miRNA-mediated silencing, DNA replication, and cell division reinforce a core theme of transcriptional control and chromatin dynamics. Plant-specific signals (cytokinin pathway) and defense response hints indicate regulatory networks linking transcription/chromatin state to signaling and immunity. Overall, the proteins likely function in transcription regulation with chromatin modification as a central theme.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006355","count":3},{"id":"GO:0006508","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0051301","count":2}]},{"hash":"689618858482469552","title":"Immune receptor signaling and angiogenesis","description":"The cluster is dominated by immune and receptor signaling terms: T cell receptor signaling (GO:0050852), B cell receptor signaling (GO:0050853), and cell surface receptor protein serine/threonine kinase signaling (GO:0007178), along with angiogenesis and VEGF receptor signaling (GO:0048010, GO:0001525). The presence of endosome transport regulation (GO:2000641) supports receptor trafficking, tying these signals together. Pollen recognition is an outlier, but the core theme centers on receptor-mediated signaling in immune and vascular contexts. ","confidence":"High","size":21,"edges":57,"triangles":64,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0048544","count":21},{"id":"GO:0001525","count":21},{"id":"GO:0007178","count":21},{"id":"GO:0022038","count":21},{"id":"GO:0050852","count":21}]},{"hash":"334226225069884908","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:2000637","count":4},{"id":"GO:0061157","count":4},{"id":"GO:0001308","count":4},{"id":"GO:1902416","count":4},{"id":"GO:0000056","count":4}]},{"hash":"732908772726175318","title":"Gene Expression and Stress Response","description":"The cluster shows enrichment for core gene expression processes (translation initiation complex formation, DNA-templated transcription, and translation reinitiation) alongside a mix of stress- and development-related terms (neural tube and forebrain development, immune defense to Gram-positive bacteria, cadmium ion response, ER stress\u2013induced apoptosis, and glucose-limited invasive growth). This suggests proteins involved in basic transcription/translation machinery with broader roles in development and stress adaptation, rather than a single cohesive pathway.","confidence":"Low","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0001843","count":2},{"id":"GO:0050830","count":2}]},{"hash":"62033948940298033","title":"Developmental signaling and reproductive processes","description":"This cluster shows a mix of terms centered on developmental signaling (Wnt secretion regulation, GPCR signaling regulation, transcription regulation) and reproductive biology (egg-laying behavior, maternal axis specification), with related processes like angiogenesis and hypoxia detection. While some terms touch on behavior and aging, the strongest common theme is development and reproduction, supporting a label focused on those functions.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":3},{"id":"GO:0001302","count":2},{"id":"GO:0008277","count":2},{"id":"GO:0070483","count":2},{"id":"GO:0051262","count":2}]},{"hash":"1584392619258234425","title":"Ubiquitination-regulated cytoskeletal remodeling","description":"This cluster centers on cytoskeletal dynamics and signaling: several terms point to stress fiber assembly and regulation of GTPase activity (Rho-family pathways) as well as protein ubiquitination and its positive regulation. These together suggest a theme of cytoskeleton remodeling tightly controlled by ubiquitination and GTPase signals, which also aligns with locomotion regulation and cellular stress responses, though a few terms (e.g., viral release, tumor cell response) reflect broader stress-related contexts.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0009408","count":2},{"id":"GO:0071228","count":2},{"id":"GO:0019076","count":2},{"id":"GO:0016567","count":2}]},{"hash":"1174336679943901813","title":"Ubiquitin-mediated protein degradation","description":"This cluster is dominated by ubiquitin-related processes, especially ubiquitin tagging and ubiquitin-dependent degradation (autoubiquitination, ERAD, and K48/K6-linked ubiquitination). The inclusion of peroxisomal protein import and various catabolic terms also aligns with ubiquitin-regulated turnover. Overall, the proteins likely function in ubiquitin-mediated protein degradation pathways.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":6},{"id":"GO:0030433","count":6},{"id":"GO:0070936","count":6},{"id":"GO:0042787","count":5},{"id":"GO:0016558","count":5}]},{"hash":"2133162829860078133","title":"Ion transport and membrane potential regulation","description":"The top terms cluster around ion homeostasis (sodium/potassium transport, ion import/export) and membrane potential dynamics (including cardiac action potential repolarization), suggesting a cohesive function in ion channel/excitation regulation; unrelated terms like development/patterning are likely contextual rather than defining.","confidence":"High","size":21,"edges":66,"triangles":74,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019233","count":16},{"id":"GO:0007275","count":16},{"id":"GO:0046827","count":12},{"id":"GO:0006351","count":12},{"id":"GO:0030007","count":12}]},{"hash":"877250836172894105","title":"Endodermal organ and ocular development","description":"The top GO terms point to development and differentiation in endoderm-derived organs (intrahepatic bile ducts, gallbladder) as well as eye-related tissues (retinal rod cell differentiation, cornea development), with some regulatory processes in stem cells and immune responses. This suggests a broad theme of organogenesis spanning endodermal organs and the eye, despite some regulatory terms not defining a single pathway.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007493","count":2},{"id":"GO:0060221","count":2},{"id":"GO:0002437","count":2},{"id":"GO:0035019","count":2},{"id":"GO:0071866","count":2}]},{"hash":"1570582592326632656","title":"Neuronal ion transport and glutamatergic signaling","description":"The strongest terms are about sodium/potassium ion transport across membranes and potassium homeostasis, which are core to neural excitability; combined with glutamatergic synaptic transmission and pain perception, this points to neural signaling, with labyrinthine layer development suggesting inner-ear neural/neuronal development as well.","confidence":"High","size":21,"edges":33,"triangles":17,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0097623","count":5},{"id":"GO:0098719","count":5},{"id":"GO:0030007","count":5},{"id":"GO:0019233","count":4},{"id":"GO:0007275","count":4}]},{"hash":"747936516605106356","title":"Nuclear transport and cell cycle regulation","description":"The cluster includes mitotic cell cycle, transcription, translation, splicing, and explicit positive/negative regulation of nuclear protein export (and import), pointing to coordination between nuclear transport and gene expression during cell division.","confidence":"Medium","size":21,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0046826","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006412","count":2}]},{"hash":"1924424630599008370","title":"Proteolysis and vascular ECM remodeling","description":"The top GO terms largely point to regulation of proteolysis and fibrinolysis (e.g., negative regulation of plasminogen activation, fibrinolysis) and extracellular matrix-related processes (e.g., regulation of ECM constituent secretion, angiotensin level regulation), which together suggest a functional theme around protease control and ECM/vessel remodeling in the vasculature. Some terms (heat response, insulin processing, neural differentiation) appear as outliers, but the core signals support a proteolysis/ECM remodeling theme in a vascular context.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010757","count":2},{"id":"GO:0009408","count":2},{"id":"GO:0002002","count":2},{"id":"GO:0003331","count":2},{"id":"GO:2000346","count":2}]},{"hash":"1079325613423875760","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097190","count":2},{"id":"GO:0031440","count":1},{"id":"GO:0042797","count":1},{"id":"GO:0045899","count":1},{"id":"GO:0006362","count":1}]},{"hash":"513138323123986329","title":"Steroid Hormone Signaling and Reproductive Development","description":"This cluster is driven by GO terms tied to steroid hormone receptor assembly, male sex differentiation, and prostate gland development, suggesting a core theme of steroid hormone signaling in male reproductive biology. However, several plant-specific or obsolete terms appear among the top terms, indicating some annotation noise that lowers confidence. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0046661","count":8},{"id":"GO:0071357","count":8},{"id":"GO:0006463","count":8},{"id":"GO:0030850","count":8},{"id":"GO:0009736","count":7}]},{"hash":"265207279965254378","title":"Cell cycle progression and ribosome biogenesis","description":"The cluster is enriched for terms tied to cell cycle phases (G1/S, S, G2/M), mitotic spindle organization, and DNA replication, along with ribosome biogenesis. This combination points to proteins involved in promoting cell growth and division, making a label centered on cell cycle progression with ribosome assembly a concise, representative summary.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0000082","count":2},{"id":"GO:0000320","count":2},{"id":"GO:0007052","count":2},{"id":"GO:0006260","count":2}]},{"hash":"1349997224016713051","title":"Ion transport and nociception signaling","description":"Top terms show sodium import, potassium export, and potassium homeostasis at the plasma membrane, indicating a core ion-transport role. While pain and thermosensation terms are present, they are commonly linked to ion channels and nociceptive signaling, supporting a cohesive label around ion transport informing sensory responses.","confidence":"Medium","size":21,"edges":66,"triangles":73,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0098719","count":7},{"id":"GO:0097623","count":7},{"id":"GO:0030007","count":7},{"id":"GO:0046827","count":6},{"id":"GO:0019233","count":6}]},{"hash":"134350842182103364","title":"Stress-Responsive Transcription and Metabolic Regulation","description":"The Top Terms show strong enrichment for cellular response to amino acid starvation, LPS, GM-CSF stimuli, and glucose metabolism, plus transcription-related processes and nuclear transport/endosome dynamics, suggesting a coordinated network that senses stress and modulates gene expression and metabolism. This label captures the common theme of stress signaling, transcriptional control, and metabolic adjustment.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0034198","count":4},{"id":"GO:0006351","count":4},{"id":"GO:2000641","count":3},{"id":"GO:0097011","count":3},{"id":"GO:0046827","count":3}]},{"hash":"431044086014682639","title":"TRPV1-mediated thermosensation and pain signaling","description":"The Top Terms include diet-induced thermogenesis, cellular response to temperature stimulus, thermosensory behavior, sensory perception of pain, and response to capsazepine, all of which point to heat/pain sensing and TRPV1-related pathways. The presence of sodium ion import and potassium ion export across the plasma membrane supports neuronal excitability involved in nociception. Some terms also hint at osmotic/osmotic-stress\u2013related apoptotic signaling and inflammatory chemokine regulation, which can accompany stress responses in sensory and immune cells. Together, these terms suggest a theme of thermosensation and pain signaling with associated ion transport and inflammatory signaling. ","confidence":"High","size":21,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002024","count":4},{"id":"GO:0071502","count":4},{"id":"GO:0019233","count":4},{"id":"GO:0098719","count":4},{"id":"GO:0097623","count":4}]},{"hash":"781293530166059341","title":"RNA processing and ribosome biogenesis","description":"Dominant signals are DNA-templated transcription, mRNA splicing, and rRNA maturation, together with ribosome biogenesis, pointing to the gene expression and ribosome assembly machinery. This cluster thus centers on RNA processing and production of ribosomes, with ER stress response and ER-to-Golgi transport reflecting general protein quality control and trafficking that support synthesis. The brain and liver development terms are tissue contexts rather than core functions here, and the absence of strong interaction data means this label should be taken as a functional summary rather than a pathway map.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0000747","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0051301","count":2}]},{"hash":"1607790507256371013","title":"Synaptic Signaling and Receptor Trafficking","description":"This cluster prominently features synaptic transmission, receptor recycling, and endosome regulation, with accompanying signaling pathways (cGMP and Rho). Together, these terms point to neuronal signaling and membrane receptor trafficking as the core theme.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0060316","count":4},{"id":"GO:0034968","count":3},{"id":"GO:0001881","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0051036","count":3}]},{"hash":"1773685635458892863","title":"Unknown","description":"The GO terms are highly diverse and largely unrelated (miRNA catabolic process; cardiac, cuticle, kidney development; calcium transport regulation; nuclear import; kinase regulation), and there are no observed edges among proteins, indicating no cohesive shared function. Therefore, this cluster is best labeled Unknown with no confidence in a unifying function.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010587","count":2},{"id":"GO:0055003","count":1},{"id":"GO:0097274","count":1},{"id":"GO:0008365","count":1},{"id":"GO:2001246","count":1}]},{"hash":"193277426123875752","title":"Unknown","description":"The GO terms span disparate nuclear processes (DNA-templated transcription, DNA replication, chromosome condensation) and unrelated metabolic pathways, with no connecting edges, so there is no coherent single function for the cluster to label confidently.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":1},{"id":"GO:0006558","count":1},{"id":"GO:0006729","count":1},{"id":"GO:0043496","count":1},{"id":"GO:0051291","count":1}]},{"hash":"2148593008077981519","title":"Neural development and stress-responsive signaling","description":"GO terms point to neural processes (brain development, glial apoptotic signaling) with additional hints of stress/inflammatory and protein quality control mechanisms (heat-stress mRNA export, ubiquitination, cell cycle regulation). This suggests a neural development/stress-response cluster rather than a single pathway, giving a plausible but not definitive label.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000728","count":2},{"id":"GO:1904668","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0061641","count":2},{"id":"GO:0002534","count":2}]},{"hash":"344652314952239694","title":"Signal Perception and Transcription Regulation","description":"GO terms emphasize detection of stimulus, regulation of transcription, and DNA-templated transcription, with hints of hormone signaling (ethylene and cytokinin) and developmental processes (secondary growth, heterocyst development). The cluster seems to group proteins involved in sensing signals and controlling transcription, despite some heterogeneity.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010105","count":1},{"id":"GO:0042173","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0080117","count":1},{"id":"GO:0051606","count":1}]},{"hash":"2063659742792950730","title":"Nuclear genome maintenance and RNA processing","description":"This cluster's top GO terms cluster around nuclear genome stability processes (DNA repair, mitotic DNA replication, spindle assembly, histone turnover, ubiquitination) together with RNA maturation and surveillance (mRNA splicing/processing, nonfunctional rRNA decay). The combination points to roles in genome maintenance and RNA metabolism within the nucleus.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0036205","count":2},{"id":"GO:0051225","count":2},{"id":"GO:1902969","count":2},{"id":"GO:0045292","count":2}]},{"hash":"513086606739967001","title":"Unknown","description":"The terms cover a mix of metabolism, transcription regulation, protein modification, cell wall organization, proteolysis, and neuronal processes, with no single cohesive function tying the proteins together.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009442","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0035609","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0006508","count":2}]},{"hash":"936874781153541986","title":"Cytokine Production Regulation","description":"The strongest recurring theme in the top terms is regulation of inflammatory cytokines (positive regulation of MIP-1\u03b1 production, positive regulation of CCL5 production, and negative regulation of IL-12 production), indicating an immune signaling focus. Other terms (fat cell differentiation, telomere maintenance, spindle assembly, SA node signaling) appear more peripheral, suggesting the cluster is somewhat heterogeneous. Overall, the shared thread is modulation of inflammatory cytokine signaling, though not exclusively, so the label is representative but not definitive.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071642","count":1},{"id":"GO:0045444","count":1},{"id":"GO:0016567","count":1},{"id":"GO:0045083","count":1},{"id":"GO:0071446","count":1}]},{"hash":"408582809113047557","title":"Unknown","description":"The top GO terms are highly diverse (immune defense, transcription, cytoskeleton remodeling, signaling, nutrient response) with no clear unifying function or pathway linking the 21 proteins, and there are no network connections to anchor a specific cluster role. ","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050830","count":2},{"id":"GO:0050731","count":2},{"id":"GO:0051013","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1306890867230814746","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0071456","count":2}]},{"hash":"1706058613356808705","title":"Nuclear Transcription Regulation","description":"This cluster is dominated by GO terms for DNA-templated transcription and its regulation, indicating a core role in nuclear gene expression; additional terms are diverse and peripheral (hormone signaling, xenobiotic response, hypoxia), suggesting transcription control as the unifying theme.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009736","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006261","count":1},{"id":"GO:0033160","count":1}]},{"hash":"1206364928962201574","title":"Epigenetic Regulation and Cell Cycle","description":"This cluster centers on chromatin modification and transcription control, with GO terms for histone methylation (H3-K79, H3-K4), multiple deubiquitination activities (K11/K63/K48-linked), and DNA-templated transcription, plus multicellular development. The inclusion of centrosome duplication ties the group to cell cycle regulation, suggesting a cohesive role in epigenetic regulation during development and division. Some terms (e.g., SA node regulation, vacuole fusion) are more peripheral but do not override the dominant theme of chromatin-mediated gene regulation.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051298","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0098907","count":2},{"id":"GO:0042144","count":2}]},{"hash":"2002164960806851183","title":"Unknown","description":"The terms span fibrinolysis and plasminogen activation, ECM secretion, cardiovascular regulation, protein deglutamylation, insulin processing, neural development, and heat response, with no clear single function tying the proteins together. Therefore a concise, representative label cannot be assigned with confidence.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010757","count":1},{"id":"GO:0009408","count":1},{"id":"GO:0002002","count":1},{"id":"GO:0003331","count":1},{"id":"GO:2000346","count":1}]},{"hash":"232562125999190963","title":"Membrane trafficking and remodeling","description":"These proteins appear to be involved in membrane dynamics across various contexts: endocytic recycling, plasma membrane tubulation, late endosome to Golgi transport, and prospore membrane formation, all point to membrane remodeling and lipid signaling (phosphatidic acid biosynthesis) as a central theme. Cleavage furrow formation ties into cytokinesis-related membrane remodeling, while ECM disassembly and some developmental terms (eye development, osteoblast fate) suggest broader roles in development. Taken together, the common thread is membrane trafficking/remodeling processes rather than a single, highly specific function.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990126","count":1},{"id":"GO:0097320","count":1},{"id":"GO:0000278","count":1},{"id":"GO:0022617","count":1},{"id":"GO:0036089","count":1}]},{"hash":"482646801417840284","title":"Unknown","description":"The top GO terms span disparate biological areas (nervous and skeletal development, plant metabolism, tRNA modification, cell division, immune processes, and protein degradation) with no cohesive function or pathway linking them, and there are no edges connecting proteins, so no single thematic label fits reliably.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":1},{"id":"GO:0007519","count":1},{"id":"GO:0019762","count":1},{"id":"GO:0031591","count":1},{"id":"GO:0035853","count":1}]},{"hash":"2286531027276362540","title":"Neuronal gene expression and synaptic signaling","description":"The cluster combines nuclear regulators of gene expression (regulation of DNA-templated transcription; chromatin remodeling) with neural-specific processes (glutamatergic synaptic transmission; brain development) and associated trafficking/signaling (receptor recycling; endosome size; Rho signaling). This suggests a cohesive theme where transcriptional control in neurons links to synaptic function and neural development, hence a label centered on neuronal gene expression influencing synaptic signaling.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":5},{"id":"GO:0060316","count":5},{"id":"GO:0034968","count":4},{"id":"GO:0001881","count":4},{"id":"GO:0051036","count":4}]},{"hash":"861127249063532340","title":"Ubiquitin-Mediated Mitotic Regulation","description":"The cluster's top GO terms center on mitosis (anaphase-promoting complex-dependent catabolic process, cell division, mitotic cell cycle) and ubiquitin pathways (K11-linked ubiquitination, ubiquitin transferase activity, autoubiquitination), indicating proteins that coordinate chromosome segregation via ubiquitin signaling; the other terms are less representative noise.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031145","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0070979","count":2}]},{"hash":"960358331283260876","title":"Neurodevelopmental signaling and endosomal trafficking","description":"The top GO terms cluster around neural development and signaling: dopaminergic synaptic transmission, CNS projection neuron axonogenesis, and dorsal-ventral neural tube patterning. Endosomal transport regulation further points to neuronal receptor trafficking, supporting a cohesive theme of neurodevelopment and neuronal signaling, with a few peripheral terms (immune/cartilage) not altering the dominant signal.","confidence":"Medium","size":20,"edges":190,"triangles":1140,"max_degree":19,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":20},{"id":"GO:0007124","count":20},{"id":"GO:1901621","count":20},{"id":"GO:1904637","count":20},{"id":"GO:0001963","count":20}]},{"hash":"1287789458637993546","title":"Central carbon metabolism","description":"This cluster is enriched for core metabolic processes: glycolysis (GO:0006096), the TCA cycle (GO:0006099), glucose metabolism (GO:0006006), and the pentose phosphate shunt (GO:0006098), plus related biosynthetic steps (e.g., glyceraldehyde-3-phosphate and terpenoid/thiamine biosynthesis). The convergence of these pathways indicates proteins involved in central carbon metabolism and energy production, with some redox-related context suggested by the oxidative stress term. ","confidence":"High","size":20,"edges":106,"triangles":442,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":11},{"id":"GO:0006096","count":9},{"id":"GO:0055114","count":6},{"id":"GO:0009228","count":5},{"id":"GO:0006006","count":4}]},{"hash":"102846434033994260","title":"Fungal cell wall synthesis and secretory trafficking","description":"The cluster is dominated by fungal-specific processes: beta-glucan (fungal-type) cell wall biosynthesis, plus SRP- and post-translational targeting to membranes, indicating secretory/ER trafficking. The cellular response to unfolded protein likewise points to ER stress handling, suggesting a cohesive theme around wall assembly and secretory machinery under stress, with a few motifs (karyogamy, heat response regulation) reflecting broader fungal biology. Overall, these terms together imply a functionally connected group centered on cell wall construction and secretory pathways in fungi.","confidence":"Medium","size":20,"edges":14,"triangles":1,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0090084","count":3},{"id":"GO:0016226","count":3},{"id":"GO:0034620","count":3},{"id":"GO:0000742","count":3}]},{"hash":"1450778764575858611","title":"Cell Division and Vesicle Trafficking","description":"This cluster centers on mitosis and proliferation (cell division, mitotic spindle assembly, cell population proliferation, multicellular organism growth) and is linked with cytoskeletal dynamics (Arp2/3-mediated actin nucleation) and secretory pathway activity (COPII vesicle budding, Golgi-to-ER transport). Together, these terms suggest a coordinated program of cell division with cytoskeleton remodeling and vesicle trafficking.","confidence":"High","size":20,"edges":167,"triangles":791,"max_degree":19,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":7},{"id":"GO:0034314","count":6},{"id":"GO:0043982","count":6},{"id":"GO:0043981","count":6},{"id":"GO:0006890","count":6}]},{"hash":"58583024083950445","title":"Neuronal signaling and development","description":"The top GO terms emphasize synaptic transmission (glutamatergic and dopaminergic), sensory perception of pain, and developmental processes (multicellular organism development, neural tube patterning), along with transcription and endosomal trafficking. This combination points to proteins involved in neuronal communication and its regulation during development, with supporting roles in intracellular transport and transcriptional control. Some terms (like pseudohyphal growth) are less aligned but do not outweigh the dominant neuronal/developmental theme.","confidence":"High","size":20,"edges":8,"triangles":1,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035249","count":11},{"id":"GO:0046827","count":9},{"id":"GO:0019233","count":9},{"id":"GO:0007275","count":9},{"id":"GO:0006351","count":9}]},{"hash":"1120991654275052155","title":"Cell Cycle Regulation & Signaling","description":"Terms converge on mitotic control and growth signaling: mitosis- and APC/C-related processes, phosphorylation/dephosphorylation cycles (kinase/phosphatase), GTPase regulation, TORC1 signaling, and hypoxia response. mRNA transport is ancillary but does not obscure the core theme of cell-cycle\u2013related signaling.","confidence":"Medium","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":8},{"id":"GO:0051028","count":6},{"id":"GO:0071902","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0031954","count":6}]},{"hash":"1691544698119018141","title":"Translation with Transport and Stress-Response Functions","description":"This cluster is dominated by translation (GO:0006412) with 6 proteins, but also includes diverse transport and stress-related terms (e.g., glycine betaine transport, cobalt ion transport, taurine transmembrane transport, SOS response, and response to antibiotic). This suggests a loose grouping of proteins centered on translation while also participating in various transport and stress-response processes, rather than a single unified function. Confidence: Low","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0046677","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0031460","count":2},{"id":"GO:0099133","count":2}]},{"hash":"966998386618086670","title":"Neural development and dopamine response","description":"This cluster has a clear emphasis on nervous system development, axonogenesis and neuron migration, plus multiple entries for cellular response to dopamine, indicating a cohesive theme of neural development and signaling. Although a couple of terms touch on unrelated processes (spermatid development, T cell signaling, reticulophagy), the predominant pattern supports a neural development/dopamine response label.","confidence":"Medium","size":20,"edges":54,"triangles":44,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0007286","count":4},{"id":"GO:0061709","count":2},{"id":"GO:1903215","count":2},{"id":"GO:0007399","count":2},{"id":"GO:1902499","count":2}]},{"hash":"1140755451290936991","title":"Rab-trafficking in proliferating and migrating cells","description":"This cluster centers on Rab-mediated signaling and vesicle trafficking, evidenced by the prominent Rab protein signal transduction term, alongside strong signals for cell growth and movement (cell population proliferation, ameboidal migration, and cell spreading). ER stress response suggests the cells are in a stressed or adaptive state where trafficking and growth are coordinated. While copper homeostasis and cytotoxic T cell degranulation are present, they appear as supportive context rather than core drivers. Confidence: Medium","confidence":"","size":20,"edges":73,"triangles":103,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008283","count":17},{"id":"GO:0032482","count":16},{"id":"GO:1903206","count":16},{"id":"GO:0034976","count":16},{"id":"GO:0050771","count":16}]},{"hash":"34693509606046488","title":"Neural development and synaptic signaling","description":"The cluster is dominated by GO terms tied to neural development and synaptic function, including axonogenesis, excitatory postsynaptic potential, long-term potentiation, visual perception, and Schwann cell development. While there are some cell-cycle terms that are more general, the strongest, most consistent signals point to neural differentiation, growth, and synaptic modulation as the shared theme of these proteins.","confidence":"Medium","size":20,"edges":22,"triangles":9,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006469","count":11},{"id":"GO:0060079","count":11},{"id":"GO:0007409","count":11},{"id":"GO:0007507","count":11},{"id":"GO:0014044","count":11}]},{"hash":"2130474441460532726","title":"Cell signaling and transcription regulation","description":"The cluster shows enrichment for terms tied to cellular signaling in response to stimuli (GM-CSF, ionomycin), neural signaling and development (dopaminergic synaptic transmission, CNS axonogenesis), and transcriptional regulation (DNA-templated transcription, p53-mediated signaling). These together point to a common theme of signal transduction leading to changes in gene expression, despite some outliers like pseudohyphal growth. ","confidence":"Medium","size":20,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0097011","count":17},{"id":"GO:0006351","count":17},{"id":"GO:2000641","count":16},{"id":"GO:0007124","count":16},{"id":"GO:1901621","count":16}]},{"hash":"1443401734611561402","title":"Unknown","description":"The top GO terms are too heterogeneous: plant hormone signaling (cytokinin, ethylene), immune signaling (IL-4), xenobiotic response, hypoxia detection, and nuclear processes (DNA replication, telomerase assembly). There is no single cohesive function that unifies these proteins, and some terms (bacterial flagellum-dependent motility, obsolete protein import regulation) may reflect annotation noise. Therefore, I cannot assign a clear, representative function to this cluster.","confidence":"","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009736","count":7},{"id":"GO:0035690","count":6},{"id":"GO:0006261","count":5},{"id":"GO:0033160","count":5},{"id":"GO:1905323","count":5}]},{"hash":"1670846302436537984","title":"Mitotic Cycle and Centrosome Regulation","description":"The top GO terms are mainly mitosis- and centrosome-related: G1/S transition of the mitotic cell cycle, mitotic cell cycle, and centrosome cycle. This points to a core function in cell division control. The presence of innate immune response and JNK cascade regulation suggests concurrent stress-signaling modulation, while ubiquitin-protein catabolic processes and DNA-templated transcription reflect broader regulatory layers linked to cell-cycle progression. Overall, the label highlights a mitosis-centric module with associated regulatory and stress-response features.","confidence":"Medium","size":20,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000082","count":5},{"id":"GO:0071276","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0045087","count":5},{"id":"GO:0046329","count":4}]},{"hash":"605785942443576050","title":"Signaling and Transcription Regulation","description":"The enriched GO terms span transcription (DNA-templated transcription) and signaling (cGMP, Ras, and PKA pathways), plus nuclear export and downstream cellular responses, indicating proteins that coordinate gene expression with signal transduction rather than a single pathway. The presence of cardiac proliferation and olfactory terms suggests tissue-specific roles but within a broader theme of regulatory control over signaling and transcription.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":14},{"id":"GO:0060038","count":13},{"id":"GO:0046827","count":13},{"id":"GO:0071805","count":13},{"id":"GO:0045013","count":13}]},{"hash":"76601305074759051","title":"Ribosome biogenesis and translation","description":"The Top Terms show strong enrichment for translation-related processes: translation, cytoplasmic translation, ribosomal large subunit assembly and export from nucleus, indicating involvement in ribosome assembly and protein synthesis. There are also cell cycle terms (exit from mitosis, cell division) that commonly accompany growth-related translation. A couple of terms (retinal ganglion cell axon guidance, ephrin receptor signaling) are neural signaling and may reflect specific proteins in the cluster; however, the core theme remains ribosome and translation machinery.","confidence":"High","size":20,"edges":5,"triangles":1,"max_degree":4,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0031290","count":3},{"id":"GO:0048013","count":3},{"id":"GO:0000027","count":3},{"id":"GO:0010458","count":3}]},{"hash":"1040702605292538010","title":"Angiogenesis and Neural Development Signaling","description":"The dominant GO terms include angiogenesis and endothelial cell migration, as well as axonogenesis and dopaminergic synaptic transmission, pointing to a theme of coordinated signaling in vascular and neural development. Hedgehog pathway regulation and p53-mediated signaling also appear, suggesting broader developmental signaling cascades. A few terms (endosome transport, pseudohyphal growth, ionomycin response) are less directly tied to metazoan development, likely reflecting shared trafficking processes or annotation noise.","confidence":"Medium","size":20,"edges":14,"triangles":1,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043536","count":6},{"id":"GO:0001525","count":6},{"id":"GO:2000641","count":5},{"id":"GO:0007124","count":5},{"id":"GO:1901621","count":5}]},{"hash":"2158631950112219501","title":"Developmental gene expression and nuclear processes","description":"The top GO terms combine several developmental signals (brain development, multicellular organism growth, single fertilization) with core nuclear gene-expression activities (mRNA splicing, ribosomal biogenesis, translation initiation, and CENP-A chromatin assembly) and related regulatory processes (ubiquitin ligase activity). This suggests a theme where development is coordinated with fundamental gene-expression and chromatin maintenance. Some terms (defense response, SREBP signaling) are less tightly aligned but do not override the overarching pattern. Confidence: Medium","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:1904668","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0061641","count":2},{"id":"GO:0050830","count":2}]},{"hash":"223606811875669992","title":"DNA replication and chromatin maintenance","description":"The cluster is dominated by GO terms tied to DNA replication, nucleosome assembly, and telomere maintenance (including D-loop disassembly) and mitotic checkpoint signaling, pointing to a shared function in genome replication and chromatin organization. A few terms related to ethanol response or plant hormone signaling appear as minor, less representative signals.","confidence":"High","size":20,"edges":123,"triangles":429,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0006334","count":3},{"id":"GO:0061820","count":3},{"id":"GO:0033314","count":2},{"id":"GO:0002674","count":2},{"id":"GO:0071897","count":2}]},{"hash":"1781996704213148824","title":"Mitochondrial import and proteostasis","description":"The terms point to mitochondrial function: regulation of membrane permeability and protein import into the mitochondrial matrix, together with ubiquitin-dependent protein catabolic processes and proteasome assembly. This pattern suggests a cluster centered on mitochondrial protein homeostasis and quality control. Some other GO terms (lipid metabolism and plant-specific processes like chlorophyll biosynthesis and stamen formation) appear as secondary annotations, but do not override the core mitochondrial theme.","confidence":"Medium","size":20,"edges":9,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":5},{"id":"GO:2000134","count":5},{"id":"GO:0070940","count":5},{"id":"GO:1903740","count":5},{"id":"GO:0010867","count":5}]},{"hash":"2126335231311585203","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":22,"triangles":7,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":3},{"id":"GO:0000398","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0000472","count":2}]},{"hash":"791313656530277850","title":"Immune signaling and cell adhesion","description":"The top GO terms indicate immune cell signaling (B cell receptor signaling, B cell proliferation, NK cell cytotoxicity) alongside cytoskeletal and adhesion processes (lamellipodium assembly, microtubule anchoring, adherens junctions, epithelial adhesion, integrin signaling, Rho regulation). This combination suggests a module governing immune cell activation, migration, and cell\u2013cell interactions, rather than a single pathway.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050853","count":2},{"id":"GO:0030032","count":1},{"id":"GO:0030593","count":1},{"id":"GO:0034453","count":1},{"id":"GO:0030890","count":1}]},{"hash":"333715153431084685","title":"Chromatin remodeling and transcription regulation","description":"The top GO terms cluster around chromatin dynamics (chromatin remodeling, nucleosome assembly) and transcriptional control (negative regulation of transcription by RNA polymerase II, positive regulation of DNA binding). While a few terms touch on specific signaling or plant/muscle contexts, the dominant pattern ties to chromatin structure and regulation of gene expression, making a concise label like \"Chromatin remodeling and transcription regulation\" appropriate.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":3},{"id":"GO:0000122","count":2},{"id":"GO:0014718","count":2},{"id":"GO:0033234","count":2},{"id":"GO:0043388","count":2}]},{"hash":"26330300750706624","title":"Nuclear Transcription Regulation and Mitosis","description":"The cluster shows enrichment for DNA-templated transcription and negative regulation of transcription by RNA polymerase II, combined with cell cycle processes like G2/M transition and mitotic spindle pole separation, pointing to proteins that coordinate gene expression with mitosis. While terms like angiogenesis and detoxification appear, the dominant signal is nuclear transcription control linked to cell-cycle progression.","confidence":"High","size":20,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0098869","count":4},{"id":"GO:0046826","count":4},{"id":"GO:0042220","count":4},{"id":"GO:0051301","count":3}]},{"hash":"122054524595258494","title":"Metal and chemical stress response with transcription","description":"The top GO terms cluster around cellular responses to metal/chemical stress (cadmium, arsenite, ionomycin) and DNA-templated transcription, suggesting a coordinated transcriptional response to toxic stimuli. Additional terms on endosome transport and pseudohyphal growth point to broader stress adaptation and cellular remodeling in eukaryotes, supporting a cohesive theme of stress-induced gene regulation, despite some distant terms.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071276","count":4},{"id":"GO:0006351","count":4},{"id":"GO:2001033","count":4},{"id":"GO:1903936","count":4},{"id":"GO:0006349","count":3}]},{"hash":"1990850701139238065","title":"Unknown","description":"The top terms reflect a mix of nervous system development and dopaminergic signaling alongside endosome transport regulation, hormone response, cell-cycle checkpoints, and even pseudohyphal growth, suggesting a heterogeneous set of proteins with no single cohesive function. Because there is no clear, unified theme tying these GO terms together, a precise, representative label cannot be assigned.","confidence":"","size":20,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071374","count":20},{"id":"GO:0007124","count":20},{"id":"GO:2000641","count":20},{"id":"GO:0000187","count":20},{"id":"GO:0007094","count":20}]},{"hash":"1494428122773380844","title":"ER stress response and protein folding","description":"This cluster is dominated by terms related to endoplasmic reticulum (ER) function, including protein folding in the ER, unfolded protein response, ER-associated degradation, and regulation of translation initiation in response to ER stress, plus ER redox/homeostasis. Together they point to ER protein quality control and stress response mechanisms.","confidence":"High","size":20,"edges":2,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0034975","count":3},{"id":"GO:0045454","count":3},{"id":"GO:0030433","count":3}]},{"hash":"2267294278907271001","title":"Regulators of trafficking and signaling","description":"This cluster centers on regulatory processes affecting trafficking (receptor recycling, endosome size) and signaling (Rho pathway, transcription regulation, synaptic transmission), with additional links to ion transport. The common theme is modulation of cellular communication and membrane trafficking rather than a single enzymatic function, justifying a label focused on regulatory roles in trafficking and signaling.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0060316","count":4},{"id":"GO:0034968","count":3},{"id":"GO:0001881","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0051036","count":3}]},{"hash":"1329117866140257999","title":"Nuclear DNA transcription and replication","description":"The top GO terms are dominated by DNA-templated transcription, DNA replication, and DNA topology, with telomerase assembly also pointing to nuclear DNA maintenance. Although some terms relate to broader stress or signaling responses, the central theme is nuclear genome expression and maintenance. ","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0045793","count":4},{"id":"GO:0006261","count":3},{"id":"GO:0033160","count":3},{"id":"GO:0035690","count":3}]},{"hash":"525494322359297446","title":"Ubiquitin Signaling and Proteasomal Degradation","description":"The cluster is dominated by ubiquitination-related terms (K48, K63, K6 linkages), histone ubiquitination and turnover, ubiquitin-dependent degradation pathways (ERAD and overall proteolysis), and autoubiquitination, with additional links to spindle assembly/mitotic checkpoint signaling and TNF pathway regulation. This points to a cohesive role in ubiquitin-mediated proteostasis and cell cycle control during mitosis. ","confidence":"High","size":20,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070535","count":5},{"id":"GO:0044810","count":5},{"id":"GO:0051865","count":5},{"id":"GO:1903265","count":5},{"id":"GO:0051225","count":4}]},{"hash":"2175428080972772838","title":"Cell Cycle and DNA Replication Termination","description":"The cluster\u2019s strongest signals are in cell division and cell cycle processes, including mitotic DNA replication termination and site-specific DNA replication termination, suggesting proteins involved in coordinating replication with mitosis. While other terms touch on transcription regulation or stress responses, the dominant theme is cell-cycle control and DNA replication termination.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0050999","count":1},{"id":"GO:0071171","count":1},{"id":"GO:1902979","count":1}]},{"hash":"2228090319743358079","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036265","count":2},{"id":"GO:0050830","count":2},{"id":"GO:1990966","count":1},{"id":"GO:0006747","count":1},{"id":"GO:0034628","count":1}]},{"hash":"346615049296361722","title":"Ubiquitin-Dependent Degradation and ERAD","description":"The top GO terms are dominated by ubiquitin-related processes (ubiquitination, K48-linked ubiquitination, ubiquitin-dependent protein catabolic/ERAD pathways) and a peroxisomal import link, suggesting a cohesive module around ubiquitin-mediated protein turnover and ERAD-related degradation.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0030433","count":11},{"id":"GO:0046621","count":10},{"id":"GO:0038018","count":10},{"id":"GO:0051865","count":10},{"id":"GO:0042787","count":10}]},{"hash":"121690441206223797","title":"Transcription and Splicing Regulation","description":"The top GO terms emphasize regulation of DNA-templated transcription and, especially, regulation of alternative mRNA splicing via the spliceosome, including negative regulation of splicing. This points to a cluster of proteins involved in transcription control and RNA processing/splicing regulation. Additional terms like blastocyst formation and protein complex oligomerization are more peripheral but do not override the main theme. Overall, labeling this cluster as transcription and splicing regulation best captures the shared function of the proteins.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0048025","count":2},{"id":"GO:0000381","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0019363","count":2}]},{"hash":"2278282638211694124","title":"Stress-Responsive Transcription and Ion Transport","description":"The cluster combines transcription-related GO terms (DNA-templated transcription, negative regulation of transcription by RNA polymerase II) with multiple transport-related terms (potassium, cobalt, monoatomic anions, glycine betaine, taurine) and SOS/antibiotic stress signals, suggesting a collection of proteins involved in stress response that couple transcriptional regulation with membrane transport and osmotic/ion balance. While not tied to a single precise function, the pattern points to a generalized stress-adaptation module. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0009432","count":3},{"id":"GO:0071805","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0046677","count":2}]},{"hash":"2049620747715694327","title":"Transmembrane Ion and Sugar Transporters","description":"The top GO terms are dominated by various transmembrane transport processes, including potassium and sodium ions as well as glucose, galactose, fructose, and xenobiotic transport. This points to a cluster of membrane transporter proteins handling ion and sugar movement across membranes. A couple of terms on osmotic stress response and extracellular matrix disassembly exist but are less central to the main function. Overall, the dominant theme is membrane transport, so this label best captures the cluster's shared function.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":2},{"id":"GO:0022617","count":2},{"id":"GO:0052106","count":1},{"id":"GO:0006970","count":1},{"id":"GO:1904659","count":1}]},{"hash":"1981196258336112939","title":"Apoptosis regulation and proteolysis","description":"The cluster's GO terms include several directly related to apoptosis (negative regulation of extrinsic apoptotic signaling, release of cytochrome c from mitochondria) and proteolysis, pointing to a common theme of cell-death regulation and protein degradation. While a few terms are more divergent (phytochelatin biosynthesis, cellulose catabolism, fungal cell wall remodeling), the strongest signal centers on mitochondrial-related apoptotic control and proteolytic activity.","confidence":"Medium","size":20,"edges":13,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0043085","count":1},{"id":"GO:0046938","count":1},{"id":"GO:1904715","count":1},{"id":"GO:0006508","count":1},{"id":"GO:0051902","count":1}]},{"hash":"336388056884154670","title":"Environmental Signal Sensing and Response","description":"These terms indicate a broad theme of sensing environmental cues and transducing that information into transcriptional or regulatory responses, spanning plant hormone signaling (cytokinin/ethylene), xenobiotic stress, chemotaxis/flagellar motility, and phosphorelay pathways, with some regulation of sporulation and protein acetylation. The cluster thus seems to represent environmental signal sensing and downstream regulation rather than a single specific process.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009736","count":7},{"id":"GO:0006355","count":6},{"id":"GO:0035690","count":5},{"id":"GO:0071973","count":5},{"id":"GO:0010105","count":5}]},{"hash":"631443431985700167","title":"Gene expression and cell cycle regulation","description":"The top terms cluster around regulation, including mRNA processing/export, splicing, chromatin assembly, and cell-cycle control, with supporting roles for ubiquitination and stress response signaling; together they point to a coherent theme of regulating gene expression and cell-cycle progression, despite some broader processes present. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060271","count":2},{"id":"GO:2000728","count":1},{"id":"GO:1904668","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0061641","count":1}]},{"hash":"348518758887877049","title":"Wnt Secretion and ER-Golgi Trafficking","description":"The top terms cluster around the secretory pathway and protein transport (positive regulation of Wnt secretion, ER exit from ER, ER-to-Golgi transport, COPI vesicle coating), pointing to a core theme of secretion and trafficking that can influence signaling in development (egg-laying regulation, maternal axis specification). This makes \u201cWnt Secretion and ER-Golgi Trafficking\u201d a coherent, specific label for the group.","confidence":"Medium","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048042","count":3},{"id":"GO:0061357","count":3},{"id":"GO:0002121","count":3},{"id":"GO:0007311","count":3},{"id":"GO:0070863","count":3}]},{"hash":"1058612956075920319","title":"Ubiquitination and proteasomal degradation","description":"Based on the top GO terms, the cluster is dominated by ubiquitination-related processes (autoubiquitination, ubiquitin-dependent proteolysis, K48/K63-linked ubiquitination, ERAD) and signals regulating NF-\u03baB and TNF pathways, with an incidental link to histone turnover. This points to a cohesive theme of ubiquitin-mediated protein degradation and its regulatory signaling roles.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":11},{"id":"GO:0042787","count":9},{"id":"GO:0043123","count":8},{"id":"GO:0070534","count":8},{"id":"GO:0070936","count":7}]},{"hash":"1133771056945458977","title":"Ubiquitin-Dependent Protein Degradation (ERAD)","description":"The cluster shows strong representation of ubiquitination-related processes: autoubiquitination, ubiquitin-dependent protein catabolic process, RING-type ligase activity leading to K48-linked ubiquitination, and references to the ERAD pathway. These point to proteins involved in tagging substrates for proteasomal degradation and ER-associated degradation, which can also modulate growth and signaling via turnover of receptors like the Wnt pathway. A peroxisome import term appears less central, but overall theme is ubiquitin-mediated protein turnover.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":7},{"id":"GO:0042787","count":6},{"id":"GO:0030433","count":6},{"id":"GO:0070936","count":6},{"id":"GO:0046621","count":5}]},{"hash":"562020673229209321","title":"Mitotic spindle and cytoskeleton dynamics","description":"This cluster is dominated by mitosis-related GO terms (mitotic cell cycle, mitotic spindle assembly, CENP-A chromatin assembly) and cytoskeletal remodeling (actin filament depolymerization, microtubule severing), pointing to coordinated cell division and cytoskeletal regulation. Less central terms such as brain development, inflammatory cytokine production, and mRNA processing may reflect pleiotropy or shared components but do not override the core mitotic/cytoskeletal theme.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0007420","count":3},{"id":"GO:0030042","count":3},{"id":"GO:0090307","count":3},{"id":"GO:0051013","count":3}]},{"hash":"2165991009637218532","title":"Wax/Suberin Lipid Biosynthesis","description":"The cluster\u2019s top GO terms cluster around lipid biosynthesis and barrier formation (long-chain fatty-acyl-CoA metabolism, ether lipid biosynthesis, wax biosynthetic process, suberin biosynthetic process), suggesting a shared function in producing lipid-based barriers. A few terms relate to endocytosis and GTPase regulation, which are less cohesive with the lipid theme, but the predominant signal is lipid barrier synthesis.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035002","count":1},{"id":"GO:0035336","count":1},{"id":"GO:0008611","count":1},{"id":"GO:0010345","count":1},{"id":"GO:0010025","count":1}]},{"hash":"306072833496880624","title":"Mitotic spindle and centromeric chromatin assembly","description":"The cluster is enriched for mitosis-related terms (mitotic spindle assembly, CENP-A chromatin assembly, cell cycle checkpoint regulation) and ubiquitination processes that commonly regulate chromosome segregation, suggesting a cohesive role in mitosis and centromere function. Some terms touch on nuclear RNA processing and neural/glial processes, but the strongest signal points to chromosome segregation machinery.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":2},{"id":"GO:2000728","count":1},{"id":"GO:1904668","count":1},{"id":"GO:0050773","count":1},{"id":"GO:0000398","count":1}]},{"hash":"1548828593547017317","title":"Developmental Gene Expression and Ubiquitin Regulation","description":"The cluster centers on transcriptional control (DNA-templated transcription, splicing) and chromatin assembly, with concurrent signals for multicellular development (skin development, developmental processes). Ubiquitin-related processes (polyubiquitination, ubiquitin ligase activity) suggest regulation of protein turnover linked to gene expression in development, and a heat-stress response term hints at regulatory flexibility. Together these imply a coordinated role in developmental gene expression and proteostasis.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0043588","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0007275","count":3},{"id":"GO:2000728","count":2}]},{"hash":"1029846034655803798","title":"Ubiquitin-Mediated Endocytosis and Vesicle Trafficking","description":"This cluster centers on ubiquitination and endocytic/vesicular transport processes, including ubiquitin-dependent endocytosis, protein ubiquitination, and intracellular transport with recycling, with a supporting role for GTPase activity regulation in trafficking. The retina and brain development terms likely reflect neural-specific roles of these core trafficking/ubiquitination pathways.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006886","count":2},{"id":"GO:0070086","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0060041","count":2},{"id":"GO:0000209","count":2}]},{"hash":"280120277425507014","title":"Unknown","description":"The Top Terms span chromatin regulation, trafficking (receptor recycling and endosome size), Rho signaling, glutamatergic synaptic activity, and developmental processes (eye and vasculature development) with no clear, single theme linking the proteins. There are no edges or triangles, suggesting little or no functional cohesion in this cluster. Therefore a generic Unknown label is appropriate.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034968","count":1},{"id":"GO:0001881","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0051036","count":1},{"id":"GO:0035023","count":1}]},{"hash":"1623525021160393361","title":"Ribosome Biogenesis: rRNA Maturation","description":"The strongest GO signals are maturation of 5.8S rRNA and LSU-rRNA from rRNA transcripts, pointing to ribosome biogenesis and ribosomal RNA processing. The presence of DNA-templated transcription and its regulation terms is sometimes linked to nucleolar functions and ribosome gene regulation, supporting a nucleolar/ribosome assembly theme. A few terms (cadmium response, IgG isotype switching, host-mediated viral activation) appear less connected and may reflect broader cellular context rather than the core cluster function. Overall, the dominant theme is rRNA maturation and ribosome biogenesis, with some peripheral notes.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000466","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0051568","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1858494206442848536","title":"Endosome-to-Golgi Transport and Rab Regulation","description":"The top GO terms cluster around intracellular vesicle trafficking, especially endosome-to-Golgi and recycling routes (plasma membrane to endosome, recycling endosome to Golgi, retrograde transport, late endosome to Golgi) and Rab signaling regulation, indicating a cohesive theme of endosomal trafficking with Rab control. A few terms (nucleosome assembly, placental morphogenesis) are less central but do not outweigh the dominant transport-focused pattern.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032483","count":2},{"id":"GO:0060669","count":2},{"id":"GO:0006334","count":2},{"id":"GO:0048227","count":1},{"id":"GO:0071955","count":1}]},{"hash":"1681493053053834213","title":"Unknown","description":"The top GO terms span a broad and inconsistent set of processes (cyclic nucleotide biosynthesis, ABA and suberin biosynthesis, transcription regulation, NF-kappaB signaling, Rap signaling, MHC biosynthesis regulation, RNA maintenance, and DNA replication initiation) with no clear common function. There are no edges or network connections (Edges 0, Triangles 0, Max Degree 0) to tie the proteins into a single cohesive pathway, so a specific, representative label cannot be confidently assigned.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009190","count":2},{"id":"GO:0009688","count":1},{"id":"GO:0090419","count":1},{"id":"GO:0010345","count":1},{"id":"GO:0034244","count":1}]},{"hash":"1106753218430740095","title":"Rab/Rap GTPase-driven vesicle trafficking","description":"The cluster centers on Rap and Rab GTPase signaling and various endosomal transport steps (plasma membrane to endosome, recycling endosome to Golgi, intracellular transport, retrograde transport), with microtubule organization supporting trafficking. This points to a cohesive role in small GTPase\u2013mediated regulation of intracellular vesicle trafficking and recycling, possibly with signaling cross-talk via cAMP/cGMP pathways.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032486","count":3},{"id":"GO:0090630","count":3},{"id":"GO:0032483","count":3},{"id":"GO:0071320","count":2},{"id":"GO:0071321","count":2}]},{"hash":"468511242440244106","title":"Membrane trafficking and cytokinesis","description":"The top GO terms point to vesicle transport and membrane remodeling (endosome-Golgi routing, Cvt/vacuolar targeting, endocytic recycling, plasma membrane tubulation) along with cell division processes (cleavage furrow formation, mitotic cell cycle) and sporulation-related membrane formation, plus lipid biosynthesis. This suggests a cohesive theme around membrane dynamics governing trafficking and division/development, hence the label. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034499","count":2},{"id":"GO:0032258","count":2},{"id":"GO:1990126","count":1},{"id":"GO:0097320","count":1},{"id":"GO:0000278","count":1}]},{"hash":"1566721762961461417","title":"Brain development and neural signaling","description":"It centers on brain development and neural signaling, highlighted by brain development, GPCR-mediated neural signaling, and glial apoptotic/inflammatory processes, with supporting evidence from gene-expression and protein-ubiquitination pathways frequently involved in neural function.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000728","count":1},{"id":"GO:1904668","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0061641","count":1},{"id":"GO:0002534","count":1}]},{"hash":"567832009426982819","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034553","count":1},{"id":"GO:0006120","count":1},{"id":"GO:0010098","count":1},{"id":"GO:0032447","count":1},{"id":"GO:0002136","count":1}]},{"hash":"994772442255510033","title":"Olfactory GPCR-cAMP Signaling in Neurons","description":"The top GO terms point to a shared theme of cAMP signaling and neuronal activity, including cellular responses to cAMP, regulation of cAMP-dependent kinase activity, and membrane potential changes, with strong emphasis on sensory perception of smell and olfactory receptor pathways. The presence of antipsychotic/drug response terms (e.g., clozapine) further supports a brain signaling context where GPCR-cAMP signaling mediates both sensory and pharmacological responses. Together these suggest a cohesive cluster centered on neuronal GPCR-cAMP signaling and olfactory receptor activity.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:2000480","count":3},{"id":"GO:0098719","count":3},{"id":"GO:0071320","count":3},{"id":"GO:0097332","count":3},{"id":"GO:0046827","count":3}]},{"hash":"1918085357462308749","title":"Neuronal chromatin remodeling and receptor trafficking","description":"Top GO terms indicate a mix of neural signaling (glutamatergic synaptic transmission, receptor recycling, endosome size regulation) and chromatin-related processes (chromatin remodeling, transcription regulation, histone methylation). The inclusion of neural development hints (forebrain neuroblast division) reinforces a neural context. This pattern suggests proteins that connect gene expression regulation with membrane trafficking at neurons, encompassing both transcriptional control and synaptic receptor handling.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035249","count":2},{"id":"GO:0001881","count":2},{"id":"GO:0051036","count":2},{"id":"GO:0060316","count":2},{"id":"GO:0034968","count":2}]},{"hash":"109566821474059336","title":"Cell-cycle and chromatin regulation","description":"The cluster centers on core processes of cell division (cell cycle, regulation of kinetochore assembly) and chromatin modulation (histone methylation, desumoylation) with transcriptional activity (DNA-templated transcription) also represented. While there are a few outlier terms (SRP-dependent targeting, flagellum organization), the dominant signals point to regulation of gene expression and chromosome segregation during cell division.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0051568","count":2},{"id":"GO:0034729","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006616","count":1}]},{"hash":"2163175722959075723","title":"Unknown","description":"The terms span plants (abscisic acid biosynthesis), transcription regulation (negative regulation of transcription elongation, transcription-related signaling), signaling pathways (NF-kappaB, Rap), RNA handling (RNA localization maintenance, miRNA processing), DNA replication initiation, neuronal structure (Purkinje cell layer organization), and cell adhesion (integrin activation). The wide diversity shows no coherent, single biological theme tying the cluster together, so a specific functional label is not confidently representational.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009688","count":1},{"id":"GO:0090419","count":1},{"id":"GO:0034244","count":1},{"id":"GO:0007249","count":1},{"id":"GO:0032487","count":1}]},{"hash":"1473862029434338958","title":"Unknown","description":"The top GO terms are a mix of kinetochore regulation, chromatin modification, and disparate developmental processes with only one term each, giving no shared function tying the proteins together.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090234","count":1},{"id":"GO:0060711","count":1},{"id":"GO:0016926","count":1},{"id":"GO:1904333","count":1},{"id":"GO:0035562","count":1}]},{"hash":"512050022432719849","title":"Mitotic Regulation and Developmental Signaling","description":"The top GO terms include strong signals for kinetochore localization and negative regulation of CDK activity, pointing to cell-cycle control. Additionally, several terms relate to neural development and synaptic morphology (cerebellar cortex formation, Bergmann glial differentiation, dendritic spine morphogenesis), suggesting a broader developmental signaling role. Immune and metabolic pathways appear but are less dominant, indicating a cluster of regulators with roles in cell-cycle control and tissue development signaling across contexts.","confidence":"Medium","size":19,"edges":169,"triangles":936,"max_degree":18,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0034501","count":19},{"id":"GO:0045736","count":19},{"id":"GO:0050852","count":16},{"id":"GO:0008285","count":16},{"id":"GO:0008286","count":16}]},{"hash":"1411624263002635941","title":"Cell Cycle Regulation and Endosomal Trafficking","description":"The top GO terms show a strong emphasis on cell cycle control (protein localization to kinetochore; negative regulation of cyclin-dependent protein kinase activity; regulation of protein stability) and intracellular trafficking (endosome transport). While there are peripheral terms related to signaling and growth, the dominant themes tie to cell cycle regulation combined with trafficking pathways, justifying this combined label.","confidence":"Medium","size":19,"edges":30,"triangles":28,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0034501","count":14},{"id":"GO:0045736","count":14},{"id":"GO:0014850","count":12},{"id":"GO:0031647","count":12},{"id":"GO:0060044","count":12}]},{"hash":"1441330525465072030","title":"Neuronal development and dopaminergic signaling","description":"The cluster shows strong enrichment for neural development and synaptic signaling terms: CNS projection neuron axonogenesis, dopaminergic synaptic transmission, and neural patterning regulation. While there are some outliers (endosome transport, immune differentiation, cartilage processes), the dominant theme points to neuronal development and dopamine-related neural communication.","confidence":"High","size":19,"edges":169,"triangles":936,"max_degree":18,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":19},{"id":"GO:0007124","count":19},{"id":"GO:1901621","count":19},{"id":"GO:1904637","count":19},{"id":"GO:0001963","count":19}]},{"hash":"1192269096854694403","title":"Multi-linkage Deubiquitinases","description":"These proteins cluster around deubiquitination activities across several ubiquitin linkages (K11, K29, K48, K6, K63) and ubiquitin-dependent protein turnover, with supporting hints from transcription regulation and chromatin-related terms. This suggests a core theme of versatile deubiquitinases modulating both protein fate and gene expression via ubiquitin signaling.","confidence":"High","size":19,"edges":12,"triangles":5,"max_degree":8,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0035871","count":6},{"id":"GO:0006355","count":5},{"id":"GO:0035523","count":5},{"id":"GO:0071108","count":5},{"id":"GO:0044313","count":5}]},{"hash":"1673204818082860599","title":"Chromatin, transcription, and mitotic regulation","description":"The proteins cluster around nuclear gene expression (DNA-templated transcription, splicing, mRNA export) and chromosome/mitosis control (CENP-A chromatin assembly, mitotic spindle assembly, cell cycle checkpoint), with ubiquitin-related regulation, suggesting a chromatin- and mitosis-focused group. Some terms like stress responses may reflect broader signaling rather than core function.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071276","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0090307","count":3},{"id":"GO:2000728","count":2},{"id":"GO:1904668","count":2}]},{"hash":"679745975408861055","title":"Mitotic Regulation and Endosomal Trafficking","description":"The top GO terms are dominated by mitosis-related processes (mitotic cell cycle; chromosome passenger complex localization to kinetochore) and endosomal/vesicle trafficking (receptor recycling; regulation of endosome size), suggesting a core function in coordinating cell division with intracellular transport. Additional terms like cilium assembly, tRNA wobble uridine modification, and responses to UV-B/pheromone appear as ancillary connections, but the central theme centers on mitosis with vesicle trafficking.","confidence":"Medium","size":19,"edges":151,"triangles":731,"max_degree":18,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":17},{"id":"GO:0010224","count":17},{"id":"GO:0006547","count":17},{"id":"GO:0001881","count":17},{"id":"GO:0019236","count":17}]},{"hash":"557440461729438156","title":"Ubiquitination and Proteasomal Degradation","description":"This cluster is dominated by ubiquitination-related processes: protein autoubiquitination, K6- and K48-linked ubiquitination, SCF-dependent ubiquitin-mediated protein catabolic processes, proteasomal degradation, and neddylation. These terms point to core participation in tagging proteins for degradation and regulating proteasome activity via ubiquitin-like modifiers. Additional terms on ERAD and peroxisomal protein import suggest broader protein quality control links, while viral processes and nucleotide-excision repair reflect ubiquitin\u2019s wider regulatory roles in those contexts. Overall, the set coherently maps to the ubiquitin-proteasome system and related modifications.","confidence":"High","size":19,"edges":46,"triangles":26,"max_degree":15,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":12},{"id":"GO:0085020","count":12},{"id":"GO:0042787","count":11},{"id":"GO:0031146","count":11},{"id":"GO:0070936","count":11}]},{"hash":"1346935485799883367","title":"Neural development and synaptic function","description":"Based on the dominant GO terms, the proteins cluster around neural development and synaptic activity, including axonogenesis, excitatory synaptic signaling, long-term potentiation, Schwann cell development, and visual perception. The presence of some cell cycle terms may reflect broader annotation, but the prevailing theme is neuronal development and synaptic function.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000086","count":8},{"id":"GO:0060079","count":8},{"id":"GO:0007409","count":8},{"id":"GO:0009738","count":8},{"id":"GO:0035774","count":8}]},{"hash":"476320038808863547","title":"cAMP Signaling and Membrane Potential Regulation","description":"The cluster's enriched terms center on cAMP signaling and its regulation (cellular response to cAMP, negative regulation of PKA activity), linked to transcriptional control (DNA-templated transcription, nuclear protein export) and membrane excitability (sodium import, regulation of membrane potential), with notes on cardiac proliferation and responses to antipsychotic drugs like clozapine. This pattern suggests a cohesive theme of cAMP-driven transcriptional regulation influencing membrane signaling in muscle and neural contexts, including drug response.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":13},{"id":"GO:2000480","count":7},{"id":"GO:0098719","count":7},{"id":"GO:0071320","count":7},{"id":"GO:0097332","count":7}]},{"hash":"2011224060646795532","title":"Transcription and chromatin dynamics","description":"The top terms center on transcription (RNA polymerase II transcription and snRNA transcription) and chromatin-related processes (nucleosome assembly, G-quadruplex DNA formation, and telomere-associated chromatin dynamics), suggesting a cohesive theme around gene expression regulation via chromatin state and DNA structure. Some hormone signaling terms appear as outliers, but the core signal points to transcriptional control and chromatin organization rather than a single pathway.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009737","count":5},{"id":"GO:0009736","count":4},{"id":"GO:0006366","count":3},{"id":"GO:0021983","count":3},{"id":"GO:0061820","count":3}]},{"hash":"80840233041840662","title":"Chromatin assembly and epigenetic regulation","description":"The top GO terms cluster around nucleosome assembly and epigenetic regulation (DNA methylation, histone modification), indicating a core theme of chromatin organization and epigenetic control. Other terms mention mitochondrial processes and development, which appear more peripheral or noisy in this set. Thus, the cluster is best described as chromatin-related, with some unrelated annotations present. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006334","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0045039","count":2},{"id":"GO:0006626","count":2},{"id":"GO:0072321","count":2}]},{"hash":"294853664377169153","title":"TGF-beta/BMP Signaling Regulation","description":"This cluster is dominated by GO terms that negatively regulate TGF-beta/BMP signaling, including negative regulation of TGF-beta receptor signaling and BMP signaling, along with cellular responses to TGF-beta and SMAD-related activity. The inclusion of peptidyl-threonine dephosphorylation supports a theme of phosphatase-mediated modulation of these pathways, and the non-canonical NF-kappaB regulation suggests broader signaling cross-talk. A couple of terms like photosystem stoichiometry adjustment and meristem identity maintenance appear tangential or likely due to annotation noise, but the core signal is consistent with regulation of growth factor signaling. Confidence: High","confidence":"","size":19,"edges":158,"triangles":776,"max_degree":18,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046827","count":17},{"id":"GO:0042347","count":16},{"id":"GO:0071560","count":16},{"id":"GO:0080005","count":16},{"id":"GO:0061191","count":16}]},{"hash":"1101769994060531372","title":"Mitotic signaling and COPII vesicle trafficking","description":"This cluster centers on mitotic processes (mitotic cell cycle, cell division) and vesicle trafficking (COPII-coated vesicle budding), with accompanying signaling and cytoskeletal regulation (ERK cascade, calcium-dependent exocytosis, focal adhesion assembly, actin remodeling). The combination suggests a theme of coordinating cell division with membrane trafficking and signaling pathways.","confidence":"Medium","size":19,"edges":58,"triangles":69,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":9},{"id":"GO:0070374","count":8},{"id":"GO:0090114","count":8},{"id":"GO:0045956","count":8},{"id":"GO:0034260","count":8}]},{"hash":"2166047179573960717","title":"Nuclear RNA processing and chromatin assembly with ubiquitin regulation","description":"These terms center on nuclear events (mRNA splicing/export, CENP-A\u2013dependent chromatin assembly, cell cycle checkpoint regulation) and ubiquitin-related control (polyubiquitination, ubiquitin ligase activity), suggesting a cohesive theme around nuclear RNA processing and chromatin/ubiquitin signaling; peripheral terms like glial apoptosis or GPCR signaling are less representative.","confidence":"Medium","size":19,"edges":91,"triangles":126,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:2000728","count":1},{"id":"GO:1904668","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0061641","count":1}]},{"hash":"1184641935516250051","title":"Androgen signaling and male reproductive development","description":"The cluster shows strong representation of GO terms tied to steroid hormone receptor complex assembly, male sex differentiation, and prostate gland development, pointing to androgen signaling and male reproductive development as the core function. Some terms (cell division, interferon response, morphine response, cadmium response) appear less connected and may reflect general cellular processes or annotation noise, so the label is plausible but not definitive.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":10},{"id":"GO:0070389","count":10},{"id":"GO:0043278","count":10},{"id":"GO:0006463","count":10},{"id":"GO:0046661","count":10}]},{"hash":"260030742497390254","title":"Neuronal development and endosomal trafficking","description":"This cluster centers on brain and nervous system development, with dendrite morphogenesis, indicating neuronal differentiation. It also includes several endosome-transport steps (endosome to lysosome, early endosome to Golgi/late endosome) and ubiquitination, suggesting coordinated regulation of protein trafficking and turnover during neuronal development.","confidence":"Medium","size":19,"edges":9,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090307","count":4},{"id":"GO:0007420","count":4},{"id":"GO:0016567","count":4},{"id":"GO:0048813","count":4},{"id":"GO:0007399","count":4}]},{"hash":"1433578527526525578","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by GO terms tied to making and using the protein-synthesis machinery: translation, ribosome biogenesis, ribosomal small subunit biogenesis, and tRNA modification. Additional terms about the cell cycle and cell division suggest a link between ribosome production and proliferation. While a few terms (e.g., antibiotic response, cellular fusion) are less central, the core signal points to ribosome assembly and function driving the cluster\u2019s proteins. ","confidence":"High","size":19,"edges":3,"triangles":0,"max_degree":3,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0046677","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0006412","count":4},{"id":"GO:0000747","count":3}]},{"hash":"1556360279908966468","title":"Neural development and apoptosis","description":"This cluster shows strong enrichment for neural development terms (forebrain development, nervous system development, neural tube closure, dendrite morphogenesis) and apoptosis (apoptotic process, intrinsic apoptotic signaling pathway in ER stress), suggesting a core theme of neurodevelopmental regulation with programmed cell death. While there are also terms related to placental development and innate immunity, these appear less central to the dominant neurodevelopmental pattern.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0001843","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0030900","count":4},{"id":"GO:0001893","count":4}]},{"hash":"523236739437000041","title":"Cellular stress response","description":"Based on the GO terms, many entries are annotated with cellular responses to stressors (gamma radiation, singlet oxygen, hypoxia, arsenite, psychosocial stress, nitroglycerin). A general theme of stress-response pathways emerges, though a few terms (placenta development, histone demethylation) appear unrelated or broader regulatory terms, suggesting the cluster is enriched for stress-related processes but also contains outliers.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033169","count":1},{"id":"GO:1990911","count":1},{"id":"GO:1904843","count":1},{"id":"GO:0071480","count":1},{"id":"GO:0000304","count":1}]},{"hash":"362080931846383217","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060079","count":3},{"id":"GO:0000082","count":3},{"id":"GO:0006541","count":3},{"id":"GO:0007595","count":3},{"id":"GO:0006351","count":3}]},{"hash":"2282712313547000154","title":"Gene Expression Regulation under Hormonal/ER Stress","description":"The cluster centers on fundamental gene expression processes (translation, transcription, mRNA splicing) and cellular stress/hormone signaling (ER unfolded protein response, cAMP and glucocorticoid responses). This suggests proteins that co-regulate gene expression in response to hormonal cues and ER stress, with some additional development and biosynthetic processes as secondary associations.","confidence":"Medium","size":19,"edges":148,"triangles":632,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0051591","count":2},{"id":"GO:0051384","count":2},{"id":"GO:0030968","count":2}]},{"hash":"591003464092283510","title":"Unknown","description":"The top GO terms are scattered across RNA processing, ubiquitination, chromatin assembly, inflammatory signaling, glial apoptosis, GPCR signaling, and brain development, with no single dominant biological theme tying all 19 proteins together. This makes it hard to assign a specific, cohesive label to the cluster.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000728","count":1},{"id":"GO:1904668","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0061641","count":1},{"id":"GO:0002534","count":1}]},{"hash":"1728133809813814914","title":"Neural development and synaptic signaling","description":"The terms cluster around neural growth and communication: axonogenesis, dopaminergic synaptic transmission, and dorsal/ventral patterning point to neural development and signaling; endosomal transport relates to synaptic trafficking and receptor turnover, while ionomycin response hints at calcium-dependent signaling in neurons. A few items (NK T differentiation, cartilage condensation) are less connected, but the neural theme is the strongest.","confidence":"Medium","size":19,"edges":137,"triangles":517,"max_degree":18,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":19},{"id":"GO:0007124","count":19},{"id":"GO:1901621","count":19},{"id":"GO:1904637","count":19},{"id":"GO:0001963","count":19}]},{"hash":"1758878486776431609","title":"Translation Machinery and Regulation","description":"The cluster is dominated by translation-related GO terms (translation, translational initiation/elongation/termination, and positive regulation of cytoplasmic translation, plus selenocysteine incorporation), indicating a cohesive group of proteins involved in protein synthesis and its control; a couple of terms related to nervous system development appear but do not override the core translation theme.","confidence":"High","size":19,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0046677","count":2},{"id":"GO:0006413","count":2},{"id":"GO:2000767","count":2},{"id":"GO:0045901","count":2}]},{"hash":"1052018956130716608","title":"Unknown","description":"The top GO terms span chromatin modification, transcription regulation, endosome dynamics (recycling and size), Rho signaling, vesicle trafficking, and even plant-specific biosynthesis pathways, plus a neuronal signaling term. This broad and disparate set shows no single cohesive function or pathway tying the 19 proteins together, and there are no edges indicating a shared interaction network, so a confident, specific label isn\u2019t supportable.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034968","count":2},{"id":"GO:0001881","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0051036","count":2},{"id":"GO:0035023","count":2}]},{"hash":"1937794089596523751","title":"Growth, signaling, and trafficking","description":"The top GO terms show a mix of growth-related regulation (positive regulation of cell size, pseudohyphal growth), signaling and neuronal-related responses (glutamatergic synaptic transmission, response to cocaine, chemotaxis), transcriptional control (DNA-templated transcription), metabolism (glucose metabolic process), and intracellular trafficking (endosome transport). This pattern points to a broad theme of how cells regulate growth and respond to stimuli through signaling networks and transport processes, rather than a single specific function.","confidence":"Medium","size":19,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006006","count":5},{"id":"GO:0045793","count":4},{"id":"GO:0001890","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0035249","count":4}]},{"hash":"1171104018454916935","title":"Bacterial biosynthesis and ion transport","description":"This cluster is driven by biosynthetic processes (lipopolysaccharide, serine, antibiotic biosynthesis) and membrane/ion transport terms (monoatomic cation transport, sodium transport, membrane repolarization), which together point to a bacterial metabolism/ membrane-physiology module. Sporulation and transcription regulation appear but are less central, reinforcing a broader bacterial functional grouping.","confidence":"Medium","size":19,"edges":21,"triangles":8,"max_degree":7,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0009103","count":4},{"id":"GO:0006564","count":4},{"id":"GO:0030435","count":3},{"id":"GO:0006355","count":3}]},{"hash":"707844417098553269","title":"Spliceosome-regulated RNA splicing and mRNA processing","description":"The top GO terms cluster around RNA splicing and regulation of alternative splicing via the spliceosome, plus mRNA export and negative regulation of mRNA splicing. Additional terms touch on cell cycle regulation, ER unfolded protein response, and protein ubiquitination, suggesting the proteins broadly participate in RNA processing with related links to cell-cycle control and protein quality pathways.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000381","count":5},{"id":"GO:0008380","count":4},{"id":"GO:0000122","count":3},{"id":"GO:0071157","count":3},{"id":"GO:0006406","count":2}]},{"hash":"2225181438450399485","title":"Nuclear transcription and RNA processing","description":"Top terms indicate transcription in the nucleus, various RNA processing steps (pre-miRNA processing, mRNA export, nuclear mRNA surveillance), and ribosome biogenesis, all central to nuclear gene expression. Some chromatin modification terms (histone acetylation regulation) further support a theme of chromatin-level control of expression. Despite some obsolescent terms, the cluster coherently centers on nuclear gene expression and RNA processing functions.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000617","count":2},{"id":"GO:0031054","count":2},{"id":"GO:0071442","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0042254","count":2}]},{"hash":"1629628364226078074","title":"Vesicle trafficking and secretion","description":"This cluster\u2019s GO terms center on intracellular vesicle transport and secretory pathways: Golgi-related processes (Golgi ribbon formation, Golgi-to-ER retrograde transport, vesicle targeting), autophagosome docking, receptor recycling, and various degranulation and mucus secretion activities. Together these indicate a shared function in vesicle formation, targeting, fusion, and regulated secretion, including immune cell degranulation and epithelial mucus secretion. ","confidence":"Medium","size":19,"edges":9,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0001921","count":1},{"id":"GO:0043320","count":1},{"id":"GO:0043312","count":1},{"id":"GO:0006903","count":1},{"id":"GO:0070254","count":1}]},{"hash":"377443724194158041","title":"Vertebrate Embryonic Development and Transcription Regulators","description":"The most represented GO terms point to developmental processes (neural tube closure, forebrain and skeletal development, multicellular organism development) together with DNA-templated transcription and cell cycle progression, indicating a module of regulatory proteins involved in embryogenesis and proliferation. Protein heterotrimerization further suggests formation of multi-subunit transcriptional or signaling complexes. Some terms relate to stress or immune responses, which may reflect cross-species annotations, but the main theme appears to be vertebrate development and transcriptional regulation.","confidence":"Medium","size":19,"edges":13,"triangles":1,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0070208","count":4},{"id":"GO:0001843","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0001501","count":4}]},{"hash":"130191052349741486","title":"Unknown","description":"The GO terms span immune signaling (NF-kappaB regulation, chemokine production), cellular responses to chemicals, epithelial polarity, cytoskeletal and spindle dynamics, protein localization, and even cardiac cell communication\u2014covering disparate biological processes with no clear, single theme. This makes a concise, representative cluster name unreliable.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":3},{"id":"GO:0071642","count":2},{"id":"GO:1901594","count":2},{"id":"GO:0086070","count":2},{"id":"GO:0090162","count":2}]},{"hash":"373915366454401173","title":"Nucleotide Salvage and Translation Components","description":"The top GO terms point to both translation (GO:0006412) and nucleotide salvage (AMP, GMP, IMP, XMP salvage), suggesting a theme around protein synthesis coupled with nucleotide recycling. The remaining terms are more diverse (regulatory and metabolic), making the core signal somewhat mixed but still centered on nucleotide salvage linked to translation. Confidence: Medium","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:2001246","count":2},{"id":"GO:0006541","count":1},{"id":"GO:0045892","count":1},{"id":"GO:0044209","count":1}]},{"hash":"1596467838497029406","title":"Mitochondrial energy metabolism and protein turnover","description":"The dominant GO terms are mitochondrial electron transport and aerobic respiration, indicating a focus on mitochondrial energy production. Additional terms for protein catabolic processes and protein oligomerization suggest coordinated protein turnover and assembly, with a note of lifespan determination linking metabolism to longevity. Some outlier terms (symbiont entry, pheromone maturation, bradykinin catabolism) may reflect annotation noise or cross-species effects, but the core theme appears to be energy metabolism and protein turnover.","confidence":"Medium","size":19,"edges":49,"triangles":63,"max_degree":12,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0010815","count":11},{"id":"GO:0009060","count":6},{"id":"GO:0006122","count":6},{"id":"GO:0046718","count":6},{"id":"GO:0071432","count":6}]},{"hash":"352745014918367456","title":"Plant Development and Gene Regulation","description":"This cluster centers on core gene expression processes (transcription regulation and ribosome biogenesis) with concurrent cell division, plus several plant-specific signaling and light-related terms (ethylene signaling, light detection, and chromophore linkage), suggesting a theme of plant development coordinated with gene regulation. Some terms appear non-plant or atypical, but the dominant pattern points to plant growth and regulatory signaling.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0007420","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0000747","count":2}]},{"hash":"626640509377287842","title":"Mitotic cell cycle and APC-dependent proteolysis","description":"The GO terms point to mitotic processes (mitotic cell cycle, cell division, sister chromatid cohesion) and ubiquitin-mediated degradation (APC-dependent catabolic process, K11-linked ubiquitination), suggesting a cohesive theme of mitotic progression coupled with targeted protein degradation, even though no interactions are observed in the current edge data.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0031145","count":3},{"id":"GO:0090344","count":2}]},{"hash":"2078019990804027985","title":"Rab GTPase\u2013driven vesicle trafficking","description":"This cluster is characterized by GO terms centered on Rab-regulated signal transduction and vesicle trafficking, including endocytosis and recycling, and general GTPase activity regulation. The apoptosis and Th2 cytokine production terms are peripheral and less indicative of a cohesive trafficking function.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032483","count":1},{"id":"GO:0097194","count":1},{"id":"GO:0048488","count":1},{"id":"GO:0032456","count":1},{"id":"GO:0043087","count":1}]},{"hash":"523305578227611466","title":"Membrane trafficking and remodeling","description":"The GO terms cluster around membrane dynamics: endocytic recycling, plasma membrane tubulation, endosome-to-Golgi transport, cytokinesis-related cleavage furrow formation, and related lipid biosynthesis, suggesting a membrane-trafficking and remodeling theme rather than a single organ or developmental pathway.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990126","count":1},{"id":"GO:0097320","count":1},{"id":"GO:0000278","count":1},{"id":"GO:0022617","count":1},{"id":"GO:0036089","count":1}]},{"hash":"840231383496305261","title":"ER-Golgi Vesicle Trafficking","description":"The top GO terms are dominated by COPII-coated vesicle budding and various ER-Golgi transport processes (retrograde Golgi-ER, ER-to-Golgi), pointing to a secretory/trafficking signature. Other terms like ribosome biogenesis and mitotic processes are present but likely reflect broader cellular growth states rather than a single core function, so the clearest theme is ER-Golgi vesicle trafficking.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090114","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0000278","count":2}]},{"hash":"2059863012820946656","title":"Developmental signaling and transcription regulation","description":"The cluster emphasizes developmental processes (neural tube closure, forebrain and skeletal development, multicellular organism development) along with DNA-templated transcription and signaling (positive regulation of GTPase activity). While there are some stress-response terms (cadmium, defense against Gram-positive bacteria), the dominant pattern points to regulation of development through transcriptional control and signaling pathways. Confidence: Medium","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0001843","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0001501","count":3},{"id":"GO:0007275","count":3}]},{"hash":"344925606797035893","title":"Lens fiber cell development and eye morphogenesis","description":"The top GO terms cluster around lens and eye formation (lens development in camera-type eye, lens fiber cell development/differentiation, camera-type eye development, visual perception), with supporting epithelial morphogenesis terms. This suggests the proteins collectively participate in lens fiber cell formation and broader eye morphogenesis.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007155","count":1},{"id":"GO:0070309","count":1},{"id":"GO:0043010","count":1},{"id":"GO:0002088","count":1},{"id":"GO:1902168","count":1}]},{"hash":"1524654686746426155","title":"Unknown","description":"The proteins show a highly diverse set of GO terms (mitotic cell cycle, morphogenesis, ion transport, cyclic nucleotide signaling, sensory perception, development, aerotaxis, antibiotic response) with no clear shared pathway or functional theme, and there are no connecting edges, so no coherent label can be assigned beyond Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0000902","count":2},{"id":"GO:0098719","count":2},{"id":"GO:0071321","count":2},{"id":"GO:0010754","count":2}]},{"hash":"2041137399394876200","title":"Ubiquitin-Mediated Protein Turnover","description":"The cluster is dominated by ubiquitination-related processes (autoubiquitination, K48/K63 linkages, and ubiquitin-dependent protein catabolic process) and by terms linking ubiquitination to regulation of signaling pathways (NF-kappaB) and receptor turnover (Wnt). This suggests a cohesive theme around ubiquitin tagging leading to protein degradation and signaling control, with a few less-central terms likely representing noise (e.g., peroxisome import). ","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051865","count":8},{"id":"GO:0070936","count":8},{"id":"GO:0042787","count":7},{"id":"GO:0070534","count":6},{"id":"GO:0030433","count":6}]},{"hash":"1721119745903514893","title":"Ubiquitination and NF-\u03baB signaling","description":"The cluster is enriched for ubiquitin-related processes (autoubiquitination, ubiquitin-dependent proteolysis) and NF-\u03baB\u2013related signaling (TNF-mediated signaling, I-kappaB phosphorylation, NF-\u03baB-inducing kinase activity). This suggests a cohesive module governing protein turnover and inflammatory signaling, with ancillary links to chromatin remodeling and antiviral responses.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":12},{"id":"GO:0042787","count":10},{"id":"GO:0033209","count":9},{"id":"GO:1901253","count":9},{"id":"GO:0007250","count":9}]},{"hash":"21445014410131040","title":"Translational initiation and RNA processing regulation","description":"The top terms are dominated by translation initiation and reinitiation processes, including IRES-dependent viral translation and regulation of translational initiation, pointing to post-transcriptional control at the protein synthesis level. The presence of spliceosome-mediated splicing and polyadenylation terms, along with miRNA-mediated translational silencing, suggests additional RNA processing roles in the same cluster. Overall, the cluster seems tied to post-transcriptional gene regulation, especially at the translation initiation stage, with supporting RNA processing activities.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0001731","count":10},{"id":"GO:0002188","count":10},{"id":"GO:0075525","count":7},{"id":"GO:0045292","count":7},{"id":"GO:0075522","count":7}]},{"hash":"1895372983317190244","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:2000637","count":1},{"id":"GO:0061157","count":1},{"id":"GO:0001308","count":1},{"id":"GO:1902416","count":1}]},{"hash":"2176165356627920947","title":"Cell Cycle and Growth","description":"The top terms are dominated by cell division and cell cycle, indicating a cluster enriched for proliferative and growth-related processes. There are also miscellaneous terms related to cell wall organization, secretion, and metabolism of peptidoglycan and cellulose, which may reflect annotation breadth or mixed-species content; however, the central theme centers on cellular proliferation and growth control.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0009254","count":1},{"id":"GO:0030245","count":1},{"id":"GO:0008360","count":1}]},{"hash":"601687461298667537","title":"Unknown","description":"The top GO terms include receptor recycling and endosome size regulation and even synaptic transmission, which could hint at neuronal trafficking, but many terms are obscure or unrelated (oxidation-reduction, histone methylation, transcription regulation, metabolic pathways), giving no clear, cohesive theme for the cluster. Therefore, I assign Unknown with None confidence. ","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0034968","count":2},{"id":"GO:0001881","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0051036","count":2}]},{"hash":"541643948155874287","title":"Developmental Regulation and Stress Response","description":"The cluster shows terms spanning embryonic development (forebrain development, neural tube closure), transcriptional regulation (DNA-templated transcription), cell division, and stress/apoptosis pathways (intrinsic apoptotic signaling in response to ER stress), as well as defense responses and metal stress. The mix suggests a broad regulatory/developmental gene set rather than a single cohesive pathway, with some noise from obsolete histone methylation terms.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0070059","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0000920","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0001843","count":4}]},{"hash":"1024529503301945169","title":"DNA Damage Response & Chromatin Remodeling","description":"This cluster centers on DNA maintenance and chromatin dynamics, with GO terms for DNA repair, histone H2A K63-linked ubiquitination, deubiquitination, and regulation of CDK activity, suggesting coordinated control of the cell cycle in response to DNA damage. Some terms (adaptive immune response, endosome transport, VEGF signaling) are more peripheral and may reflect broader signaling roles or incidental annotations. Overall, the dominant theme is DNA damage response and chromatin modification.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045737","count":2},{"id":"GO:0006281","count":2},{"id":"GO:1901315","count":2},{"id":"GO:0002250","count":2},{"id":"GO:2000780","count":2}]},{"hash":"1384109969520267516","title":"Nuclear Chromatin and Telomere Regulation","description":"The set of top GO terms centers on chromatin-related processes (nucleosome assembly, G-quadruplex DNA, snRNA transcription) and telomere biology (telomeric D-loop disassembly, telomere protein localization). Ubiquitin-dependent protein catabolic process also ties to protein turnover involved in chromatin maintenance. While some terms (cytokinin signaling, viral process) are peripheral or broad, the dominant pattern points to nuclear chromatin regulation and telomere dynamics.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0009736","count":4},{"id":"GO:0016032","count":4},{"id":"GO:0061820","count":3},{"id":"GO:1901347","count":3}]},{"hash":"1566611700648042599","title":"Cytokinesis and Membrane Trafficking Regulators","description":"This cluster\u2019s top GO terms point to regulators of GTPase signaling (including Ras), protein modification (ubiquitination and poly-ADP-ribosylation), and negative regulation of signaling pathways, combined with processes in membrane remodeling such as endocytic recycling, plasma membrane tubulation, and cleavage furrow formation. The presence of mitotic cell cycle and ECM disassembly terms suggests involvement in cell division and extracellular remodeling, consistent with coordination of cytoskeletal dynamics and membrane trafficking during cytokinesis. The diverse but related functions imply a cohesive theme around regulating cell division-related trafficking and signaling rather than a single enzymatic activity. Confidence in this label is Medium.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0070212","count":2},{"id":"GO:0046580","count":2}]},{"hash":"1604446242654464296","title":"Unknown","description":"The proteins show a scattered mix of GO terms including DNA replication and telomere maintenance, but also plant hormone signaling, immune signaling, hypoxia detection, xenobiotic response, and even bacterial motility, with no clear shared function linking most members. Because there is no dominant theme or cohesive interaction pattern among the top terms, there isn\u2019t a coherent biological module to name beyond Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006261","count":1},{"id":"GO:0009736","count":1},{"id":"GO:0033160","count":1},{"id":"GO:0035690","count":1},{"id":"GO:1905323","count":1}]},{"hash":"2181634600270937734","title":"Ubiquitin-regulated vesicle trafficking","description":"The GO terms highlight endocytic recycling, endosomal vesicle fusion, vacuole fusion, SNARE complex regulation, and intracellular protein transport, together with K48- and K11-linked deubiquitination. This suggests a cohesive function where ubiquitin processing governs vesicle trafficking and membrane fusion processes, possibly connecting TORC1 signaling to trafficking control; a transcription-related term appears ancillary. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071108","count":2},{"id":"GO:0035871","count":2},{"id":"GO:0006351","count":2},{"id":"GO:1990126","count":1},{"id":"GO:0099022","count":1}]},{"hash":"411923358017585072","title":"Centrosome and centriole biogenesis","description":"This cluster is dominated by GO terms tied to centriole cohesion, centrosome duplication, and centriole replication, which strongly point to centrosome/centriole biogenesis and cell-cycle\u2013related assembly. Other terms (NF-kappaB regulation, TNF signaling, endosome transport, etc.) are minor or tangential, but do not override the centriole-centric themes. Therefore, the cluster most plausibly represents proteins involved in centrosome and centriole duplication/replication.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010457","count":1},{"id":"GO:0051298","count":1},{"id":"GO:0007099","count":1},{"id":"GO:0032088","count":1},{"id":"GO:0033209","count":1}]},{"hash":"892437949933095213","title":"Unknown","description":"The top terms span ion transport (potassium, acetate, hydrogen peroxide), various stress and signaling responses (hyperosmotic, salt stress, cAMP), and several tissue- or development-specific processes (lateral ventricle development, eye morphogenesis, pancreatic juice and corticotropin secretion). There isn't a single coherent function that ties these terms together for the cluster, so a specific label isn\u2019t supported.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":4},{"id":"GO:0071474","count":3},{"id":"GO:0021670","count":3},{"id":"GO:0048593","count":3},{"id":"GO:0051458","count":3}]},{"hash":"721434108557737703","title":"Mitochondrial Transport and Metabolism","description":"The top GO terms are dominated by mitochondrial-related transport processes (NAD transmembrane transport, iron import into the mitochondrion, thiosulfate transport, deoxynucleotide transport) and regulation of mitochondrial membrane permeability, alongside energy-related terms like adaptive thermogenesis and liver regeneration. This pattern suggests a functional cluster centered on mitochondrial transport across membranes and associated metabolic activities, rather than a single signaling pathway. Hence, a name focusing on mitochondrial transport and metabolism is most representative.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097421","count":2},{"id":"GO:1990845","count":2},{"id":"GO:0060546","count":2},{"id":"GO:0097274","count":2},{"id":"GO:0070542","count":2}]},{"hash":"1937320069496477035","title":"Muscle development and calcium signaling","description":"The top GO terms are dominated by skeletal muscle fiber development and cardiac myofibril assembly, plus regulation of calcium release into the cytosol, pointing to a cluster of proteins involved in muscle differentiation, sarcomere assembly, and excitation-contraction signaling. Additional terms about protein phosphorylation and GTPase regulation fit signaling pathways that coordinate muscle growth and structural remodeling. Some terms like urea homeostasis and metanephric tubule development appear as noise/outliers, but the core theme remains muscle development and Ca2+-dependent signaling.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048741","count":4},{"id":"GO:0071902","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0031954","count":3},{"id":"GO:0051260","count":3}]},{"hash":"948996319695867002","title":"Lens development and fiber cell differentiation","description":"The cluster is dominated by lens and eye development terms (lens fiber cell morphogenesis, camera-type eye development, lens development in camera-type eye, lens fiber cell differentiation) with visual perception and epithelium morphogenesis supporting this theme, indicating roles in lens fiber formation; a couple of outlier terms relate to nucleolar transcription and rRNA regulation that are less relevant.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070309","count":2},{"id":"GO:0043010","count":2},{"id":"GO:0002088","count":2},{"id":"GO:0070307","count":2},{"id":"GO:0007601","count":2}]},{"hash":"189607582622655135","title":"Neural development and endosomal trafficking","description":"The top GO terms cluster around neural development and signaling (axonogenesis of CNS projection neurons, dopaminergic synaptic transmission, dorsal/ventral patterning) and vesicle trafficking (regulation of endosome transport). This suggests a functional module linked to neural differentiation processes that depend on endosomal trafficking, with additional developmental signals (p53 regulation, NK T differentiation, cartilage condensation) indicating broader developmental roles. Confidence: Medium","confidence":"","size":18,"edges":139,"triangles":618,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":18},{"id":"GO:0007124","count":18},{"id":"GO:1901621","count":18},{"id":"GO:1904637","count":18},{"id":"GO:0001963","count":18}]},{"hash":"32455282228843263","title":"Unknown","description":"The top GO terms are highly diverse, including telomere maintenance regulation, response to cocaine, endosome transport, pseudohyphal growth, neural signaling and dopaminergic synaptic transmission, p53 signaling, and NK T cell differentiation. This breadth suggests no single cohesive function tying all proteins together, so a unified, intuitive label isn\u2019t supported. ","confidence":"","size":18,"edges":20,"triangles":7,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0032212","count":17},{"id":"GO:0042220","count":17},{"id":"GO:0051973","count":17},{"id":"GO:2000641","count":16},{"id":"GO:0007124","count":16}]},{"hash":"707353410397047634","title":"Neuronal development and synaptic signaling","description":"The cluster shows strong representation of GO terms related to neural development (axonogenesis in CNS projection neurons, dorsal/ventral neural tube patterning) and synaptic function (dopaminergic neurotransmission), with endosome transport supporting vesicle trafficking essential for neurons. While a few terms are non-neuronal, the dominant theme centers on neural development and synaptic activity.","confidence":"Medium","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":18},{"id":"GO:0007124","count":18},{"id":"GO:1901621","count":18},{"id":"GO:1904637","count":18},{"id":"GO:0001963","count":18}]},{"hash":"1734636228298968427","title":"Ion Transport and Membrane Regulation","description":"This cluster shows a set of GO terms focused on ion movement across membranes and related membrane potential dynamics: regulation of sodium and potassium transport, monoatomic cation transmembrane transport, membrane repolarization, and calcium release within the Golgi. Although several terms are unrelated, the recurring theme is ion homeostasis and membrane activity, justifying a label around ion transport and membrane regulation.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":5},{"id":"GO:0086009","count":5},{"id":"GO:0009103","count":5},{"id":"GO:0002028","count":5},{"id":"GO:0046272","count":5}]},{"hash":"1012770450892248472","title":"Muscle development and neuromuscular synapse formation","description":"This cluster centers on muscle differentiation (myoblast fusion) and neural connectivity (axonogenesis, excitatory postsynaptic potentials, long-term potentiation), suggesting coordinated muscle fiber formation with synaptic maturation. The presence of multicellular development and cell-cycle terms supports developmental remodeling, while occasional annotation noise (e.g., abscisic acid signaling) may reflect cross-species assignments. Overall, the dominant theme is muscle development linked to neuromuscular signaling.","confidence":"Medium","size":18,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":8},{"id":"GO:0000278","count":8},{"id":"GO:0007520","count":7},{"id":"GO:0007409","count":7},{"id":"GO:0060291","count":7}]},{"hash":"1997214435201982802","title":"Apoptosis and innate immune signaling regulation","description":"The top GO terms point to regulators of cell fate and innate signaling: negative regulation of apoptotic and necroptotic pathways, modulation of Toll-like receptor signaling, and ubiquitination\u2013all common ways cells control survival and immune responses. There are also terms related to cell-cycle regulation, suggesting broader roles in coordinating proliferation with survival. Taken together, this cluster appears to encode regulators of apoptosis/necroptosis and innate immune signaling, with ancillary involvement in cell-cycle control.","confidence":"Medium","size":18,"edges":10,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0060544","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0043066","count":2},{"id":"GO:0000209","count":2},{"id":"GO:0034121","count":2}]},{"hash":"1053198857764547531","title":"Immune signaling and stress response regulators","description":"It includes terms centered on immune signaling (NF-kappaB activation, interferon production, inflammasome regulation) and cellular stress responses (stress granule localization, ubiquitin-proteasome/ERAD pathways, calcium transport), with a few broader developmental or contractile terms that can accompany stress-adaptation. The shared theme is regulation of immune and cellular stress responses, rather than a single specific pathway.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097050","count":3},{"id":"GO:0043123","count":2},{"id":"GO:0043588","count":2},{"id":"GO:0030433","count":2},{"id":"GO:1901896","count":2}]},{"hash":"1843731609015413718","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0090307","count":3},{"id":"GO:0071276","count":2},{"id":"GO:0051568","count":2},{"id":"GO:0043547","count":2}]},{"hash":"1038940343586581981","title":"Neural stress response and brain development","description":"The terms point to nervous system roles, with brain development and glial apoptosis, plus neural signaling via GPCR/PLC pathways. Supporting signs of stress-responsive mRNA processing/export and ubiquitin-mediated regulation suggest a cluster focused on neural development and stress-response regulation rather than a single, isolated pathway.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000728","count":6},{"id":"GO:1904668","count":6},{"id":"GO:0000398","count":6},{"id":"GO:0061641","count":6},{"id":"GO:0002534","count":6}]},{"hash":"1647496486089201849","title":"Lung branching morphogenesis and basement membrane remodeling","description":"The strongest signals come from GO terms tied to epithelial tube branching in lung morphogenesis and basement membrane disassembly, indicating a cluster focused on lung development and extracellular matrix remodeling. While there are additional terms related to hormonal response and immune or developmental processes, the central theme appears to be morphogenesis with ECM dynamics.","confidence":"Medium","size":18,"edges":143,"triangles":675,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0034769","count":9},{"id":"GO:0051603","count":9},{"id":"GO:0050790","count":9},{"id":"GO:0097067","count":9},{"id":"GO:0060441","count":9}]},{"hash":"589928264389395634","title":"Neural signaling and ion transport","description":"The cluster\u2019s top GO terms strongly point to nervous system signaling: glutamatergic synaptic transmission and sensory perception of pain. Supporting this theme are ion homeostasis terms (potassium and sodium transport), which are key to neuronal excitability, along with endosomal transport that can relate to receptor trafficking in neurons. Some terms touch on transcription and development, suggesting broader regulatory roles, but the most cohesive signal across the terms is neural signaling together with ion transport.","confidence":"Medium","size":18,"edges":12,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":6},{"id":"GO:0019233","count":6},{"id":"GO:0007275","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0030007","count":6}]},{"hash":"1704891989082250067","title":"Neuronal signaling and endosomal transport","description":"The cluster is dominated by terms tied to neuronal development and signaling (dopaminergic synaptic transmission, CNS projection neuron axonogenesis, neural patterning) along with endosomal trafficking (regulation of early to late endosome transport) and related regulatory processes, suggesting a cohesive theme around neuronal communication and intracellular transport. Some terms are broader or less related, but the neural emphasis is clear.","confidence":"Medium","size":18,"edges":99,"triangles":261,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046827","count":18},{"id":"GO:2000641","count":16},{"id":"GO:0007124","count":16},{"id":"GO:1901621","count":16},{"id":"GO:1904637","count":16}]},{"hash":"555190177182278467","title":"Ubiquitin-Mediated Proteolysis in Mitosis","description":"This cluster is dominated by ubiquitin-dependent protein degradation pathways, including SCF- and APC/C-mediated proteolysis, and is strongly enriched for mitotic cell cycle and cell division terms. While a few terms touch on related regulatory processes (e.g., histone methylation, ERAD, cadmium response), the core theme centers on ubiquitin-dependent proteolysis driving mitotic progression.","confidence":"High","size":18,"edges":19,"triangles":3,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0070979","count":3},{"id":"GO:0030433","count":2},{"id":"GO:2001162","count":2},{"id":"GO:0042787","count":2}]},{"hash":"1486583232675264088","title":"Neural development and signaling","description":"Based on the prominent GO terms: regulation of neuron-related transport and signaling, axonogenesis of CNS projection neurons, dopaminergic synaptic transmission, and signaling pathway regulation (p53 mediator, Smoothened), along with calcium signaling (ionomycin response) and endosome transport. While a few terms are unrelated (cartilage condensation, NK T cell differentiation, yeast pseudohyphal growth, aging stress), the overall pattern points to neural development and neuronal communication processes.","confidence":"Medium","size":18,"edges":125,"triangles":436,"max_degree":16,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":17},{"id":"GO:0007124","count":17},{"id":"GO:1901621","count":17},{"id":"GO:1904637","count":17},{"id":"GO:0001963","count":17}]},{"hash":"530903417740141572","title":"Vesicle trafficking and secretion","description":"The top GO terms are dominated by vesicle transport and secretory processes, including Golgi ribbon formation, ER-to-Golgi vesicle transport, receptor recycling, and degranulation in immune cells, along with autophagosome docking and protein targeting to vacuolar membranes. While a couple of terms relate to development and neural plasticity, the common thread is movement and secretion of cellular cargo through vesicular pathways, supporting a label of vesicle trafficking and secretion for this cluster.","confidence":"Medium","size":18,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0090161","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0060291","count":3},{"id":"GO:0001893","count":3},{"id":"GO:0001921","count":2}]},{"hash":"1297817365801799258","title":"Neuronal development and dopaminergic signaling","description":"The top GO terms cluster around neural development and neural signaling: sensory perception of pain, dopaminergic synaptic transmission, neural tube patterning, and transcriptional regulation linked to development. Additional terms on endosome transport and transcription suggest coordinated trafficking and gene expression supporting neuronal function, indicating proteins focused on neuronal development and dopamine-based signaling.","confidence":"High","size":18,"edges":10,"triangles":0,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019233","count":14},{"id":"GO:0007275","count":14},{"id":"GO:0046827","count":12},{"id":"GO:0006351","count":12},{"id":"GO:2000641","count":11}]},{"hash":"897686820186619823","title":"Unknown","description":"The top GO terms span a mix of endosome transport, fungal morphology, neural development and signaling, immune differentiation, and cartilage processes, with no single cohesive theme tying them together. This diversity suggests no clear, representative function for the cluster, so an Unknown label is most appropriate.","confidence":"","size":18,"edges":134,"triangles":562,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":18},{"id":"GO:0007124","count":18},{"id":"GO:1901621","count":18},{"id":"GO:1904637","count":18},{"id":"GO:0001963","count":18}]},{"hash":"1716299924099329115","title":"Neural development and endosome trafficking","description":"The top GO terms strongly point to neural development processes (axonogenesis, dopaminergic synaptic transmission, neural tube patterning) and intracellular trafficking (regulation of early-to-late endosome transport), suggesting a module where endosomal trafficking supports neural development signaling. While terms like NK T differentiation and cartilage condensation indicate broader development, the most cohesive theme across the cluster is neural development linked to endosome transport and signaling regulation. ","confidence":"Medium","size":18,"edges":3,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":18},{"id":"GO:0007124","count":18},{"id":"GO:1901621","count":18},{"id":"GO:1904637","count":18},{"id":"GO:0001963","count":18}]},{"hash":"315948041535147396","title":"Unknown","description":"The terms cover muscle development, kidney morphogenesis, immune signaling, and protein ubiquitination, suggesting diverse, unrelated roles. There is no common pathway or process linking the majority of proteins, and the network has no edges, making a cohesive label unreliable. Thus the cluster is Unknown.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048741","count":3},{"id":"GO:0007519","count":2},{"id":"GO:0002467","count":2},{"id":"GO:0042787","count":2},{"id":"GO:2000312","count":2}]},{"hash":"538785595371902765","title":"Deoxyribonucleotide Biosynthesis","description":"These terms converge on deoxyribonucleotide production and DNA precursor metabolism, including TMP biosynthesis, dGTP metabolism, nucleoside monophosphate phosphorylation, and salvage of deoxyguanosine. The mitochondrial electron transport term is present but the recurring theme is nucleotide biosynthesis and related phosphorylation, indicating a cluster of proteins involved in producing DNA building blocks.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":5},{"id":"GO:0006230","count":3},{"id":"GO:0046070","count":3},{"id":"GO:0046940","count":3},{"id":"GO:0046092","count":3}]},{"hash":"1655706267817766259","title":"Pancreatic insulin secretion and ER protein folding","description":"The top terms include pancreas development, insulin secretion in response to glucose, and protein folding in the endoplasmic reticulum, which together suggest a secretory\u2013ER\u2013processing role typical of pancreatic cells handling insulin. The other terms in the list are diverse (e.g., plant hormone responses, neuron signaling), indicating some noise, but the dominant signals point to pancreatic insulin processing. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031016","count":2},{"id":"GO:0035773","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0080028","count":1}]},{"hash":"617126027883799408","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071374","count":2},{"id":"GO:0090084","count":2},{"id":"GO:1901621","count":2},{"id":"GO:0006458","count":2},{"id":"GO:0070843","count":2}]},{"hash":"814898781818896144","title":"ESCRT-driven mitosis and endosomal trafficking","description":"This cluster centers on core mitotic processes (cell cycle, cell division, spindle assembly, chromosome condensation, nucleus organization) and membrane remodeling/trafficking linked to ESCRT function (intralumenal vesicle formation, multivesicular body-lysosome fusion, viral budding via host ESCRT). The convergence of mitotic and ESCRT-associated vesicle pathways suggests proteins in this cluster coordinate division with ESCRT-mediated membrane remodeling. ","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0070676","count":2},{"id":"GO:2000641","count":1},{"id":"GO:1901673","count":1}]},{"hash":"1162299857458717272","title":"Ubiquitin-Proteasome Regulation of Cell Cycle","description":"Most terms point to ubiquitin signaling and proteasomal degradation (polyubiquitination, SCF-dependent proteasomal degradation, ERAD pathway, regulation of ubiquitin ligase activity), which are central to controlling mitosis and cell proliferation. Transcription-related terms and histone methylation are linked downstream or as co-regulated processes. Together, they define a cohesive theme around ubiquitin-mediated proteostasis influencing cell cycle and gene expression.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000209","count":3},{"id":"GO:0008283","count":3},{"id":"GO:0051568","count":3},{"id":"GO:0034729","count":3},{"id":"GO:0031146","count":3}]},{"hash":"827632446414998213","title":"Ion channels in sensory signaling","description":"These proteins cluster around ion transport (potassium and sodium) and membrane potential maintenance (resting potential regulation), together with mechanosensory and thermosensory signaling (touch and thermosensory behavior), suggesting ion channels involved in sensory transduction. An immune-related term is present but does not override the dominant ion-channel/sensory theme.","confidence":"Medium","size":18,"edges":139,"triangles":619,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071805","count":15},{"id":"GO:0098914","count":15},{"id":"GO:0030322","count":15},{"id":"GO:0060075","count":15},{"id":"GO:0050976","count":15}]},{"hash":"1748437928228654689","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032435","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0008284","count":2},{"id":"GO:0009718","count":1}]},{"hash":"206107903234668125","title":"Stress Response and Metabolic Signaling","description":"The GO terms cluster around environmental stress responses (gamma radiation, xenobiotic stimulus, hypoxia detection) and metabolic/growth signaling (glucose metabolism, TORC1 signaling, multicellular growth). Although a few terms touch on development and RNA processing, the dominant theme is cellular stress response paired with metabolic regulation, justifying this label.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071480","count":2},{"id":"GO:0006006","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0035264","count":2},{"id":"GO:0038202","count":2}]},{"hash":"1670762517779644824","title":"DNA repair and telomere maintenance","description":"Top GO terms center on DNA repair, double-strand break repair, and telomere maintenance, with spindle assembly also linked to chromosome handling during division; these reflect a genome-maintenance/function cluster. The presence of reproductive and developmental terms likely reflects tissue-specific roles or annotation noise, but the dominant theme is genome integrity and chromosome maintenance.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0008033","count":2},{"id":"GO:0006302","count":1},{"id":"GO:0008209","count":1},{"id":"GO:0032212","count":1}]},{"hash":"1363404892843712045","title":"RNA processing and translation regulation","description":"Proteins are enriched for RNA processing and translation control terms: regulation of mRNA splicing via spliceosome, mRNA polyadenylation, mRNA stability in response to stress, mRNA modification, regulatory ncRNA- and miRNA-mediated gene silencing, and eIF4F complex assembly. This points to a cohesive role in post-transcriptional RNA regulation and translation initiation control.","confidence":"High","size":18,"edges":35,"triangles":39,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1900363","count":5},{"id":"GO:0048025","count":5},{"id":"GO:0035278","count":5},{"id":"GO:0010610","count":5},{"id":"GO:0016556","count":5}]},{"hash":"53380387113527494","title":"ER stress/UPR and ER-to-Golgi trafficking","description":"The top GO terms point to endoplasmic reticulum\u2013focused processes: unfolded protein response in the ER, protein localization to the ER, and COPII-coated vesicle budding (ER-to-Golgi transport), plus calcium homeostasis and oxidative stress responses. These co-occur to form a coherent theme around ER stress signaling and the secretory pathway, with some host\u2013virus interaction terms that may reflect how ER stress modulates viral replication. Overall, the cluster seems best described as ER stress and secretory pathway components.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044828","count":2},{"id":"GO:0044829","count":2},{"id":"GO:0060304","count":2},{"id":"GO:0070972","count":2},{"id":"GO:0090114","count":2}]},{"hash":"28800836110354455","title":"Renin-angiotensin system and kidney development","description":"The cluster centers on GO terms related to the renin-angiotensin system (regulation of blood volume, aldosterone production, and angiotensin maturation) and mesonephros development, pointing to renal endocrine signaling and kidney maturation as the core theme. Some terms like antigen processing, digestion, and drinking behavior appear less directly connected but may reflect broader physiological roles; however, the dominant signal is renal/angiotensin-related functions.","confidence":"Medium","size":18,"edges":81,"triangles":122,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0002016","count":2},{"id":"GO:0070305","count":2},{"id":"GO:0016540","count":2},{"id":"GO:0019886","count":2},{"id":"GO:0002003","count":2}]},{"hash":"754965317527867421","title":"Renin-angiotensin axis in kidney function","description":"The top GO terms center on regulation of blood volume and aldosterone production via the renin-angiotensin system, angiotensin maturation, and mesonephros development, pointing to kidney physiology and development. Additional terms like drinking behavior and some immune or protein-processing terms can be linked to systemic homeostasis and renal functions, but the dominant theme is the RA axis governing kidney development and fluid balance.","confidence":"High","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002016","count":2},{"id":"GO:0030163","count":2},{"id":"GO:0016540","count":2},{"id":"GO:0070305","count":2},{"id":"GO:0019886","count":2}]},{"hash":"1615699096382545327","title":"Unknown","description":"The top GO terms are highly heterogeneous, spanning DNA replication and telomerase assembly alongside diverse signaling and stress responses (cytokinin and ethylene signaling, IL-4 response, xenobiotic response, hypoxia detection, and bacterial motility). There isn\u2019t a single coherent function uniting these proteins, so a clear, representative label cannot be assigned.","confidence":"","size":18,"edges":16,"triangles":0,"max_degree":13,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006261","count":3},{"id":"GO:0009736","count":3},{"id":"GO:0033160","count":3},{"id":"GO:0035690","count":3},{"id":"GO:1905323","count":3}]},{"hash":"1025993482889411283","title":"Golgi-ER Vesicle Transport and Mitosis","description":"The cluster is enriched for COPII-coated vesicle budding and ER\u2013Golgi transport terms, together with mitotic spindle assembly and mitotic cell cycle terms, indicating a cohesive module linking secretory pathway trafficking with cell division. Ribosome biogenesis and brain development terms add breadth but do not override the central theme of vesicle trafficking intertwined with mitosis. This makes \"Golgi-ER Vesicle Transport and Mitosis\" a concise, representative label.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090114","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0000278","count":2}]},{"hash":"1533947525901934733","title":"Membrane trafficking and cytokinesis","description":"The terms cluster around membrane dynamics\u2014endocytic recycling, plasma membrane tubulation, endosome-to-Golgi transport, cleavage furrow formation, and related membrane formation activities (including prospore membrane formation) and phosphatidic acid biosynthesis\u2014pointing to membrane remodeling and trafficking during cell division. Development-related terms appear infrequently and do not define a cohesive program for the cluster. Thus, the core theme is membrane trafficking and division-related remodeling.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990126","count":1},{"id":"GO:0097320","count":1},{"id":"GO:0000278","count":1},{"id":"GO:0022617","count":1},{"id":"GO:0036089","count":1}]},{"hash":"1250916887441727664","title":"Nuclear mRNA decay and Pol II elongation control","description":"The cluster\u2019s top GO terms cluster around deadenylation-dependent decapping and decay of nuclear-transcribed mRNA, deadenylation/decapping processes, and regulation of transcription elongation by RNA polymerase II, along with mRNA processing body assembly. These points suggest a cohesive theme of RNA turnover and transcription elongation regulation, despite a few outlier terms. Confidence: Medium","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000290","count":1},{"id":"GO:0033147","count":1},{"id":"GO:0010606","count":1},{"id":"GO:0000288","count":1},{"id":"GO:0006368","count":1}]},{"hash":"1553521250067010794","title":"Ubiquitin-regulated protein turnover","description":"The top terms are dominated by ubiquitin-related processes (autoubiquitination, regulation of deubiquitination, and free ubiquitin chain polymerization), pointing to ubiquitin signaling controlling protein tagging and turnover. Other terms touch unrelated areas (tRNA processing, dendrite extension, heart development), but the ubiquitin-centered cluster is the most coherent theme.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000235","count":1},{"id":"GO:0003197","count":1},{"id":"GO:0010768","count":1},{"id":"GO:0051865","count":1},{"id":"GO:0033160","count":1}]},{"hash":"789046553851863579","title":"Unknown","description":"The cluster\u2019s top GO terms span plant hormone signaling (cytokinin, ethylene), immune signaling (interleukin-4), xenobiotic response, hypoxia detection, plus core nuclear processes (DNA-templated transcription and replication) and even bacterial motility and telomerase assembly. The broad, cross-kingdom mix and the absence of connecting edges or a single cohesive biological theme indicate there is no clear, shared function tying these proteins together. ","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009736","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0006261","count":3},{"id":"GO:0033160","count":3},{"id":"GO:0035690","count":3}]},{"hash":"512389168398160554","title":"Neuronal receptor trafficking and calcium signaling","description":"The top terms point to membrane trafficking and calcium dynamics in neurons: receptor recycling, regulation of endosome size, membrane protein ectodomain proteolysis, calcium import across the plasma membrane, and glutamatergic synaptic transmission. These together suggest a theme of endosomal trafficking and calcium-mediated signaling at synapses. Some terms related to transcription and histone methylation may reflect annotation noise or proteins with multiple roles, but the core signal is trafficking and calcium in neurons.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034968","count":2},{"id":"GO:0001881","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0051036","count":2},{"id":"GO:0035023","count":2}]},{"hash":"1791894009614766105","title":"Cardiac signaling and electrophysiology","description":"Based on the top GO terms, this cluster centers on heart development and cardiac muscle proliferation, and is linked to membrane potential regulation, sodium ion transport, and cAMP signaling\u2014key aspects of cardiac electrophysiology. While some terms are broader (transcription, nuclear export, general drug responses), the recurrent cardiac-specific terms suggest proteins involved in cardiac signaling pathways and electrical function.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0007507","count":2},{"id":"GO:2000480","count":2},{"id":"GO:0098719","count":2}]},{"hash":"537483264998036474","title":"Unknown","description":"The top terms are highly diverse (nucleotide biosynthesis, chromatin-related processes, development, cilium movement), with each term represented only once and no shared biological theme. There are no edges or clustering signals to tie these proteins into a common function, so a coherent label cannot be inferred.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042464","count":1},{"id":"GO:0051568","count":1},{"id":"GO:1902176","count":1},{"id":"GO:0021591","count":1},{"id":"GO:0006228","count":1}]},{"hash":"1894402010240474550","title":"Mitochondrial Metabolism & Transport","description":"This cluster centers on mitochondrial processes and metabolite transport, with terms like NAD transmembrane transport, iron import into the mitochondrion, thiosulfate and deoxynucleotide transport, and regulation of mitochondrial membrane permeability, plus adaptive thermogenesis. These collectively point to proteins involved in mitochondrial energy production and metabolite exchange, occasionally linked to broader contexts such as liver regeneration and necroptosis regulation.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097274","count":7},{"id":"GO:0097421","count":6},{"id":"GO:1990845","count":6},{"id":"GO:0060546","count":6},{"id":"GO:0070542","count":6}]},{"hash":"1725838085673536407","title":"Cardiac development and calcium/NFAT signaling","description":"This cluster is dominated by GO terms related to heart development, cardiac myofibril assembly, and positive regulation of the calcineurin-NFAT signaling cascade, all of which point to calcium-dependent signaling essential for cardiac muscle development and function. Additional terms like regulation of GTPase activity and calcium-release channel activity fit into this calcium/NFAT signaling theme, while visual perception terms may reflect shared signaling components rather than retina-specific roles. Overall, the strongest, coherent theme is cardiac development coupled to calcium/NFAT signaling pathways.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":4},{"id":"GO:0022400","count":3},{"id":"GO:0060316","count":3},{"id":"GO:0035774","count":3},{"id":"GO:0043547","count":3}]},{"hash":"1608246743199513598","title":"Membrane Transport and Nucleotide Catabolism","description":"The top GO terms point to membrane transport activities (sodium-independent organic anion transport; potassium ion transmembrane transport) and to catabolic processes of nucleotides and related energy carriers (ADP, NAD+, IDP, CoA, diphosphoinositol polyphosphates). This suggests a cluster spanning both transport functions and energy/metabolite turnover, rather than a single, cohesive enzymatic pathway. The lack of interactions (Edges 0) supports a broad, heterogeneous set that converges on these general themes.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043252","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0035774","count":2},{"id":"GO:1901639","count":1},{"id":"GO:2000233","count":1}]},{"hash":"1785131348578293272","title":"Calcium-NFAT signaling in muscle remodeling","description":"The terms cluster around calcium-dependent signaling (calcineurin-NFAT), muscle remodeling (fiber-type transitions, cardiac hypertrophy, connective tissue replacement) and calcium-release channels, suggesting a cohesive theme of calcium-regulated muscle signaling and tissue remodeling. A few terms such as excitatory postsynaptic potential and xenobiotic response are present but secondary to the dominant muscle-focused pattern.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1905205","count":2},{"id":"GO:0014898","count":2},{"id":"GO:0060079","count":2},{"id":"GO:0051531","count":2},{"id":"GO:0033173","count":2}]},{"hash":"190417501301350005","title":"Cytoskeletal regulation and brain development","description":"The cluster groups proteins tied to regulation of the actin cytoskeleton and GTPase signaling (regulation of GTPase activity, filopodium assembly) with related processes in cell division (mitotic spindle orientation). Developmental brain processes appear (forebrain neuroblast division, third ventricle development), and intracellular transport aspects (pigment granule transport) likely depend on cytoskeletal dynamics. This points to a cohesive theme of cytoskeletal regulation shaping cell morphology, division, and neural development.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043087","count":2},{"id":"GO:1900748","count":1},{"id":"GO:0021873","count":1},{"id":"GO:0000132","count":1},{"id":"GO:0051489","count":1}]},{"hash":"362236799900417257","title":"Unknown","description":"The GO terms for this cluster are extremely diverse (plant- and animal-related development, immune regulation, tRNA modification, and mitotic localization) with no clear shared function, so a single high-level label cannot be confidently assigned.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0042092","count":1},{"id":"GO:0007399","count":1},{"id":"GO:0007519","count":1},{"id":"GO:0045496","count":1}]},{"hash":"1140153723951228171","title":"Ciliary and Flagellar Assembly and Motility","description":"The cluster is dominated by GO terms related to cilium and flagellum biology (axoneme assembly, cilium movement, flagellated sperm motility, microtubule severing, and tubulin modifications like polyglycylation and polyglutamylation), pointing to roles in building and driving ciliary/flagellar movement. A unrelated transcription term appears but is not representative of the main theme. ","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0003353","count":1},{"id":"GO:0030516","count":1},{"id":"GO:0018094","count":1},{"id":"GO:0018095","count":1}]},{"hash":"2075993005981276498","title":"Endomembrane Transport and Golgi-Endosome Cycling","description":"The top GO terms point to intracellular protein transport with a focus on endosome-to-Golgi and recycling endosome-to-Golgi pathways, plus related retrograde transport and vacuolar/organellar acidification. This suggests a cohesive function in vesicle trafficking within the endomembrane system and secretory pathway, rather than outside-cell processes. The development terms appear incidental noise relative to the dominant trafficking theme.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060036","count":1},{"id":"GO:0015991","count":1},{"id":"GO:0007035","count":1},{"id":"GO:0033336","count":1},{"id":"GO:0042777","count":1}]},{"hash":"47404750341830401","title":"DNA-Templated Transcription Regulators","description":"This cluster\u2019s strongest signal is DNA-templated transcription, suggesting proteins involved in regulating transcription. The accompanying terms point to signaling-related modulation (cGMP signaling and receptor regulation), indicating transcription factors or coregulators that respond to signaling cues. Some deubiquitination and histone-related terms are present but less coherent with the main theme, so the transcription regulation interpretation remains the most plausible overall.","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:0010754","count":2},{"id":"GO:0007608","count":2},{"id":"GO:0071321","count":2},{"id":"GO:0061408","count":2}]},{"hash":"1505969174031452603","title":"Stress Signaling and Kinase Activity","description":"The terms cluster around cellular responses to various stimuli (BDNF, prolactin, anoxia), regulation of phosphorylation (autophosphorylation), calcium-related processes, and cytoskeletal dynamics (myosin II disassembly, calcium-dependent adhesion), with an additional note on necroptosis. This points to a theme of signaling and phosphorylation driving stress responses and potential cell fate decisions, rather than a single tight pathway.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990416","count":1},{"id":"GO:0010961","count":1},{"id":"GO:0031952","count":1},{"id":"GO:0071454","count":1},{"id":"GO:1990637","count":1}]},{"hash":"410185104961600481","title":"Unknown","description":"The proteins\u2019 GO terms span signaling, kinase activity regulation, calcium handling, nuclear import, and various developmental processes, with several terms obsolete. This scattered mix shows no single cohesive function or pathway linking the cluster, so a definite, descriptive label cannot be assigned.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":2},{"id":"GO:0055003","count":1},{"id":"GO:0097274","count":1},{"id":"GO:0008365","count":1},{"id":"GO:1905205","count":1}]},{"hash":"8704476280922104","title":"Immune signaling and inflammatory response","description":"The top GO terms cluster around innate and adaptive immune processes: Toll signaling, inflammatory response, regulation of cytokine production (IL-1, IL-8, IFN-beta), dendritic cell cytokine regulation, and B cell proliferation. These collectively point to a shared function in coordinating immune signaling and inflammatory responses, despite a single plant growth term appearing as a noise outlier.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030011","count":2},{"id":"GO:0050711","count":1},{"id":"GO:0002730","count":1},{"id":"GO:0071225","count":1},{"id":"GO:0010080","count":1}]},{"hash":"1651935050549427528","title":"Ribosome biogenesis and translation","description":"This cluster is dominated by GO terms related to ribosome production and function, including cytoplasmic translation, ribosomal subunit biogenesis, ribosomal subunit export from the nucleus, and tRNA modification, signaling a core theme of ribosome assembly and protein synthesis. Additional terms about cell division and cyclin-dependent kinase regulation suggest coupling of growth/translation with the cell cycle, but the central motif remains ribosome biogenesis and translation.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0045737","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0043087","count":2},{"id":"GO:0002181","count":2}]},{"hash":"1385182869828134721","title":"Membrane Trafficking and Assembly","description":"The top GO terms point to endomembrane system organization, protein localization to the plasma membrane, and assembly processes such as ruffles and focal adhesions, along with autophagosome assembly, suggesting a membrane- and cytoskeleton\u2013associated cluster; despite some unrelated or obsolete terms and no observed interactions, these themes collectively imply membrane trafficking and remodeling functions.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042070","count":1},{"id":"GO:0035855","count":1},{"id":"GO:0032288","count":1},{"id":"GO:0031321","count":1},{"id":"GO:2000786","count":1}]},{"hash":"1495352625184785472","title":"Microtubule Organization & Golgi Trafficking","description":"These proteins show a cohesive set of functions centered on the microtubule cytoskeleton and vesicle trafficking: tubulin folding/assembly, centrosome/Golgi maintenance, post-Golgi vesicle transport, and cytoskeleton organization. This suggests a role in organizing the microtubule network and directing Golgi-related trafficking, which can influence cell shape and development, including nervous system formation.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015031","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0007021","count":1},{"id":"GO:0007010","count":1},{"id":"GO:0006892","count":1}]},{"hash":"1465529404593823292","title":"Protein synthesis machinery","description":"Based on the top GO terms, these proteins are mainly involved in translation and ribosome-related processes, including translation, translation initiation, prolyl-tRNA aminoacylation, and maturation of SSU-rRNA. While a couple of terms (osteoblast differentiation, immune signaling) appear incidental, the dominant theme is components of the protein synthesis machinery.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006450","count":1},{"id":"GO:0006433","count":1},{"id":"GO:0031564","count":1},{"id":"GO:0006508","count":1}]},{"hash":"1283634146125415508","title":"Cerebellar development and neural signaling","description":"The cluster prominently features terms tied to neural development in the cerebellum, including Bergmann glial cell differentiation and cerebellar cortex formation, along with broader neural signaling and axon regeneration processes. While there are also cell cycle and immune signaling terms present, the clearest shared theme centers on cerebellar development and neural signaling, suggesting these proteins may participate in cerebellar maturation and neuronal connectivity. ","confidence":"Medium","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0034501","count":12},{"id":"GO:0045736","count":12},{"id":"GO:0050852","count":12},{"id":"GO:0008285","count":12},{"id":"GO:0008286","count":12}]},{"hash":"1810874576641521164","title":"Mitochondrial Transport and Metabolism","description":"The GO terms cluster around mitochondrial transport and energy metabolism: transmembrane transport of NAD and deoxynucleotides, thiosulfate transport, and iron import into mitochondria, plus regulation of mitochondrial membrane permeability. Coupled with terms about adaptive thermogenesis and liver regeneration, the set points to a coordinated mitochondrial energy metabolism module rather than a single signaling pathway.","confidence":"Medium","size":17,"edges":4,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0097421","count":5},{"id":"GO:1990845","count":5},{"id":"GO:0060546","count":5},{"id":"GO:0097274","count":5},{"id":"GO:0070542","count":5}]},{"hash":"593628489001569847","title":"Protein quality control and stress responses","description":"This cluster centers on ubiquitin-mediated regulation, ER-associated degradation, aggresome formation, and autophagy, with oxidative stress and apoptosis signals, indicating a cohesive proteostasis program activated during cellular stress.","confidence":"High","size":17,"edges":58,"triangles":112,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0070301","count":5},{"id":"GO:0016579","count":5},{"id":"GO:0002862","count":4},{"id":"GO:0070842","count":4},{"id":"GO:0030433","count":4}]},{"hash":"1858426701148006057","title":"Cortical development and synaptic signaling","description":"The cluster is dominated by neural-related GO terms: layer formation in the cerebral cortex, dendrite extension, regulation of synapse structure or activity, and GABA secretion/neurotransmission, pointing to brain development and synaptic function. While some terms touch peripheral tissues (hair follicle/adrenal development, eye morphogenesis), the strongest signals center on CNS maturation and cortical connectivity, suggesting a cohort of proteins involved in neural development and synaptic signaling.","confidence":"Medium","size":17,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0001662","count":3},{"id":"GO:0048820","count":3},{"id":"GO:0030325","count":2},{"id":"GO:0010719","count":2},{"id":"GO:0048593","count":2}]},{"hash":"300199418267911699","title":"Ubiquitin-Driven Growth and Signaling","description":"The cluster shows strong signals for ubiquitination (autoubiquitination and K48-linked ubiquitination) and negative regulation of growth and signaling pathways (organ growth, TNF signaling, necroptosis), indicating regulation of protein stability to modulate cell fate and immune signaling. Additional terms on protein localization to bud neck/spindle pole body and histone catabolic processes suggest cell-cycle and chromatin turnover roles, which can be coordinated by ubiquitin-based regulation. Overall, these proteins likely act as ubiquitin-dependent regulators of growth, signaling, and cell-cycle processes.","confidence":"High","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":"autophagy","top_go_terms":[{"id":"GO:0046007","count":6},{"id":"GO:0097271","count":6},{"id":"GO:0055114","count":5},{"id":"GO:0046621","count":5},{"id":"GO:0051865","count":5}]},{"hash":"275941573059933095","title":"Neural development and signaling","description":"Many top GO terms point to neural development and function, including CNS projection neuron axonogenesis, dopaminergic synaptic transmission, and dorsal/ventral neural tube patterning. Endosome transport regulation can support neuronal vesicle trafficking, reinforcing a neural theme. Some terms (NK T cell differentiation, cartilage condensation) appear as outliers, suggesting broader developmental connections or noise, but the dominant pattern supports neural development and signaling.","confidence":"Medium","size":17,"edges":125,"triangles":530,"max_degree":16,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":17},{"id":"GO:0007124","count":17},{"id":"GO:1901621","count":17},{"id":"GO:1904637","count":17},{"id":"GO:0001963","count":17}]},{"hash":"843831396185552486","title":"Nucleocytoplasmic RNA Export and Splicing","description":"This cluster is enriched for GO terms related to export of ribosomal large subunit and mRNA from the nucleus, mRNA binding and import of splicing factors/snRNPs, and tRNA transport, pointing to RNA processing and transport across the nuclear envelope as the shared function. Some xenobiotic response terms appear but are less central to the main theme.","confidence":"High","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0000055","count":4},{"id":"GO:0042493","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0006406","count":4},{"id":"GO:0006609","count":3}]},{"hash":"1725937898607062813","title":"Developmental signaling and neural function","description":"The top GO terms cluster around development (multicellular organism development) and neural-related processes (visual perception, dopaminergic synaptic transmission, Hedgehog pathway regulation), with supporting roles for endosome transport and signaling-related stress responses (ionomycin response, p53 mediator). Despite diversity (including pseudohyphal growth across fungi), the shared theme is regulation of signaling pathways that govern development and neural processes, often involving intracellular trafficking. This makes \"Developmental signaling and neural function\" a representative label.","confidence":"Medium","size":17,"edges":36,"triangles":39,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0009636","count":15},{"id":"GO:0007275","count":15},{"id":"GO:0007601","count":15},{"id":"GO:0000278","count":15},{"id":"GO:2000641","count":14}]},{"hash":"59603228264868546","title":"Neural development and dopaminergic signaling","description":"This cluster is dominated by GO terms tied to neural development and function, including CNS projection neuron axonogenesis and dopaminergic synaptic transmission, suggesting a shared role in neural development and dopamine-mediated signaling. Other terms about endosome transport and gene regulation appear as ancillary connections, but the neural terms are the strongest thread.","confidence":"Medium","size":17,"edges":46,"triangles":46,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046827","count":17},{"id":"GO:2000641","count":16},{"id":"GO:0007124","count":16},{"id":"GO:1901621","count":16},{"id":"GO:1904637","count":16}]},{"hash":"724185261100721482","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032147","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0071374","count":1},{"id":"GO:0090084","count":1},{"id":"GO:1901621","count":1}]},{"hash":"957814326406523296","title":"Developmental signaling and neuronal differentiation","description":"Top GO terms cluster around intracellular trafficking (endosome transport), neural development (axonogenesis, dorsal/ventral patterning), dopaminergic synaptic transmission, and regulatory signaling (p53 mediator, Hedgehog-related pathways), with additional developmental processes like cartilage condensation and NK T cell differentiation. This pattern suggests a shared theme of developmental signaling coupled with intracellular transport, especially pertaining to neural contexts, rather than a single isolated function.","confidence":"Medium","size":17,"edges":110,"triangles":422,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":17},{"id":"GO:0007124","count":17},{"id":"GO:1901621","count":17},{"id":"GO:1904637","count":17},{"id":"GO:0001963","count":17}]},{"hash":"171212001650043748","title":"Unknown","description":"The GO terms span diverse biological contexts (neural development and signaling, dopaminergic synaptic transmission, immune differentiation, endosome transport, and even yeast pseudohyphal growth), with no clear, shared function tying them together, so no coherent label can be assigned.","confidence":"","size":17,"edges":46,"triangles":31,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046827","count":17},{"id":"GO:2000641","count":16},{"id":"GO:0007124","count":16},{"id":"GO:1901621","count":16},{"id":"GO:1904637","count":16}]},{"hash":"1704560691284530700","title":"Unknown","description":"The top GO terms span very different biological themes (ER unfolded protein response, mitotic cell cycle, DNA repair and transcription, vesicle formation, spermatogenesis, immune signaling, and sensory perception), and the cluster shows little connectivity (Edges=1, Triangles=0, Max Degree=1). There isn\u2019t a single cohesive function that ties these proteins together, so a generic Unknown label is most appropriate.","confidence":"","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030968","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0070676","count":3},{"id":"GO:0007288","count":2},{"id":"GO:0032608","count":2}]},{"hash":"1756046807279941628","title":"Proteostasis and Stress Response","description":"The terms point to protein quality control and stress-related pathways: ER-associated degradation and proteasomal protein degradation, oxidative stress response, and energy-demanding proteostasis processes. While there are also some cell cycle/chromatin assembly terms, the strongest signals are from proteostasis and stress response mechanisms across organelles, suggesting a cluster centered on maintaining protein homeostasis under stress. ","confidence":"Medium","size":17,"edges":22,"triangles":2,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0046034","count":1},{"id":"GO:0071712","count":1},{"id":"GO:0033314","count":1},{"id":"GO:1901800","count":1},{"id":"GO:0034551","count":1}]},{"hash":"4073645966260313","title":"Mitotic Cell Cycle and DNA Replication","description":"The dominant GO terms point to cell-cycle control, G1/S and G2/M transitions, and DNA replication, indicating a co-regulated module of division and DNA synthesis. Rho signaling and translation appear as additional context but are less central, and some terms relate to development; overall, the core theme is cell division machinery.","confidence":"Medium","size":17,"edges":20,"triangles":13,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007266","count":4},{"id":"GO:0006412","count":4},{"id":"GO:0006977","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0007399","count":3}]},{"hash":"2032555803578769795","title":"Metabolic and circadian transcription regulation","description":"Most frequent GO terms cluster around lipid metabolism and adipogenesis (intracellular triglyceride homeostasis; positive regulation of fat cell differentiation), growth signaling (response to insulin-like growth factor stimulus), and nutrient-responsive transcription control (negative regulation of ribosomal protein gene transcription in response to nutrients). The presence of circadian rhythm and miRNA transcription further supports a theme of transcriptional programs tied to metabolic status and circadian cues. Some terms related to immune processing and neural development appear as outliers, but the dominant signal points to metabolism-linked transcriptional regulation with circadian involvement.","confidence":"Medium","size":17,"edges":47,"triangles":68,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0045348","count":5},{"id":"GO:0036091","count":5},{"id":"GO:1990418","count":4},{"id":"GO:0035470","count":4},{"id":"GO:0061614","count":4}]},{"hash":"889305865192674302","title":"Microtubule Cytoskeleton Organization","description":"The GO terms cluster around organizing and regulating the microtubule network\u2014polarity, spindle dynamics, and microtubule-based transport in neurons\u2014pointing to a cohesive role in cytoskeletal organization across cell types. An outlier plant-related term is present but does not override the central theme.","confidence":"High","size":17,"edges":15,"triangles":0,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0010938","count":1},{"id":"GO:0001560","count":1},{"id":"GO:0032487","count":1},{"id":"GO:0098971","count":1},{"id":"GO:0009904","count":1}]},{"hash":"71858181924758085","title":"Mitochondrial membrane regulation and protein import","description":"The top GO terms point to core mitochondrial functions, especially regulation of mitochondrial membrane permeability and protein import into the mitochondrial matrix, suggesting the cluster centers on mitochondrial maintenance and metabolism. While a few terms relate to cell-cycle regulation or RNA processing, the strongest signals are mitochondrial, so the name reflects the dominant theme of mitochondrial handling and associated processes.","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":4},{"id":"GO:2000134","count":4},{"id":"GO:0070940","count":4},{"id":"GO:1903740","count":4},{"id":"GO:0010867","count":4}]},{"hash":"361391377894999583","title":"Nuclear transcription and endosome trafficking","description":"The cluster\u2019s top GO terms center on DNA-templated transcription and regulation of protein export from the nucleus, alongside regulation of endosome transport. This suggests a cohesive theme around gene expression control coupled with intracellular signaling and vesicle trafficking, with additional developmental and signaling-context terms that reflect broader roles in cellular communication. Confidence in this labeling is medium due to the presence of heterogeneous terms (e.g., development and dopaminergic signaling) that broaden the theme beyond a single, tight function. ","confidence":"Medium","size":17,"edges":49,"triangles":45,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":11},{"id":"GO:0046827","count":10},{"id":"GO:0019233","count":10},{"id":"GO:0007275","count":10},{"id":"GO:0046826","count":8}]},{"hash":"1858824999602875803","title":"Neural development and JNK signaling","description":"Enrichment centers on nervous system development, hippocampus development, dendrite morphogenesis, and axon extension, complemented by regulation of the JNK cascade and related phosphorylation/stability controls. Together these terms suggest a cluster of proteins involved in neural differentiation and neurite growth with MAPK/JNK pathway regulation. The T cell receptor signaling term appears as an outlier, but the neural development theme dominates.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0050852","count":12},{"id":"GO:0000278","count":12},{"id":"GO:0007399","count":11},{"id":"GO:0046330","count":11},{"id":"GO:0021766","count":11}]},{"hash":"1381795102453211722","title":"H/ACA snoRNPs for RNA maturation and telomere maintenance","description":"The top GO terms cluster around rRNA maturation (5.8S and LSU), pseudouridine synthesis of rRNA and snRNA, and rRNA processing, plus telomerase RNA localization to Cajal bodies and telomere maintenance via telomerase. This points to the H/ACA snoRNP\u2013mediated RNA modification and maturation pathway, which also relates to telomerase RNA biology. A translation term may reflect nucleolar ribosome biogenesis, but the core theme is RNA processing/modification and telomere biology.","confidence":"High","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:1903146","count":2},{"id":"GO:0000463","count":2},{"id":"GO:1903955","count":2},{"id":"GO:0000466","count":2}]},{"hash":"2103397151270486058","title":"Adipose lipid metabolism, circadian rhythm, and immune signaling","description":"The cluster shows strong representation of fat tissue\u2013related lipid processes (intracellular triglyceride homeostasis, positive fat cell differentiation) along with immune-related activity (IL-4 response, MHC class II biosynthesis) and circadian rhythm. This combination points to adipose tissue\u2013centered functions that integrate metabolism with immune and temporal regulation, even though a few terms are more distant (e.g., dorsal identity, lactation). Overall, the core theme appears to be adipose lipid metabolism coupled with immune and circadian signaling.","confidence":"Medium","size":17,"edges":17,"triangles":11,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071353","count":5},{"id":"GO:1990418","count":4},{"id":"GO:0035470","count":4},{"id":"GO:0035356","count":4},{"id":"GO:0007623","count":4}]},{"hash":"1480107878765737296","title":"Post-transcriptional gene regulation","description":"The cluster\u2019s GO terms center on RNA processing and post-transcriptional control\u2014mRNA polyadenylation, alternative splicing, and mRNA modification, plus regulation of mRNA stability under stress\u2014and extend to RNA silencing (ncRNA/miRNA) and translation initiation complex assembly, indicating a cohesive theme of regulating gene expression after transcription.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":2},{"id":"GO:0048025","count":2},{"id":"GO:0035278","count":2},{"id":"GO:0010610","count":2},{"id":"GO:0016556","count":2}]},{"hash":"194928045888033261","title":"Neural transcription and cAMP signaling in antipsychotic response","description":"This cluster is driven by prominent GO terms for DNA-templated transcription and cAMP-related signaling, with several entries tied to neural signaling and responses to antipsychotic drugs (including clozapine). The presence of membrane potential regulation and sodium ion transport supports a neuronal context, suggesting a theme of transcriptional regulation linked to neural signaling and pharmacologic response. Confidence in this label is moderate because a few terms (e.g., cardiac muscle proliferation) are less directly connected to the core neural/drug response theme.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":13},{"id":"GO:2000480","count":8},{"id":"GO:0098719","count":8},{"id":"GO:0071320","count":8},{"id":"GO:0097332","count":8}]},{"hash":"2022164786044870444","title":"Unknown","description":"The top GO terms include synaptic vesicle maturation; obsolete histone H4-R3 methylation; negative regulation of transcription by RNA polymerase II; arginine methylation; cell growth and cellular senescence; cobalamin biosynthesis; oxidative phosphorylation; germ cell development; and gene conversion at mating-type locus. These terms span neuronal, chromatin/ transcriptional, metabolic, and developmental processes with no cohesive shared pathway or interactions, and there are no edges linking proteins, so a single cohesive label cannot be confidently assigned.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016188","count":2},{"id":"GO:0043985","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0019919","count":2},{"id":"GO:0016049","count":2}]},{"hash":"39282840226491114","title":"Mitochondrial Transport and Energy Metabolism","description":"This cluster is dominated by GO terms related to mitochondrial transport and metabolic regulation, including iron import into the mitochondrion, NAD transmembrane transport, deoxynucleotide transport, thiosulfate transport, and regulation of mitochondrial membrane permeability, with supportive signals from adaptive thermogenesis and response to fatty acids. Together these imply a cohesive theme of mitochondrial transport coupled to energy homeostasis and metabolic adaptation.","confidence":"High","size":17,"edges":29,"triangles":6,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0097421","count":13},{"id":"GO:1990845","count":13},{"id":"GO:0060546","count":13},{"id":"GO:0097274","count":13},{"id":"GO:0070542","count":13}]},{"hash":"1349480032035979843","title":"Mitotic cell cycle and transcription regulation","description":"This cluster is dominated by GO terms related to cell division, especially mitosis and the G2/M transition, along with DNA-templated transcription and mRNA transport, plus regulatory signaling activities (kinase and GTPase regulation). The combination suggests proteins involved in coordinating cell cycle progression with gene expression, rather than a single specialized pathway. Confidence: High","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0000086","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0071456","count":3}]},{"hash":"296570613711726383","title":"Ribosome biogenesis and translation","description":"This cluster is dominated by GO terms related to ribosome assembly and function: maturation of LSU rRNA, ribosome biogenesis, translation, and cytoplasmic translation, indicating the proteins are primarily involved in ribosome biogenesis and protein synthesis. A few terms (e.g., single fertilization, spinal cord development) are less connected to this core function and may reflect broader annotations, but the primary theme is clear.","confidence":"High","size":17,"edges":4,"triangles":1,"max_degree":2,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000463","count":5},{"id":"GO:0042273","count":4},{"id":"GO:0007338","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0042254","count":3}]},{"hash":"2224863700280341714","title":"cAMP signaling and transcriptional regulation (antipsychotic response)","description":"The cluster shows a cohesive theme around cAMP signaling and transcriptional control, with multiple terms for cellular responses to cAMP, regulation of PKA activity, and DNA-templated transcription. The presence of GO terms for responses to antipsychotic drugs (e.g., clozapine) reinforces a pharmacological response angle, making this a plausible unified function. While membrane potential and ion transport terms appear, they are less central to the main pattern of cAMP/PKA-regulated transcription tied to drug response.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:2000480","count":3},{"id":"GO:0098719","count":3},{"id":"GO:0071320","count":3},{"id":"GO:0097332","count":3}]},{"hash":"96019892222176656","title":"Ubiquitin-Dependent Protein Degradation and Signaling","description":"The cluster contains multiple ubiquitin-related processes (ubiquitin-dependent protein catabolic process, autoubiquitination, ERAD) and turnover of signaling components (Wnt receptor catabolic process, histone catabolism). It also includes pathways influenced by ubiquitin-regulated degradation, such as TNF signaling and JNK cascade regulation, pointing to a cohesive theme of protein turnover driving signaling and growth control. This label captures the core shared function across the GO terms.","confidence":"High","size":17,"edges":49,"triangles":67,"max_degree":12,"top_function":"autophagy","top_go_terms":[{"id":"GO:0046621","count":7},{"id":"GO:0033151","count":7},{"id":"GO:0038018","count":7},{"id":"GO:0051865","count":7},{"id":"GO:0090073","count":7}]},{"hash":"260698041498427729","title":"Unknown","description":"Top GO terms span cell cycle, cytoskeleton dynamics, development, and metal stress responses, with no single dominant function linking all terms; plus the cluster has no edges, indicating a heterogeneous set of annotations rather than a cohesive module.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019076","count":2},{"id":"GO:0000902","count":2},{"id":"GO:0007095","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0035023","count":2}]},{"hash":"442555500964258945","title":"Chromatin Assembly and Histone Modification","description":"Top GO terms center on nucleosome assembly and multiple histone H3 modifications (K27 acetylation, K4/K27 methylation), suggesting chromatin organization and epigenetic regulation as the cluster\u2019s core function. Some developmental morphogenesis and drug-response terms appear but are likely secondary noise.","confidence":"High","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006334","count":8},{"id":"GO:1901674","count":5},{"id":"GO:0080182","count":5},{"id":"GO:0098532","count":5},{"id":"GO:2001040","count":5}]},{"hash":"2182974868986863210","title":"ER-Golgi vesicle trafficking and cell cycle signaling","description":"The top GO terms show strong enrichment for ER-to-Golgi transport, COPII vesicle budding, and retrograde Golgi-ER transport, plus positive regulation of GTPase activity, which together point to a vesicle trafficking program. Additional terms related to TORC1 signaling, cell division, mitotic spindle assembly, and ribosome biogenesis suggest this trafficking system is coordinated with growth and proliferation. Brain development appears as a broader associated process, but the core signal is vesicle trafficking coupled to cell growth/division. ","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":6},{"id":"GO:0043547","count":5},{"id":"GO:0090114","count":5},{"id":"GO:1904263","count":5},{"id":"GO:0051301","count":5}]},{"hash":"1492959166153183287","title":"Neural development and morphogenesis","description":"The terms show strong emphasis on neural development (neural tube closure, forebrain development) and morphogenesis (cell morphogenesis, skeletal system development, multicellular organism development), with transcriptional regulation (DNA-templated transcription) as a common mechanism. While a few entries touch on stress or immune responses, the overall pattern points to developmental regulation and neural tissue formation.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0001843","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0001501","count":2}]},{"hash":"1540071727093732123","title":"Neural RNA Processing and Ubiquitin Regulation","description":"The top GO terms point to RNA processing activities (mRNA export and splicing) and ubiquitin-related regulation (polyubiquitination and ubiquitin ligase activity), with additional links to chromatin assembly, cell cycle control, and neural-specific processes (brain development and glial apoptotic signaling). This suggests a cohesive theme where RNA processing and protein turnover are coordinated in neural contexts, possibly in response to stress, rather than a single isolated function. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000728","count":5},{"id":"GO:1904668","count":5},{"id":"GO:0000398","count":5},{"id":"GO:0061641","count":5},{"id":"GO:0002534","count":5}]},{"hash":"941732095647162827","title":"Cell Cycle and Immune Signaling","description":"The top GO terms point to core cell cycle and DNA processing activities (DNA replication, DNA-templated transcription, mitotic cell cycle, cell morphogenesis) alongside immune-related signaling (GM-CSF stimulus response, LPS response, T cell receptor signaling). This mix suggests a cluster of proteins involved in coordinating cell proliferation with immune signaling and stress responses, with a few peripheral terms like pinocytosis and sperm capacitation not central to the main theme.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097011","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0000902","count":2},{"id":"GO:0071222","count":2}]},{"hash":"2044626380681079606","title":"Unknown","description":"This cluster lists GO terms spanning core gene expression processes (spliceosome-mediated splicing, translation, nuclear import) and diverse developmental/structural processes (muscle assembly, cuticle development, organ/tissue development), with no single coherent functional theme linking all terms. Because there isn\u2019t a clear, shared biological function among the top terms, a specific representative label cannot be justified.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000349","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0055003","count":2},{"id":"GO:0097274","count":2},{"id":"GO:0008365","count":2}]},{"hash":"2139844969232621289","title":"RNA processing and splicing regulation","description":"This cluster is driven by GO terms related to mRNA polyadenylation, spliceosome-mediated splicing, snoRNA splicing, and deadenylation-independent decay, indicating a core theme of RNA processing and mRNA surveillance. While there are a few other signals like p38MAPK and translation regulation, the RNA-centric terms dominate, supporting a label centered on RNA processing and splicing. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098789","count":3},{"id":"GO:0006378","count":3},{"id":"GO:0045292","count":3},{"id":"GO:0071805","count":3},{"id":"GO:2000766","count":2}]},{"hash":"1297738679271505915","title":"ER-Golgi Vesicle Transport","description":"The top GO terms cluster around vesicle trafficking between the endoplasmic reticulum and the Golgi apparatus, including forward ER-to-Golgi transport, retrograde Golgi-to-ER transport, and COPII-coated vesicle budding, which together point to a secretory pathway function. Other terms like brain development, transcription, and histone methylation are present but less central to the dominant trafficking theme.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006888","count":5},{"id":"GO:0007420","count":4},{"id":"GO:0006890","count":4},{"id":"GO:0034729","count":3},{"id":"GO:0051568","count":3}]},{"hash":"1082131215829841151","title":"Nuclear transcription, RNA processing, and cell-cycle regulation","description":"The top GO terms cluster around nuclear gene-expression processes: DNA-templated transcription, mRNA splicing, and mRNA export, along with chromatin assembly (CENP-A) and regulation of ubiquitin ligase activity, plus cell-cycle checkpoint control. While forebrain development and cytokine production appear, the dominant theme is gene-expression regulation and genome maintenance during the cell cycle, making this label represent the core of the cluster.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0030900","count":3},{"id":"GO:0051301","count":3},{"id":"GO:2000728","count":2},{"id":"GO:1904668","count":2}]},{"hash":"1039134081088243478","title":"Mitochondrial metabolism and transport","description":"The GO terms are dominated by mitochondrial-related processes (NAD and iron transport into mitochondria, regulation of membrane permeability), fatty acid responsiveness, and metabolic regulation, with additional terms linked to liver regeneration and adaptive thermogenesis\u2014collectively pointing to mitochondrial energy metabolism and transport as the unifying theme. ","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0097421","count":2},{"id":"GO:1990845","count":2},{"id":"GO:0060546","count":2},{"id":"GO:0097274","count":2}]},{"hash":"569669260417476048","title":"Regulatory Signaling and Epigenetic Modulators","description":"This cluster\u2019s GO terms center on the regulation of signaling pathways (NF-kappaB, vitamin D receptor, retinoic acid receptor) and on gene expression control (epigenetic programming, protein ubiquitination, SMAD-related processes, PML body organization, MHC class I biosynthesis). Although the terms span diverse systems (plants to animals) and processes, the common thread is involvement in modulating signaling and transcription rather than executing a single pathway, suggesting a broad regulatory role for these proteins.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900458","count":1},{"id":"GO:0043123","count":1},{"id":"GO:2000653","count":1},{"id":"GO:0070562","count":1},{"id":"GO:0048384","count":1}]},{"hash":"855881378097931391","title":"Unknown","description":"The GO terms are highly diverse (BDNF response, magnesium homeostasis, protein autophosphorylation, anoxia response, prolactin response, calcium-dependent adhesion, myosin II disassembly, tetramerization, and necroptosis) with no single clear functional theme linking the proteins. This makes a concise, representative label difficult to justify; a catch-all Unknown best reflects the lack of a coherent shared function.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990416","count":1},{"id":"GO:0010961","count":1},{"id":"GO:0031952","count":1},{"id":"GO:0071454","count":1},{"id":"GO:1990637","count":1}]},{"hash":"703420295409265152","title":"Unknown","description":"The top GO terms include short-term memory, vocalization, autophagy and vesicle trafficking, immunological synapse and complement activation, plant defense, and more, with no single shared function tying the proteins together and no interaction data to suggest a coherent pathway.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007614","count":2},{"id":"GO:0030242","count":1},{"id":"GO:0032258","count":1},{"id":"GO:0034497","count":1},{"id":"GO:0001771","count":1}]},{"hash":"1529814464699212414","title":"Unknown","description":"The top GO terms cover a diverse set of functions (mRNA stability regulation, calcium release in the sarcoplasmic reticulum, immune signaling, retinal development, xenobiotic response, and cardiac hypertrophy) with no clear, shared biological pathway or theme. The lack of a cohesive functional signal and no network cohesion (edges/triangles) suggest no single dominant function for this cluster. ","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043488","count":2},{"id":"GO:0010880","count":1},{"id":"GO:0036006","count":1},{"id":"GO:0046549","count":1},{"id":"GO:0050852","count":1}]},{"hash":"1451912297198486475","title":"Unknown","description":"The top GO terms are highly diverse, ranging from nucleocytoplasmic transport and nuclear pore localization to cell cycle processes, ubiquitin-related pathways (noted as obsolete), dendrite development, pancreatic juice secretion, and DNA replication. With no clear shared function or theme across most terms, there isn\u2019t a coherent biological label that accurately represents the cluster.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046784","count":1},{"id":"GO:0010697","count":1},{"id":"GO:0035185","count":1},{"id":"GO:0030433","count":1},{"id":"GO:0051441","count":1}]},{"hash":"2068660928552855480","title":"Neural development and ciliary signaling","description":"This cluster strongly links neural development terms (ganglion development, embryonic neurocranium morphogenesis, dorsal/ventral neural tube patterning, ventral spinal cord patterning) with ciliary/retinal functions (receptor localization to non-motile cilium, photoreceptor cell maintenance). A few sugar catabolic terms are present but do not dominate the theme. Overall, the theme is neural development intertwined with ciliary signaling.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0005990","count":1},{"id":"GO:0000272","count":1},{"id":"GO:0019391","count":1},{"id":"GO:0061548","count":1},{"id":"GO:0097500","count":1}]},{"hash":"999669847735516032","title":"Unknown","description":"The top terms mix neuronal signaling (glutamatergic synaptic transmission) with intracellular trafficking (Golgi to endosome transport, multivesicular body sorting, endocytosis) and a few unrelated processes (female pregnancy, cocaine catabolic process, tRNA biosynthesis). Given zero edges/triangles and no consistent single function linking all proteins, there isn\u2019t a clear, cohesive theme to name a specific function for this cluster. ","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007565","count":2},{"id":"GO:0035249","count":2},{"id":"GO:0043065","count":2},{"id":"GO:0006508","count":1},{"id":"GO:0050784","count":1}]},{"hash":"1676768021700896038","title":"Motile cilium and flagellum assembly and motility","description":"Top GO terms cluster around cilium/flagellum movement, axoneme assembly, microtubule modifications, and sperm motility, pointing to coordinated assembly and regulation of motile cilia and flagella. The inclusion of tubulin PTMs (polyglycylation/polyglutamylation), axoneme-related processes, and small GTPase signaling reinforces a core theme of cilium/flagellum biogenesis and motility.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003353","count":3},{"id":"GO:0030516","count":3},{"id":"GO:0018094","count":3},{"id":"GO:0018095","count":3},{"id":"GO:0007288","count":3}]},{"hash":"1280710974799138358","title":"Neuronal endosomal recycling and SNARE regulation","description":"Based on the top GO terms, the cluster centers on endocytic recycling and endosome trafficking (endocytic recycling, Golgi to endosome transport, endosome organization, receptor recycling, regulation of Rab signaling) and a SNARE-related regulatory theme (negative regulation of SNARE complex assembly). Some terms also indicate neuronal synaptic function and dendrite morphogenesis (glutamatergic synaptic transmission, positive regulation of dendrite morphogenesis), suggesting these proteins participate in neuronal synaptic maintenance via endosomal trafficking.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990126","count":1},{"id":"GO:0035249","count":1},{"id":"GO:0035544","count":1},{"id":"GO:0006895","count":1},{"id":"GO:0032483","count":1}]},{"hash":"2223315146985918659","title":"Embryonic organogenesis and vascular development","description":"Most terms cluster around embryonic development with emphasis on heart and placental vascular formation (labyrinthine layer vessels, VEGF response, placenta development). Additional terms reference spinal cord development and apoptosis during organogenesis, as well as signaling events (VEGF, insulin receptor, phosphorylation). Overall, the proteins appear tied to embryonic organogenesis and vessel formation.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0097011","count":3},{"id":"GO:0008286","count":3},{"id":"GO:0097194","count":3},{"id":"GO:0021510","count":3},{"id":"GO:0035924","count":3}]},{"hash":"424370423133500919","title":"Unknown","description":"The top terms present a wide and inconsistent mix of functions (cuticle development, connective tissue regulation, nuclear import, kinase activity regulation, oxidative generation, cytokinesis, calcium signaling, cardiac hypertrophy, photoreceptor morphogenesis, membrane tubulation) with no clear shared biology or interaction pattern. With zero edges and diverse GO terms, there isn\u2019t a coherent theme to label this cluster beyond Unknown.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008365","count":1},{"id":"GO:1905205","count":1},{"id":"GO:0006607","count":1},{"id":"GO:0006469","count":1},{"id":"GO:0042554","count":1}]},{"hash":"297233702349097521","title":"Unknown","description":"There are no edges or GO-term signals linking the 17 proteins, and the Top Terms field is empty, so there is no clear shared function to name. The ReCIPE note with degree 0.75 appears to reflect a computational artifact rather than biological coherence.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1499533213337879425","title":"Bacterial Motility, Signaling, and Sporulation","description":"The terms point to bacterial development and behavior: flagellum-driven motility, chemotaxis, and sporulation, tied together by phosphorelay/two-component signaling and transcriptional regulation, with supporting post-translational modification. Some plant-hormone terms may be less relevant noise, but the core pattern clearly reflects bacterial signaling and lifecycle control.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009736","count":6},{"id":"GO:0006355","count":6},{"id":"GO:0071973","count":5},{"id":"GO:0010105","count":5},{"id":"GO:0042173","count":5}]},{"hash":"1168950866790617494","title":"Unknown","description":"The GO terms shown are highly diverse and touch on cytoskeletal regulation, cell migration, development, metabolism, immune differentiation, mitochondrial dynamics, platelet activation, and behavior, with no dominant shared function or clear protein-protein connectivity (edges/triangles = 0). This lack of a cohesive theme makes it inappropriate to assign a specific, concise function label, so Unknown is the best representation.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032956","count":1},{"id":"GO:1904140","count":1},{"id":"GO:0072015","count":1},{"id":"GO:0031999","count":1},{"id":"GO:1904693","count":1}]},{"hash":"471296373828446192","title":"Ribosome assembly and translation initiation","description":"The cluster is dominated by GO terms related to translation and ribosome assembly: formation of translation initiation complexes, translational initiation, translation itself, and cytosolic ribosome assembly. A few terms (germ cell proliferation, skeletal development, endosome/ER-to-Golgi transport) appear incidental and do not define the core function. Overall, the proteins seem tied to the translational machinery, justifying this label despite some outliers.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001732","count":1},{"id":"GO:0006413","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0042256","count":1}]},{"hash":"2140609967638671242","title":"Drosophila Developmental Morphogenesis","description":"Based on the top GO terms, this cluster centers on developmental morphogenesis, including wing morphogenesis, chaeta morphogenesis, and chaeta development, as well as spermatid nucleus elongation. Additional related processes like intracellular transport (ER-Golgi and intraflagellar transport) support the cellular changes underlying morphogenesis. A single immune-related term (antigen processing via MHC II) appears to be an annotation artifact rather than a primary cluster theme. Overall, the label captures the dominant developmental/morphogenetic theme.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000132","count":2},{"id":"GO:0007476","count":2},{"id":"GO:0008407","count":2},{"id":"GO:0035735","count":2}]},{"hash":"1575288367633204275","title":"Unknown","description":"This cluster's GO terms span developmental processes (gastrulation, skin development, muscle contraction), immune signaling (NF-kappaB regulation, interferon production), protein processing/localization (GPI anchor biosynthesis, ERAD), and stress responses (stress granule localization), with no clear shared pathway or strong connectivity (Edges: 0). The functions are too diverse to assign a specific, representative label.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904103","count":1},{"id":"GO:0006506","count":1},{"id":"GO:0043123","count":1},{"id":"GO:0043588","count":1},{"id":"GO:0030433","count":1}]},{"hash":"1498223351865115813","title":"Neural RNA processing and protein ubiquitination","description":"The Top Terms show RNA processing roles (mRNA export regulation in response to heat stress; mRNA splicing) alongside ubiquitination-related processes (ubiquitin ligase activity, polyubiquitination), with supporting involvement in chromatin assembly and cell cycle checks. Additional terms touch on neural development and glial apoptosis, suggesting a neural context where RNA processing and protein regulation govern gene expression and cellular stress responses. The cluster thus appears to center on neural-related RNA processing and protein regulation rather than a single, isolated pathway.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000728","count":2},{"id":"GO:1904668","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0061641","count":2},{"id":"GO:0002534","count":2}]},{"hash":"135337950677636030","title":"Antigen presentation and immune defense","description":"This cluster shows a clear enrichment for antigen processing and presentation via MHC class I and II, along with a positive defense response to bacteria, pointing to an immune-related function focused on antigen presentation and immune activation. Other terms about responses to curcumin, catechin, and mercury hint at broader stress responses but do not define a cohesive, alternative primary function. Confidence in this thematic label is moderate because the signal is driven by a small set of immune-related GO terms with few supporting interactions in the data. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904643","count":1},{"id":"GO:0007155","count":1},{"id":"GO:0046689","count":1},{"id":"GO:1902168","count":1},{"id":"GO:0042590","count":1}]},{"hash":"420032098220134940","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007338","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0032212","count":2},{"id":"GO:0071447","count":2},{"id":"GO:1903204","count":2}]},{"hash":"665755495822818562","title":"Membrane trafficking and signaling regulators","description":"The terms point to proteins that modulate membrane-associated processes and signaling: negative regulation of NF-kappaB and TNF signaling, endosome transport from the plasma membrane, negative regulation of protein localization to the cell surface, and palmitoylation that anchors or targets proteins to membranes. While there are miscellaneous terms (vacuole fusion, sebaceous gland development, amino acid export), the common thread appears to be regulators of membrane trafficking and cell-surface signaling rather than a single enzymatic function. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":2},{"id":"GO:0033209","count":2},{"id":"GO:0048227","count":2},{"id":"GO:1902072","count":2},{"id":"GO:1902306","count":2}]},{"hash":"1931015526514589492","title":"Neural Development and Stress-Responsive RNA Processing","description":"This cluster combines brain development and glial apoptotic processes with RNA processing activities (mRNA splicing/export) and ubiquitin-related regulation, suggesting a theme of neural development coupled with stress-responsive RNA processing and protein quality control.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000728","count":2},{"id":"GO:1904668","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0061641","count":2},{"id":"GO:0002534","count":2}]},{"hash":"2065111924673611658","title":"Unknown","description":"There are no shared GO terms, no edges or triangles, and no top terms to guide labeling. ReCIPE re-added 4 proteins, but the absence of functional signals provides no clear common function for the cluster.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1276466454937866152","title":"Chromatin regulation and transcription control","description":"Most terms point to regulation of DNA-templated transcription, histone methylation, and chromatin binding, suggesting a chromatin-centric cluster. A few terms involve endosome trafficking, Rho signaling, and synaptic transmission, which may reflect multifunctional roles or annotation noise, but the dominant theme remains chromatin regulation.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0051568","count":2},{"id":"GO:0034968","count":1},{"id":"GO:0001881","count":1},{"id":"GO:0051036","count":1}]},{"hash":"424967940620045427","title":"Unknown","description":"The terms include nervous system development, skeletal muscle development, plant brassinosteroid signaling, glucosinolate catabolism, wybutosine biosynthesis, mitotic spindle localization, germinal center formation, ubiquitin-dependent proteolysis, and swimming. This wide mix across animal, plant, development, metabolism, and cell-cycle processes does not reveal a single cohesive function or pathway linking the proteins, suggesting the cluster is heterogeneous. ","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":1},{"id":"GO:0007519","count":1},{"id":"GO:0019762","count":1},{"id":"GO:0031591","count":1},{"id":"GO:0035853","count":1}]},{"hash":"2077766067943872944","title":"Unknown","description":"The Top Terms are highly diverse, spanning metal ion response, innate immune signaling (TLR1 pathway and lipopeptide detection), ubiquitination, dopamine signaling, and kidney size regulation. With no edges or coherent shared biological process, there is no clear, single theme tying the proteins together, so a specific label isn\u2019t supported.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071287","count":1},{"id":"GO:1903215","count":1},{"id":"GO:0034130","count":1},{"id":"GO:0016567","count":1},{"id":"GO:1902499","count":1}]},{"hash":"1994330492061906341","title":"Developmental morphogenesis across tissues","description":"The top GO terms span various developmental and morphogenetic processes across different tissues (neural differentiation, tracheal cartilage morphogenesis, fin and limb development, lung morphogenesis, smooth muscle interactions, etc.), indicating a broad theme of organogenesis rather than a single pathway. Therefore, a concise label capturing multi-tissue developmental morphogenesis fits best.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071542","count":1},{"id":"GO:2000052","count":1},{"id":"GO:0060535","count":1},{"id":"GO:0033336","count":1},{"id":"GO:1990874","count":1}]},{"hash":"1648015480346248965","title":"Unknown","description":"Top terms span DNA replication and telomere-related processes alongside plant hormone signaling, immune signaling, xenobiotic response, hypoxia detection, and bacterial motility; these diverse terms show no single cohesive function tying the proteins together, and there are no edges to suggest a shared pathway. ","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006261","count":1},{"id":"GO:0009736","count":1},{"id":"GO:0033160","count":1},{"id":"GO:0035690","count":1},{"id":"GO:1905323","count":1}]},{"hash":"679296094584827012","title":"Mitotic Regulation and Trafficking","description":"The top GO terms are dominated by mitosis-related processes (kinetochore localization, negative regulation of CDK activity, and protein stability regulation), with additional links to intracellular transport and morphogenesis. This suggests a theme of regulating cell division and endomembrane trafficking rather than a single pathway, making mitotic control and trafficking the most representative label.","confidence":"Medium","size":16,"edges":64,"triangles":135,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0034501","count":14},{"id":"GO:0045736","count":14},{"id":"GO:0014850","count":10},{"id":"GO:0060997","count":10},{"id":"GO:0031647","count":10}]},{"hash":"1627819883445278811","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":116,"triangles":508,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000398","count":12},{"id":"GO:0031047","count":11},{"id":"GO:0006260","count":11},{"id":"GO:0048026","count":11},{"id":"GO:0006311","count":10}]},{"hash":"1215399168843296455","title":"Ubiquitin-Dependent ERAD Proteolysis","description":"The top GO terms show a clear emphasis on ubiquitin-mediated degradation, especially the ubiquitin-dependent ERAD pathway and ER-associated protein catabolism, including autoubiquitination. This points to a cohesive theme of protein quality control and turnover via the ubiquitin-proteasome system. Some other terms appear peripheral or noisy (e.g., TNF signaling, insecticide response, mitochondrial fusion), which may reflect broader stress responses or annotations rather than core function. ","confidence":"High","size":16,"edges":86,"triangles":219,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":6},{"id":"GO:0051865","count":5},{"id":"GO:1903265","count":5},{"id":"GO:0033132","count":4},{"id":"GO:0014070","count":4}]},{"hash":"1259192354648351865","title":"Nuclear import and cell division machinery","description":"This cluster is dominated by nucleocytoplasmic transport and nuclear events in cell division: NLS-bearing protein import and ribosomal protein import into nucleus, plus meiotic and mitotic nuclear processes. The GTPase activity regulation fits transport and mitosis control, while viral process and other terms are ancillary connections rather than core functions. Overall, the evident theme is movement of proteins into the nucleus combined with cell-cycle\u2013related nuclear dynamics.","confidence":"Medium","size":16,"edges":58,"triangles":123,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0006607","count":5},{"id":"GO:0007143","count":4},{"id":"GO:0007084","count":4},{"id":"GO:0016032","count":4}]},{"hash":"432315300028842462","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000637","count":2},{"id":"GO:0061157","count":2},{"id":"GO:0001308","count":2},{"id":"GO:1902416","count":2},{"id":"GO:0000056","count":2}]},{"hash":"241729955431620571","title":"Cell Polarity and Migration Signaling","description":"The top GO terms cluster around cell polarity (apical/basal polarity maintenance), cell movement (ameboidal migration, negative chemotaxis, axonogenesis regulation), and signaling pathways that coordinate these processes (including T cell receptor signaling and mating projection growth) along with membrane trafficking/reticulophagy and secretory pathway regulation. This suggests a coherent theme of polarity-driven migration and associated signaling, making the label a good fit.","confidence":"Medium","size":16,"edges":117,"triangles":521,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010796","count":4},{"id":"GO:0031384","count":4},{"id":"GO:0061709","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0050852","count":3}]},{"hash":"1243542032476375629","title":"Ubiquitin-like protein modifications","description":"This cluster is dominated by GO terms for neddylation, urmylation, ufmylation, and sumoylation, which are all ubiquitin-like modifier conjugation pathways, as well as related lipidation. This suggests a common theme of attaching small modifiers to proteins to regulate function or stability. A few other terms (e.g., tRNA thiolation, thiamine biosynthesis) appear less central, but the strongest signal remains ubiquitin-like modification processes.","confidence":"High","size":16,"edges":15,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0045116","count":7},{"id":"GO:0032447","count":6},{"id":"GO:0002143","count":6},{"id":"GO:0045892","count":6},{"id":"GO:1990592","count":6}]},{"hash":"1731864274385416896","title":"Unknown","description":"There is no clear shared function among the terms; the top GO terms include neuron projection extension, regulation of chromatin binding, differentiation, and several obsolete regulatory terms, with only singleton annotations and no edges connecting proteins. This sparse, dispersed set does not reveal a cohesive biological theme, so a specific label isn\u2019t justifiable.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990138","count":1},{"id":"GO:0035563","count":1},{"id":"GO:0010725","count":1},{"id":"GO:0010569","count":1},{"id":"GO:0051572","count":1}]},{"hash":"1144884594677564640","title":"NF-kappaB and TLR immune signaling regulation","description":"The top GO terms cluster around immune signaling (NF-kappaB signaling, TLR signaling regulation), plus modulation of apoptosis/necroptosis and transcriptional control via ubiquitination. This suggests a group of proteins that regulate immune-response signaling and transcriptional output to influence cell fate, with some transcriptional repression and cell-cycle regulation as supporting themes. The plant abscisic acid term seems likely to be annotation noise rather than core to the cluster. Overall, the label reflects a coherent theme of immune signaling regulation and transcriptional control.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060544","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0043066","count":1},{"id":"GO:0000209","count":1},{"id":"GO:0034121","count":1}]},{"hash":"404894873766110050","title":"Neural development and dopaminergic signaling","description":"This cluster is anchored by neural-focused terms: cerebellar cortex development and dopaminergic synaptic transmission, plus neural patterning regulation via Hedgehog signaling. While other terms touch general cellular processes (endosome transport, autophagy), the prominent themes center on neural development and neuronal communication.","confidence":"Medium","size":16,"edges":118,"triangles":532,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":16},{"id":"GO:0007124","count":16},{"id":"GO:1901621","count":16},{"id":"GO:1904637","count":16},{"id":"GO:0001963","count":16}]},{"hash":"21264587615941218","title":"Amino Acid Catabolism and Central Metabolism","description":"Most top GO terms describe catabolic processes for amino acids (L-alanine, L-aspartate, L-lysine via saccharopine) and the involvement of the TCA cycle, suggesting a cluster of proteins focused on extracting energy from amino acids and funneling carbons into central metabolism. Additional terms include fatty acid transport and sphingomyelin biosynthesis, indicating broader roles in lipid metabolism. A single Notch signaling term is present but does not dominate the cluster's function, so the overall theme is metabolic catabolism feeding core metabolism.","confidence":"Medium","size":16,"edges":119,"triangles":546,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0033512","count":9},{"id":"GO:0042853","count":7},{"id":"GO:0006099","count":6},{"id":"GO:0006686","count":6},{"id":"GO:0019878","count":6}]},{"hash":"1770534951614843513","title":"Unknown","description":"The GO terms are diverse and span nuclear/nucleic-acid processes (chromosome condensation, RNase MRP-dependent mRNA decay, snoRNA processing, regulation of DNA binding, deubiquitination) as well as a pollen sperm cell differentiation and multiple stress/transport-related processes (potassium ion starvation response, histidine transport into vacuole, nitrogen starvation). There isn\u2019t a single clear shared function or pathway tying these terms together, so a cohesive, specific label isn\u2019t supported.","confidence":"","size":16,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030261","count":1},{"id":"GO:0000294","count":1},{"id":"GO:0034965","count":1},{"id":"GO:0048235","count":1},{"id":"GO:0042981","count":1}]},{"hash":"394530980871111895","title":"Gene expression and reproductive development","description":"This cluster is dominated by GO terms for transcription (DNA-templated transcription) and ribosome biogenesis, indicating active gene expression and protein synthesis, with supporting signals for cell division and cytoskeletal regulation (Arp2/3). Reproductive-related terms such as male gonad development and conjugation with cellular fusion further tie these processes to development and mating. While some terms are more general, the core theme centers on gene expression and growth in a reproductive context.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0008584","count":5},{"id":"GO:2000601","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0000747","count":3}]},{"hash":"401042423924023444","title":"Unknown","description":"The top GO terms cover a wide range of processes across different tissues (endosome transport, fungal growth, neural tube patterning, calcium signaling, dopaminergic synaptic transmission, p53 signaling, NK T cell differentiation, neuron axonogenesis, aging responses, and cartilage condensation) with no single cohesive function connecting them. This heterogeneity suggests there is no single biological theme represented by the cluster.","confidence":"","size":16,"edges":12,"triangles":4,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":16},{"id":"GO:0007124","count":16},{"id":"GO:1901621","count":16},{"id":"GO:1904637","count":16},{"id":"GO:0001963","count":16}]},{"hash":"1283439541651244689","title":"DNA replication and growth regulation","description":"The strongest terms center on DNA replication and DNA-templated transcription, with additional signals for cell size regulation and metabolic processes, together pointing to a theme of growth coupled with genome synthesis. Some seemingly unrelated terms may be noise, but the core cluster appears to reflect replication-associated growth control and related trafficking/metabolic aspects.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":15},{"id":"GO:0045793","count":15},{"id":"GO:0001890","count":15},{"id":"GO:0006006","count":15},{"id":"GO:0006351","count":15}]},{"hash":"1110466870962231923","title":"Developmental signaling and differentiation","description":"Top terms span neural development, signaling, calcium signaling, and developmental differentiation (cartilage, immune). The shared theme is regulation of signaling pathways guiding development across tissues, so this label fits the cluster's broad functional scope.","confidence":"Medium","size":16,"edges":99,"triangles":325,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":16},{"id":"GO:0007124","count":16},{"id":"GO:1901621","count":16},{"id":"GO:1904637","count":16},{"id":"GO:0001963","count":16}]},{"hash":"2235015222383066668","title":"Neural development and dopaminergic signaling","description":"The top GO terms cluster around neural development and synaptic signaling, including CNS projection neuron axonogenesis and dopaminergic synaptic transmission, with related signaling regulation (p53 pathway, calcium response) and endosomal trafficking that supports neuronal function. While there are a few non-neural terms present, the dominant theme is neural development and neuronal signaling.","confidence":"Medium","size":16,"edges":87,"triangles":247,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":16},{"id":"GO:0007124","count":16},{"id":"GO:1901621","count":16},{"id":"GO:1904637","count":16},{"id":"GO:0001963","count":16}]},{"hash":"1254211903137971115","title":"Peroxisomal lipid metabolism and mitochondrial apoptosis regulation","description":"This cluster centers on peroxisomal and mitochondrial lipid and amino acid catabolism (ketone body biosynthesis/catabolism, acetyl-CoA catabolic, L-isoleucine catabolic, glyoxysome organization) and metabolic stress responses (response to starvation). It also includes terms about regulation of mitochondrial membrane permeability and apoptotic signaling, suggesting a link between lipid metabolism and apoptosis control. Together, these terms define a module where lipid processing feeds into mitochondrial pathways and modulates cell survival, hence the name.","confidence":"Medium","size":16,"edges":29,"triangles":25,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0046951","count":1},{"id":"GO:0010111","count":1},{"id":"GO:0046356","count":1},{"id":"GO:0014070","count":1},{"id":"GO:0046952","count":1}]},{"hash":"596188522180411608","title":"DNA Replication and Cell Cycle Regulation","description":"The cluster is enriched for GO terms related to DNA replication (including replication and initiation) and mitotic DNA replication checkpoint signaling, which together point to core replication machinery and cell cycle control. Additional terms like transcription initiation and protein targeting appear but seem secondary or noisy relative to the replication/cell cycle theme. Overall, this set most clearly represents replication-linked cell cycle regulation. ","confidence":"Medium","size":16,"edges":66,"triangles":121,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0030433","count":2},{"id":"GO:0019079","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0006367","count":2}]},{"hash":"1128904964149871523","title":"Diverse Stimulus-Response Signaling","description":"This cluster includes GO terms for cytokinin and ethylene signaling, hypoxia and light detection, xenobiotic response, and interleukin-4 signaling, indicating responsiveness to a wide range of environmental and immune signals. It also contains nuclear/ DNA maintenance terms like DNA replication, DNA topology changes, telomerase assembly, and nuclear import regulation, suggesting these proteins participate in coordinating signaling with genome maintenance. Therefore a label reflecting broad stimulus responsiveness is appropriate.","confidence":"Medium","size":16,"edges":24,"triangles":13,"max_degree":10,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009736","count":8},{"id":"GO:0006261","count":8},{"id":"GO:0033160","count":8},{"id":"GO:0035690","count":8},{"id":"GO:1905323","count":8}]},{"hash":"2245810903275850217","title":"Olfactory-cAMP signaling and neural drug response","description":"The top GO terms cluster around cAMP signaling (cellular response to cAMP, negative regulation of PKA activity), regulation of membrane potential, and sensory perception of smell, with additional hints of neural pharmacology (response to antipsychotic drugs and clozapine). Together these point to a neural context where olfactory signaling and cAMP pathways are modulated, including drug responsiveness. Some terms (ion import, cardiac proliferation) are less directly tied, but do not override the central olfactory/cAMP-neural theme.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000480","count":2},{"id":"GO:0098719","count":2},{"id":"GO:0071320","count":2},{"id":"GO:0097332","count":2},{"id":"GO:0046827","count":2}]},{"hash":"1634839861023030159","title":"Unknown","description":"The top GO terms span plant cytokinin signaling, chlorophyll biosynthesis regulation, animal morphine response, male sex differentiation, interferon response, and several obsolete terms, indicating no single cohesive function. The diverse and cross-kingdom signals imply the cluster lacks a common biological theme, so a safe label is Unknown with no confidence.","confidence":"","size":16,"edges":25,"triangles":7,"max_degree":8,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0043278","count":12},{"id":"GO:0009736","count":11},{"id":"GO:1902325","count":11},{"id":"GO:0046661","count":11},{"id":"GO:0051348","count":11}]},{"hash":"2164149264694043179","title":"Neuronal development and synaptic signaling","description":"The dominant GO terms describe neural development and synapse-related processes: excitatory postsynaptic potential, axon extension, dendrite morphogenesis, hippocampus and nervous system development, and cellular response to dopamine. These themes indicate proteins involved in neural circuit formation and synaptic activity. Some terms (T cell receptor signaling, mitotic cell cycle) may reflect shared signaling components or annotation noise, but do not override the overall neuronal theme.","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060079","count":16},{"id":"GO:0045773","count":16},{"id":"GO:1903351","count":16},{"id":"GO:0021766","count":16},{"id":"GO:0048813","count":16}]},{"hash":"1774238117083132255","title":"Unknown","description":"The top GO terms span plant hormone biosynthesis (abscisic acid) and suberin formation, general transcription regulation, signaling pathways, immune-related processes, and neural structure terms, with no clear single biological theme tying all proteins together. This mix suggests either annotation noise or multi-functional proteins rather than a cohesive, identifiable cluster function. ","confidence":"","size":16,"edges":15,"triangles":0,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0009688","count":4},{"id":"GO:0090419","count":4},{"id":"GO:0010345","count":4},{"id":"GO:0034244","count":4},{"id":"GO:0007249","count":4}]},{"hash":"1313406710081423951","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071374","count":1},{"id":"GO:0090084","count":1},{"id":"GO:1901621","count":1},{"id":"GO:0006458","count":1},{"id":"GO:0070843","count":1}]},{"hash":"444342266554390302","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning immune defense, transcriptional regulation, nuclear transport, endosome trafficking, growth, and neuronal signaling, with no single unifying biological theme. Edges are absent, indicating little functional connectivity in the cluster. This makes it hard to assign a specific, representative label beyond Unknown.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050830","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0046826","count":2},{"id":"GO:0000122","count":2},{"id":"GO:2000641","count":1}]},{"hash":"988818227308219076","title":"Ribosome Biogenesis and Translation in Cell Cycle","description":"The top GO terms cluster around ribosome biogenesis (small and large subunits, nuclear export), cytoplasmic translation, tRNA modification, and cell division/cell cycle processes, indicating a coordinated program of ribosome production and protein synthesis linked to cell-cycle progression.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000747","count":4},{"id":"GO:1901001","count":4},{"id":"GO:0090529","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0042274","count":4}]},{"hash":"397462260343834657","title":"Membrane remodeling during division and morphogenesis","description":"This cluster centers on processes that tie membrane dynamics to cell division and morphogenesis, including mitotic cell cycle, cleavage furrow formation, and plasma membrane tubulation, plus endocytic recycling and phosphatidic acid biosynthesis that support membrane trafficking and lipid signaling. Some terms also reflect developmental membrane remodeling (sporulation membrane formation, eye development, ECM disassembly), suggesting a broader role in membrane-associated shaping during growth and development.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0000902","count":3},{"id":"GO:0016310","count":2},{"id":"GO:1990126","count":2},{"id":"GO:0097320","count":2}]},{"hash":"1587833781244216748","title":"Cellular stress response and protein homeostasis","description":"The cluster shows enrichment in stress-related and protein-handling processes, including ER-Golgi vesicle transport, heat-stress\u2013driven mRNA export, ubiquitination, and splicing, along with cell-cycle regulation and chromatin assembly. These together point to a broad stress-response/quality-control module, with additional inflammatory and apoptotic signaling components reflecting remodeling under stress.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:2000728","count":2},{"id":"GO:1904668","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0061641","count":2}]},{"hash":"798348459773758382","title":"Antiviral innate immune signaling and cell cycle regulation","description":"The cluster is enriched for innate antiviral responses, including cellular response to type I interferon and dsRNA, and general innate immune response terms, suggesting a core antiviral signaling theme. The presence of mitotic cell cycle and cell division terms implies a link between immune signaling and cell cycle regulation. Stress-related terms like cadmium and hydrogen peroxide appear as secondary responses but do not dominate the theme. ","confidence":"High","size":16,"edges":48,"triangles":41,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071357","count":7},{"id":"GO:0051301","count":7},{"id":"GO:0045087","count":7},{"id":"GO:0050689","count":7},{"id":"GO:0071360","count":7}]},{"hash":"819848102600477859","title":"Nuclear signaling, cell cycle, and cilium assembly","description":"This cluster is dominated by GO terms related to nuclear processes (cell division, APC/C-dependent catabolic process, snoRNP assembly, and regulation of protein modification) and steroid signaling (steroid hormone receptor complex assembly and glucocorticoid pathway regulation), with additional emphasis on cilium-related biology (regulation of non-motile cilium assembly and photoreceptor outer segment localization). While innate immune response and lead ion response appear, the core theme appears to be nuclear regulation of the cell cycle and ciliary/sensory functions, sometimes modulated by steroid signaling.","confidence":"Medium","size":16,"edges":15,"triangles":0,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":14},{"id":"GO:0000492","count":13},{"id":"GO:0006463","count":13},{"id":"GO:2000324","count":13},{"id":"GO:0045087","count":13}]},{"hash":"908253393221433839","title":"Nuclear RNA Processing and Ribosome Biogenesis","description":"The cluster centers on nuclear RNA-processing events (rRNA maturation, mRNA splicing, mRNA export regulation) and chromatin-related assembly, suggesting a cohesive focus on ribosome biogenesis and related RNA processing with some cell-cycle regulation aspects; a few outliers (inflammatory cytokine term) exist but do not dominate the set.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0007584","count":3},{"id":"GO:2000728","count":2},{"id":"GO:1904668","count":2}]},{"hash":"1934320912874065811","title":"Unknown","description":"The top GO terms span ER-Golgi transport, mRNA processing (export and splicing), ubiquitination, chromatin assembly, cell cycle checkpoints, inflammatory cytokine production, glial apoptosis, and GPCR signaling, showing no single dominant theme. Because there isn't a cohesive function linking these terms for this cluster, a specific label cannot be confidently assigned.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:2000728","count":1},{"id":"GO:1904668","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0061641","count":1}]},{"hash":"2165683328430682628","title":"Neurodevelopment and Nuclear Organization","description":"The top GO terms point to brain development (forebrain neuroblast division, third ventricle development) alongside nuclear processes (DNA-templated transcription, nuclear membrane organization). The presence of diverse developmental and nuclear terms, plus no observed interactions among proteins (edges 0), suggests a broad cluster linked to neurodevelopmental regulation and nuclear dynamics rather than a single pathway. Confidence reflects partial cohesion: Moderate.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034638","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0071763","count":2},{"id":"GO:1900748","count":1},{"id":"GO:0021873","count":1}]},{"hash":"859178612230814059","title":"Cell Cycle Regulation and Transcription Control","description":"The cluster centers on mitotic control and transcriptional regulation, including positive regulation of spindle pole separation, CDK activity, and the canonical Wnt signaling pathway, all of which point to cell cycle progression and transcriptional control as the core theme. A few terms related to tissue-specific development (mammary gland) or obsolete/viral annotations appear but do not redefine the main function.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019086","count":1},{"id":"GO:0060749","count":1},{"id":"GO:0010696","count":1},{"id":"GO:0010165","count":1},{"id":"GO:0000411","count":1}]},{"hash":"1333820371444775016","title":"ER-Golgi Vesicle Trafficking and Cell Cycle","description":"The dominant GO terms point to ER-to-Golgi and Golgi-to-ER vesicle transport (including COPII-coated budding), indicating a core role in ER-Golgi vesicular traffic. Additional terms for cell division and mitotic spindle assembly suggest a coupling to cell cycle processes, while brain development and multicellular growth imply a developmental context in which trafficking is essential. Overall, the cluster seems to be centered on ER-Golgi transport with links to cell proliferation and development.","confidence":"Medium","size":16,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0007420","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0008283","count":2}]},{"hash":"700189592041915379","title":"Ubiquitin-Dependent Proteolysis (ERAD)","description":"The top GO terms cluster around ubiquitination and degradation, including protein autoubiquitination and ubiquitin-dependent ERAD pathways, as well as ER-associated protein catabolic processes. While other terms appear (e.g., cell cycle regulation, metabolism) they are less cohesive, making ubiquitin-mediated degradation the most representative theme for this cluster. Confidence: Medium","confidence":"","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1900087","count":2},{"id":"GO:0008152","count":1},{"id":"GO:1902475","count":1},{"id":"GO:0033132","count":1},{"id":"GO:0051865","count":1}]},{"hash":"2033725361720866264","title":"ER-Golgi-Endosome Transport","description":"GO terms cluster around endomembrane trafficking, including ER exit, Golgi-to-endosome transport, and localization to early endosomes, plus plasma membrane-to-endosome trafficking. This suggests a cohesive role for these proteins in vesicle trafficking along the secretory and endocytic pathways, with some peripheral terms contributing noise.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045599","count":1},{"id":"GO:0048227","count":1},{"id":"GO:1900452","count":1},{"id":"GO:0008625","count":1},{"id":"GO:0070863","count":1}]},{"hash":"871770186090968887","title":"Secretory pathway glycosylation and sphingolipid metabolism","description":"The top GO terms cluster around protein processing in the secretory pathway (ER-to-Golgi transport and N-linked glycosylation) together with lipid metabolism/signaling (sphingolipid, sphingosine, and related lipid processes). A few terms are older or less informative (obsolete Wnt terms, detoxification, transport), but the dominant theme links secretory pathway functions with membrane lipid turnover. This suggests a module focused on secretory protein processing coupled to lipid metabolism.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":1},{"id":"GO:0006487","count":1},{"id":"GO:1902068","count":1},{"id":"GO:0006668","count":1},{"id":"GO:0098869","count":1}]},{"hash":"2038728915220815150","title":"Diverse catabolic metabolism","description":"Top GO terms point to multiple substrate-specific catabolic processes (lipids like triglycerides and monoacylglycerols, phosphatidylserine, aromatic compounds via beta-ketoadipate and stilbene pathways, uracil) and related lipid signaling regulation, indicating a cluster of proteins involved in broad degradation and turnover of diverse metabolites rather than a single pathway.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":10},{"id":"GO:2000124","count":10},{"id":"GO:0052651","count":8},{"id":"GO:0006660","count":8},{"id":"GO:0055114","count":7}]},{"hash":"1271950614512911781","title":"Mitochondrial Ion and Metabolite Transport","description":"The cluster\u2019s GO terms center on transmembrane transport activities, especially of ions and metabolites (phosphate, thiosulfate, NAD) and iron import into mitochondria, which points to mitochondrial transport functions linked to metabolism and energy regulation. Some terms reference systemic metabolic processes (adaptive thermogenesis, liver regeneration) that are connected to mitochondrial function, supporting a unifying theme of mitochondrial/ membrane transport and metabolic regulation. While not every term fits perfectly, the overall pattern supports this label with moderate confidence.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":3},{"id":"GO:0006970","count":2},{"id":"GO:0097421","count":2},{"id":"GO:1990845","count":2},{"id":"GO:0060546","count":2}]},{"hash":"452808298272751969","title":"Lipid metabolism and lipoprotein remodeling","description":"The cluster\u2019s top GO terms are dominated by lipid-related processes: phospholipid catabolic and biosynthetic pathways (phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol), cholesterol metabolism, triglyceride biosynthesis, and remodeling of HDL and VLDL particles, plus lipid storage. This pattern strongly indicates a cohesive function in lipid metabolism and lipoprotein remodeling, though a single annotation (dorsal appendage formation) appears incidental. ","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046338","count":2},{"id":"GO:0031161","count":1},{"id":"GO:0046843","count":1},{"id":"GO:0034638","count":1},{"id":"GO:0019432","count":1}]},{"hash":"1535572650473198279","title":"Unknown","description":"The cluster shows a mix of terms spanning chromatin regulation, trafficking, signaling, and miscellaneous cellular processes (histone methylation regulation, receptor recycling, transcription regulation, endosome size, Rho signaling, glutamatergic synaptic transmission, tRNA processing, spermatogenesis, microtubule anchoring). With no clear, shared functional theme across the proteins and several terms being obsolete, there isn\u2019t a cohesive label that accurately captures the group.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0034968","count":3},{"id":"GO:0001881","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0051036","count":3},{"id":"GO:0035023","count":3}]},{"hash":"308338489854498567","title":"Mitochondrial Metabolite Transport","description":"The GO terms cluster around mitochondrion-centered transport and metabolism, including NAD transmembrane transport, iron import into the mitochondrion, thiosulfate transport, and deoxynucleotide transport, along with regulation of mitochondrial membrane permeability and energy-related processes like adaptive thermogenesis. These recurring themes indicate a function focused on mitochondrial metabolite transport and related regulation.","confidence":"High","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0097421","count":1},{"id":"GO:1990845","count":1},{"id":"GO:0060546","count":1},{"id":"GO:0097274","count":1},{"id":"GO:0070542","count":1}]},{"hash":"1070176776961047336","title":"Peroxisome Biogenesis & Metabolism","description":"This cluster is dominated by peroxisome-related terms: peroxisome organization, fission, and regulation of size, with brown fat differentiation connecting to peroxisomal function in adipocytes. Catabolic processes like beta-ketoadipate and glucuronoside catabolism further support a peroxisomal metabolic theme, suggesting the proteins are involved in peroxisome biogenesis and lipid/xenobiotic metabolism.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050873","count":2},{"id":"GO:0044375","count":2},{"id":"GO:0016559","count":2},{"id":"GO:0007031","count":2},{"id":"GO:0042952","count":1}]},{"hash":"110533370948968931","title":"Calcium signaling and developmental transcription regulation","description":"The cluster shows several calcium signaling-related terms (positive regulation of calcium release into cytosol and regulation of ryanodine receptor activity), suggesting calcium signaling as a core theme. Additionally, the presence of terms for positive regulation of DNA binding and NLS-bearing protein import into the nucleus points to transcriptional regulation, while developmental terms (cardiac myofibril assembly, kidney development, connective tissue remodeling) hint at roles in developmental processes. Taken together, the proteins likely participate in calcium-regulated transcriptional control across development. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060316","count":3},{"id":"GO:0043388","count":3},{"id":"GO:0055003","count":2},{"id":"GO:0097274","count":2},{"id":"GO:0008365","count":2}]},{"hash":"330801698933467948","title":"Neural development and morphogenesis","description":"The top GO terms center on neural development and morphogenesis (neural tube closure, forebrain development, cell morphogenesis), supported by transcriptional and cell cycle processes typically involved in development. Some terms reflect generic stress or defense responses, which may be incidental, but do not override the main developmental theme. Confidence: Medium","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000902","count":2},{"id":"GO:0001843","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0070059","count":2}]},{"hash":"1959444791313710457","title":"DNA-Templated Transcription and RNA Processing","description":"This cluster is dominated by GO terms for regulation and execution of DNA-templated transcription and RNA processing (mRNA splicing and snoRNA metabolism), suggesting a nucleus-centric transcription/RNA biology theme. A few outlier terms (pseudohyphal growth, retrotransposition, muramyl dipeptide response, and Rho signaling) may reflect broader or incidental annotations, but the core signal points to transcription control and RNA processing.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0007124","count":1},{"id":"GO:0032197","count":1},{"id":"GO:0009793","count":1}]},{"hash":"1797987447816942163","title":"Transcriptional Regulation and Endosomal Trafficking","description":"The terms center on regulation of transcription and chromatin processes, plus endosomal trafficking and signaling (receptor recycling, endosome size, Rho signaling, glutamatergic transmission). This suggests a cluster coordinating gene expression with membrane trafficking and synaptic signaling, with auxiliary regulation of autophagy and catalytic activity. While some terms are peripheral, the core pattern ties transcriptional control to intracellular trafficking and signaling.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":7},{"id":"GO:0034968","count":6},{"id":"GO:0001881","count":6},{"id":"GO:0051036","count":6},{"id":"GO:0035023","count":6}]},{"hash":"467183986924799856","title":"Unknown","description":"The cluster\u2019s top GO terms are a mix of immune signaling (interferon response, cytokine production), nuclear gene regulation (splicing, mRNA export, chromatin assembly, ubiquitination, hormone receptor complex assembly), and developmental processes (male differentiation, prostate development). With no clear single theme and no edges connecting proteins, there isn\u2019t a cohesive function to name; thus Unknown is most appropriate.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071357","count":1},{"id":"GO:0046661","count":1},{"id":"GO:0030850","count":1},{"id":"GO:0006463","count":1},{"id":"GO:2000728","count":1}]},{"hash":"325845380844008201","title":"Unknown","description":"The proteins show a highly diverse set of GO terms, including porphyrin biosynthesis (two terms) but also cellular responses to amines and arsenic, telomere-related DNA processes, nucleosome assembly, G-quadruplex DNA formation, and plant cytokinin signaling. There isn\u2019t a single dominant function or pathway tying them together, so a cohesive, specific label isn\u2019t supported. At best, porphyrin/heme biosynthesis appears, but it\u2019s only a small fraction of the annotations.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071418","count":1},{"id":"GO:0006782","count":1},{"id":"GO:0071243","count":1},{"id":"GO:0006780","count":1},{"id":"GO:0061820","count":1}]},{"hash":"332052659242575306","title":"DNA repair and chromatin regulation","description":"The terms point to genome maintenance: DNA repair (GO:0006281), DNA damage response signals, and deubiquitination of K48-linked chains (GO:0071108) that modulate repair pathways. TE silencing (GO:0010526) and RNA processing-related terms suggest chromatin-level regulation. A calcium/NFAT term exists but is less central, making the main theme genome maintenance and chromatin regulation.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051533","count":1},{"id":"GO:0070940","count":1},{"id":"GO:0006379","count":1},{"id":"GO:0051209","count":1},{"id":"GO:0010526","count":1}]},{"hash":"1806134740575506675","title":"Skeletal and connective tissue development with mechanosensing","description":"The top GO terms highlight bone development and connective tissue development (bone, lung connective tissue, otolith morphogenesis) together with a cellular response to mechanical stimulus, pointing to a shared theme of tissue development influenced by mechanical cues. While there are some immune and signaling terms present, they seem less central to this core theme, suggesting the label captures the dominant function of the cluster.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060348","count":3},{"id":"GO:0071260","count":3},{"id":"GO:0002730","count":2},{"id":"GO:1903215","count":2},{"id":"GO:1902499","count":2}]},{"hash":"1481985259810020642","title":"Chromatin, RNA processing, and ubiquitin signaling","description":"The proteins show enrichment for chromatin assembly (CENP-A), mRNA splicing/export, and ubiquitin-related regulatory processes, with links to cell cycle control. While neural development terms appear, the core signal centers on gene expression regulation and protein fate via chromatin state, RNA processing, and ubiquitination.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060041","count":2},{"id":"GO:0051013","count":2},{"id":"GO:2000728","count":1},{"id":"GO:1904668","count":1},{"id":"GO:0050773","count":1}]},{"hash":"474217737467948553","title":"Chromatin modification and transcription regulation","description":"The cluster is enriched for GO terms related to chromatin state and transcription: DNA-templated transcription, nucleosome assembly, and multiple histone modifications (H3K4/H3K27 methylation, acetylation). Together these indicate chromatin remodeling/epigenetic regulation of gene expression. A few terms like placenta morphogenesis or sodium transport are less directly related and likely peripheral, but the dominant pattern is chromatin modification and transcription control.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:1901674","count":2},{"id":"GO:0006334","count":2},{"id":"GO:0080182","count":2},{"id":"GO:0098532","count":2}]},{"hash":"1258959317716784986","title":"Unknown","description":"The GO terms for this cluster are highly diverse, spanning regulatory processes in fungi (regulation of pseudohyphal growth; urmylation), developmental terms in animals (spinal cord development; epithelial cell differentiation), and assorted cellular processes (tRNA wobble thiolation; redox homeostasis; cysteine modification; glycerol metabolism; mitotic M phase; peptidyl-tyrosine dephosphorylation). There are no shared terms or edges linking the proteins, so there is no clear common function to label. Therefore label Unknown with no confidence.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000220","count":1},{"id":"GO:0032447","count":1},{"id":"GO:0021510","count":1},{"id":"GO:0002143","count":1},{"id":"GO:0045454","count":1}]},{"hash":"2146414923214303554","title":"Unknown","description":"The top GO terms here are diverse across digestion, development, cell cycle transitions, and protein processing with no clear shared function or pathway linking the proteins. There are no edges or triangles, so the cluster does not cohere around a specific biological theme, just a set of independent regulatory or developmental processes.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033234","count":2},{"id":"GO:0097050","count":2},{"id":"GO:0051281","count":2},{"id":"GO:0014718","count":2},{"id":"GO:0097264","count":2}]},{"hash":"696793296252657839","title":"Muscle contraction and calcium handling","description":"The top GO terms are dominated by muscle-related processes (muscle contraction, ventricular cardiac muscle cell action potential, calcium transport and buffering), and there is an emphasis on calcium regulation (calcium sequestering, ATPase-coupled calcium transporter activity). Although a few terms refer to skin development or taste, the strongest signal across the cluster is functions related to muscle activity and calcium dynamics, suggesting these proteins commonly participate in excitation-contraction coupling and calcium homeostasis in muscle cells.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071712","count":1},{"id":"GO:0051284","count":1},{"id":"GO:0043588","count":1},{"id":"GO:0050882","count":1},{"id":"GO:1901896","count":1}]},{"hash":"464339569502309092","title":"RNA metabolism in germline and meiosis","description":"This cluster combines RNA processing/regulation terms (mRNA destabilization, primary miRNA processing, RNA editing, cap-independent translational regulation) with germline and meiotic processes (stem cell maintenance, meiotic cell cycle, karyogamy, germarium-derived cyst encapsulation), suggesting a coordinated RNA-based regulatory module during germline development and meiosis.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061157","count":1},{"id":"GO:0000742","count":1},{"id":"GO:0007329","count":1},{"id":"GO:0030708","count":1},{"id":"GO:0019827","count":1}]},{"hash":"1600227349928365105","title":"Unknown","description":"No enriched GO terms and no interactions observed; cannot infer a shared function from the available data.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1020983671874189780","title":"Glutamatergic synaptic receptor recycling","description":"The terms emphasize receptor recycling, endosome size regulation, and glutamatergic synaptic transmission, pointing to a role in glutamatergic receptor trafficking and endosomal dynamics at the synapse; regulation of Rho signaling aligns with cytoskeletal changes needed for endocytosis.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0060316","count":5},{"id":"GO:0034968","count":4},{"id":"GO:0001881","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0051036","count":4}]},{"hash":"1078659693984010696","title":"Unknown","description":"The GO terms are a mix of membrane trafficking (receptor recycling, regulation of endosome size, Rho signaling, glutamatergic transmission) and nuclear processes (histone methylation, regulation of transcription, rRNA processing). There isn\u2019t a single cohesive theme linking these functions for this cluster, so a non-specific label is most appropriate.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034968","count":1},{"id":"GO:0001881","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0051036","count":1},{"id":"GO:0035023","count":1}]},{"hash":"1797158095286503527","title":"Nuclear transcription and RNA processing regulators","description":"This cluster centers on DNA-templated transcription and chromatin modification (H3K4/H3K79 methylation), plus RNA processing steps (mRNA splicing and export, including regulation under heat stress). It also includes related regulatory processes such as ubiquitin ligase activity, and developmental or cellular organization roles (lens differentiation, P granule organization, dendrite development). The shared pattern is nuclear gene expression control from transcription through RNA processing and related regulatory pathways.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0051568","count":2},{"id":"GO:0034729","count":2},{"id":"GO:0070306","count":2},{"id":"GO:0030719","count":2}]},{"hash":"972824115928789387","title":"Immune signaling with RNA processing and translation control","description":"The terms show a blend of immune-related regulation (T cell proliferation, monocyte differentiation, glucocorticoid response) and post-transcriptional gene regulation (translation and elongation, mRNA decay, snoRNA splicing). The presence of p38MAPK cascade supports a stress/ inflammatory signaling context. Together, they suggest a cluster involved in coordinating immune responses with RNA processing and translation control, rather than a single narrow function.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000766","count":1},{"id":"GO:0045647","count":1},{"id":"GO:0038066","count":1},{"id":"GO:0034247","count":1},{"id":"GO:0042129","count":1}]},{"hash":"1010742966756834726","title":"Photosynthesis and Aromatic Compound Catabolism","description":"The top GO terms point to photosynthetic metabolism, with strong signals for photosynthesis, nonphotochemical quenching, nitrate assimilation, and proton transmembrane transport, suggesting a photosynthesis-centered functional theme. The presence of aromatic compound catabolic processes (toluene and carbazole) indicates additional metabolic versatility, which can occur in environmental or photosynthetic bacteria. An anomalous term related to NF-kappaB signaling is likely incidental. Overall, the cluster appears to reflect photosynthesis-linked metabolism with auxiliary hydrocarbon degradation capabilities.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0042128","count":6},{"id":"GO:0015979","count":6},{"id":"GO:0042203","count":5},{"id":"GO:0046381","count":5},{"id":"GO:0010196","count":5}]},{"hash":"1380298735866144206","title":"Cell cycle regulation and transcription signaling","description":"These terms cluster around cell-cycle control (CDK activity, spindle pole separation), transcription regulation (RNA polymerase II CTD phosphorylation, transcription by galactose), and proliferative signaling (canonical Wnt pathway) with links to mammary gland development. The common theme is coordination of cell division with transcriptional programs and growth signals.","confidence":"Medium","size":15,"edges":102,"triangles":418,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019086","count":9},{"id":"GO:0060749","count":9},{"id":"GO:0010696","count":9},{"id":"GO:0010165","count":9},{"id":"GO:0000411","count":9}]},{"hash":"722213688537955357","title":"Neural development and synaptic vesicle regulation","description":"It is dominated by neural-related terms\u2014brain development, substantia nigra development, and regulation of synaptic vesicle exocytosis\u2014together with related processes like cell polarity and gene expression control, pointing to proteins involved in neural development and synaptic machinery.","confidence":"High","size":15,"edges":49,"triangles":88,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007420","count":13},{"id":"GO:0010796","count":13},{"id":"GO:0031384","count":13},{"id":"GO:2000300","count":13},{"id":"GO:0010628","count":12}]},{"hash":"1455368176857821284","title":"Neural development and synaptic signaling","description":"The top terms are dominated by neural-related processes: visual perception, axonogenesis, excitatory postsynaptic potential, and long-term synaptic potentiation, pointing to neuronal development and synaptic function as the core theme. Additional terms like Schwann cell and heart development, and myoblast fusion suggest broader developmental roles but do not outweigh the neural emphasis; the ABA signaling term appears as an outlier but does not define the cluster\u2019s function.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":11},{"id":"GO:0000278","count":11},{"id":"GO:0000086","count":10},{"id":"GO:0060079","count":10},{"id":"GO:0007520","count":10}]},{"hash":"123856489971521239","title":"Neuronal development and endosomal trafficking","description":"This cluster centers on neural development and signaling, with terms like CNS projection neuron axonogenesis, dopaminergic synaptic transmission, and regulation of endosome transport, pointing to a theme of neural differentiation and intracellular trafficking. Some terms (pseudohyphal growth, NK T cell differentiation, cartilage condensation) are less clearly connected and may reflect broader or off-target annotations, but they do not outweigh the neural-development focus. Confidence: Medium.","confidence":"","size":15,"edges":18,"triangles":7,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":15},{"id":"GO:0007124","count":15},{"id":"GO:1901621","count":15},{"id":"GO:1904637","count":15},{"id":"GO:0001963","count":15}]},{"hash":"2089992083119098395","title":"Neurodevelopmental Signaling","description":"The cluster\u2019s top GO terms point to neural development and signaling, including axonogenesis of CNS neurons, dopaminergic synaptic transmission, and regulation of signaling pathways (e.g., hedgehog/smoothened, p53). While there are some non-neural developmental terms (endosome trafficking, cartilage condensation, NK T differentiation), the strongest and most frequent themes relate to neural development and neuronal signaling processes.","confidence":"Medium","size":15,"edges":79,"triangles":214,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":15},{"id":"GO:0007124","count":15},{"id":"GO:1901621","count":15},{"id":"GO:1904637","count":15},{"id":"GO:0001963","count":15}]},{"hash":"1931407143603064616","title":"Cellular stress response and DNA repair","description":"The top GO terms span responses to multiple stresses (psychosocial stress, nitroglycerin, gamma radiation, singlet oxygen, arsenite, hypobaric hypoxia) and a term related to DNA damage repair regulation, along with an epigenetic modification term. This suggests a cohesive module of proteins involved in sensing and responding to cellular stress while maintaining genome integrity, rather than a single narrowly defined pathway.","confidence":"Medium","size":15,"edges":16,"triangles":3,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0033169","count":6},{"id":"GO:1990911","count":6},{"id":"GO:1904843","count":6},{"id":"GO:0071480","count":6},{"id":"GO:0000304","count":6}]},{"hash":"1063821965494860512","title":"Neural signaling and endosomal transport","description":"This cluster is dominated by neural-related processes\u2014dopaminergic synaptic transmission and CNS neuron axonogenesis\u2014and a strong signal for endosomal trafficking (early to late endosome transport), suggesting a module of neuronal communication integrated with vesicle trafficking. A few terms touch on development and immune or cartilage processes, but the core theme centers on neuronal signaling and endosome dynamics.","confidence":"Medium","size":15,"edges":104,"triangles":442,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":15},{"id":"GO:0007124","count":15},{"id":"GO:1901621","count":15},{"id":"GO:1904637","count":15},{"id":"GO:0001963","count":15}]},{"hash":"411551196425473471","title":"Photosynthesis and Plant Stress Response","description":"The terms prominently feature photosynthesis alongside stress responses (oxidative stress, amino acid starvation, cadmium), with peroxisome import suggesting plant organelle dynamics. There are also DNA replication and transcription terms indicating general cellular processes, but the strongest plant-specific signals are photosynthesis and stress-related pathways. Confidence: Medium","confidence":"","size":15,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0034198","count":3},{"id":"GO:0034599","count":2},{"id":"GO:0018279","count":2}]},{"hash":"1200835038246257382","title":"Neurodevelopmental Signaling and Trafficking","description":"This cluster centers on neural development and neuronal signaling activities, with terms like axonogenesis, dopaminergic transmission, and dorsal/ventral patterning; plus components of calcium signaling (ionomycin) and intracellular trafficking (endosome transport) that support neuronal processes. Some entries touch on broader development and signaling (p53-mediated signaling, NK T differentiation, cartilage condensation), but the dominant theme links neural development and signaling pathways.","confidence":"Medium","size":15,"edges":48,"triangles":58,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":15},{"id":"GO:0007124","count":15},{"id":"GO:1901621","count":15},{"id":"GO:1904637","count":15},{"id":"GO:0001963","count":15}]},{"hash":"2279720084898660694","title":"Mitochondrial protein import and membrane regulation","description":"The top GO terms are centered on mitochondrial function, especially regulation of mitochondrial membrane permeability and import of proteins into the mitochondrial matrix, with supporting terms related to lipid metabolism and cell cycle control. This suggests a cluster of proteins involved in mitochondrial import machinery and membrane dynamics, with downstream links to energy metabolism and cell-cycle regulation. Confidence: Medium","confidence":"","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070940","count":10},{"id":"GO:0046902","count":9},{"id":"GO:2000134","count":9},{"id":"GO:1903740","count":9},{"id":"GO:0010867","count":9}]},{"hash":"2077402336663781383","title":"Developmental Signaling Across Tissues","description":"Top GO terms point to signaling and development across diverse cell types: neural development (axonogenesis, dopaminergic synaptic transmission, CNS projection neurons) and dorsal-ventral patterning, immune differentiation (NK T cells), and cartilage condensation. Supporting processes include endosome transport regulation and calcium signaling (ionomycin response) that modulate signal transduction, as well as p53-mediated signaling. The shared feature is participation in signaling pathways that guide development and cell fate across tissues, rather than a single, unified function, hence a broad label.","confidence":"Medium","size":15,"edges":72,"triangles":164,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":15},{"id":"GO:0007124","count":15},{"id":"GO:1901621","count":15},{"id":"GO:1904637","count":15},{"id":"GO:0001963","count":15}]},{"hash":"119805834039873113","title":"Ubiquitin-Mediated Regulation and Immune Signaling","description":"The top GO terms cluster around ubiquitination and ubiquitin-protein transferase activities (ERAD, autoubiquitination, free ubiquitin chain polymerization, K29-linked ubiquitination), with immune signaling contexts (TRIF-dependent TLR signaling and T cell receptor signaling) and related processes like transcriptional regulation and DNA repair, indicating a cohort of proteins centered on ubiquitin-regulated regulation and immune pathways.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0035666","count":1},{"id":"GO:0070911","count":1},{"id":"GO:0051443","count":1},{"id":"GO:0051865","count":1}]},{"hash":"70970189606290426","title":"Cardiac electrophysiology and ion transport","description":"This cluster is dominated by GO terms tied to ion movement and membrane potential, including sodium import, potassium transmembrane transport, and atrial cardiac muscle cell repolarization, plus membrane stabilization and cGMP signaling, which together point to cardiac electrical activity systems. Some transcription-related terms appear but are less central to the cluster's core function.","confidence":"Medium","size":15,"edges":76,"triangles":199,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":9},{"id":"GO:0006351","count":9},{"id":"GO:0019233","count":8},{"id":"GO:0007275","count":8},{"id":"GO:0098719","count":6}]},{"hash":"984746677791340693","title":"Mitotic cell cycle and ER-Golgi trafficking","description":"The cluster shows strong representation of mitosis-related processes (mitotic spindle assembly, mitotic cell cycle, cell division, cell population proliferation) alongside vesicle trafficking between the ER and Golgi (COPII budding, retrograde transport, ER-to-Golgi transport). A ribosome biogenesis term is present but appears less central, and brain development is more context-specific; overall the dominant theme links cell division machinery with the secretory pathway. This justifies a label around mitosis coupled with vesicle trafficking.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090114","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0090307","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0000278","count":3}]},{"hash":"319687409183171","title":"Mitosis and DNA Replication","description":"The cluster is dominated by GO terms tied to cell division, with mitotic cell cycle (4), DNA replication (3), and centrosome cycle (3) pointing to core mitotic machinery and genome duplication processes. While other terms appear (cadmium response, innate immune response, development, endosome transport), they are less represented and do not define the primary theme. Thus the proteins most likely participate in cell division-related functions.","confidence":"High","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0071276","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0019233","count":3},{"id":"GO:0007098","count":3}]},{"hash":"186763860561185620","title":"Cell Cycle and Signaling Regulators","description":"The top GO terms are heavily centered on DNA replication and the mitotic cell cycle, pointing to a core involvement in cell proliferation. Additional terms span endosome transport, developmental signaling ( Hedgehog, p53 pathway regulation), calcium signaling responses, dopaminergic synaptic transmission, and developmental processes like cartilage condensation. This mix suggests a broad regulatory network that coordinates cell division with diverse signaling and developmental processes, rather than a single cohesive pathway.","confidence":"Medium","size":15,"edges":12,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006260","count":15},{"id":"GO:0000278","count":15},{"id":"GO:2000641","count":14},{"id":"GO:0007124","count":14},{"id":"GO:1901621","count":14}]},{"hash":"814573341593908336","title":"Potassium Ion Homeostasis and Membrane Potential","description":"Based on the prominent GO terms, the cluster centers on regulation of membrane potential and potassium ion transport/homeostasis, key to excitability in neurons and cardiac cells (e.g., resting potential, repolarization, K+ homeostasis). A few terms touch transcription or development, but the dominant pattern is electrophysiology and ion balance.","confidence":"High","size":15,"edges":90,"triangles":284,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":13},{"id":"GO:0019233","count":13},{"id":"GO:0007275","count":13},{"id":"GO:0006351","count":13},{"id":"GO:0071805","count":10}]},{"hash":"1320184509623562193","title":"Neural stress response and brain development","description":"The cluster includes brain development and glial apoptotic processes, suggesting neural-context biology. Additional terms indicate stress-responsive regulation of gene expression and protein turnover (mRNA export under heat stress, splicing, ubiquitination), pointing to a regulatory network in neural cells under stress that can intersect with inflammation and cell cycle control. The set is somewhat heterogeneous, so this label captures a best-fit high-level theme rather than a single tightly linked function.","confidence":"Medium","size":15,"edges":75,"triangles":171,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":3},{"id":"GO:2000728","count":2},{"id":"GO:1904668","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0061641","count":2}]},{"hash":"361796607625068071","title":"Meiosis-Associated Chromatin Remodeling","description":"The cluster is driven by terms pointing to chromatin dynamics and histone modification (nucleosome mobilization, histone exchange/acetylation, heterochromatin boundary formation) and meiotic/cell-cycle processes (male meiosis I, G2/M transition). This suggests proteins functioning together to remodel chromatin during meiosis and cell-cycle progression, despite some obsolete GO terms.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070940","count":2},{"id":"GO:0001207","count":1},{"id":"GO:1900051","count":1},{"id":"GO:0002574","count":1},{"id":"GO:0010971","count":1}]},{"hash":"663571151444910310","title":"Neural development and dopaminergic signaling","description":"The top GO terms are dominated by nervous system development (GO:0007399), dopaminergic synaptic transmission (GO:0001963), neural tube patterning (GO:1904637), and glial cell survival regulation, all pointing to neural development and neurotransmission. Additional terms about endosome transport and MAPK signaling reflect broader cellular signaling/trafficking themes that support neuronal signaling. While a few terms are less directly related (e.g., pseudohyphal growth), the prevailing pattern emphasizes neural development and dopaminergic signaling.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071374","count":14},{"id":"GO:0007124","count":14},{"id":"GO:2000641","count":14},{"id":"GO:0000187","count":14},{"id":"GO:0007094","count":14}]},{"hash":"96096011157419497","title":"Reproductive Development and Growth Signaling","description":"The top terms include placenta development and sperm capacitation, both reproductive processes, along with DNA replication and cell size regulation, suggesting a growth/ cell-cycle\u2013related theme within reproductive contexts. Metabolic signaling (response to glucose) and proteasomal regulation also align with coordinated growth and signaling in these tissues.","confidence":"Medium","size":15,"edges":50,"triangles":119,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0045793","count":4},{"id":"GO:0001890","count":4},{"id":"GO:0071333","count":4},{"id":"GO:0032435","count":4}]},{"hash":"1305502108506502856","title":"RNA processing and post-transcriptional regulation","description":"Most top GO terms point to mRNA handling (export, splicing regulation, stability, modification) and related post-transcriptional control, suggesting a core theme around RNA metabolism. A few terms reference mitosis or cytoskeletal processes, which are less representative of the cluster\u2019s main signal. Thus, the label captures the dominant RNA-focused function for this cluster.","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":2},{"id":"GO:0070676","count":2},{"id":"GO:0051013","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0046360","count":1}]},{"hash":"896452908342398569","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0050830","count":2},{"id":"GO:0000447","count":2}]},{"hash":"1235812322066903929","title":"Telomere-Chromatin Maintenance","description":"The terms cluster around telomere biology and chromatin organization (telomeric D-loop disassembly, nucleosome assembly, G-quadruplex DNA, snRNA transcription, and protein localization to telomeres), suggesting a nuclear/chromatin maintenance role. Some terms are obsolete or less cohesive (e.g., cytokinin signaling), but the dominant theme is telomere- and chromatin-related processes.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0061820","count":3},{"id":"GO:0009736","count":3},{"id":"GO:1901347","count":3},{"id":"GO:0072362","count":3},{"id":"GO:0006334","count":3}]},{"hash":"2040950774147426712","title":"Unknown","description":"The top GO terms are heterogeneous: innate immune response, regulation of Rho protein signal transduction, blood vessel development, asymmetric neuroblast division, cytokinin-activated signaling pathway, mitotic cell cycle, negative regulation of chlorophyll biosynthetic process, obsolete GO terms, and male sex differentiation. The mix indicates no single cohesive function linking the proteins, and several terms are plant- or obsolete-specific, so a clear label is not supported.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0001568","count":2},{"id":"GO:0055059","count":1},{"id":"GO:0009736","count":1}]},{"hash":"1263518989402829774","title":"Nociception and Thermoception with Transcriptional Regulation","description":"The cluster shows two intertwined themes: core transcriptional machinery (mRNA processing and DNA-templated transcription) and nociceptive/thermoceptive signaling (pain perception, thermoception, and detection of chemical/mechanical stimuli), along with inflammatory mediator regulation and vasopressin secretion. This suggests proteins that participate in neuronal gene expression control that modulates pain and temperature sensing, possibly linking neural signaling to immune/hormonal responses. Confidence: Medium","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006397","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0071642","count":3},{"id":"GO:1901594","count":3},{"id":"GO:0071651","count":3}]},{"hash":"1983399402393373777","title":"Ciliary and flagellar axoneme assembly and motility","description":"The cluster is dominated by GO terms related to cilium and flagellum function\u2014cilium movement, axoneme assembly, sperm flagellum motility, and microtubule-based modifications such as polyglycylation and polyglutamylation\u2014indicating proteins involved in axoneme structure and movement. A few terms on mitotic spindle elongation reflect shared microtubule machinery but the overall theme centers on ciliary/flagellar motility.","confidence":"High","size":15,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0003353","count":1},{"id":"GO:0030516","count":1},{"id":"GO:0018094","count":1},{"id":"GO:0018095","count":1},{"id":"GO:0007288","count":1}]},{"hash":"2226974538972064641","title":"Cardiac Ion Transport and Membrane Potential","description":"This cluster is dominated by GO terms for sodium and potassium ion transport, intracellular potassium homeostasis, and regulation of membrane potential, pointing to ion transport and excitability in cardiac or other excitable cells. Additional terms related to cardiac muscle proliferation and signaling modulation (adenylate cyclase, Ras) fit the broader signaling environment of such cells, though they are less central. Overall, the common theme is ion transport linking to membrane potential in cardiac/excitable tissues.","confidence":"High","size":15,"edges":5,"triangles":0,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0098719","count":7},{"id":"GO:0071805","count":7},{"id":"GO:0030007","count":7},{"id":"GO:0042391","count":6},{"id":"GO:0034465","count":6}]},{"hash":"1073865393365640472","title":"Unknown","description":"The top GO terms span epithelial polarity, apoptosis in different cell types, transcription, inflammatory mediator production, and even cardiac signaling, with no clear unifying pathway. The diversity suggests multiple, unrelated roles for these proteins rather than a single cohesive function, so a specific functional label cannot be confidently assigned.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090162","count":2},{"id":"GO:2000171","count":2},{"id":"GO:0033028","count":2},{"id":"GO:0097284","count":2},{"id":"GO:0006351","count":2}]},{"hash":"282557435853807822","title":"Unknown","description":"The terms suggest mixed plant hormone signaling and chloroplast-related processes, but many items are obsolete and there is no single shared function across all proteins. As a result, there is no clear theme to label, so Unknown is the safest choice.","confidence":"","size":15,"edges":12,"triangles":1,"max_degree":10,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0009736","count":9},{"id":"GO:1902325","count":9},{"id":"GO:1903071","count":9},{"id":"GO:0046661","count":9},{"id":"GO:0051348","count":9}]},{"hash":"1527485986178907093","title":"Drosophila oogenesis and Wnt secretion","description":"The top GO terms cluster around maternal specification of the dorsal/ventral axis in oocytes and regulation of egg-laying, plus positive regulation of Wnt protein secretion and ER-Golgi trafficking steps (ER to Golgi transport and exit from ER). This points to proteins involved in Drosophila oogenesis and the secretory pathway affecting maternal-effect signaling. A few other terms (miRNA silencing and nucleotide salvage) are less connected to this theme and may reflect broader cellular housekeeping; however, the dominant pattern supports a maternal-development and secretion-focused cluster.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035278","count":2},{"id":"GO:0044206","count":1},{"id":"GO:0006223","count":1},{"id":"GO:0044211","count":1},{"id":"GO:0048042","count":1}]},{"hash":"351965338363362219","title":"Craniofacial neural crest and eye development","description":"The top GO terms cluster around neural crest development, face and forebrain formation, and embryonic eye structures (e.g., facial development, olfactory pit, embryonic camera-type eye development) with involvement of retinoic acid signaling. This points to a cohesive developmental module governing craniofacial patterning and early eye/olfactory structure formation, despite a few unrelated catabolic terms.","confidence":"High","size":15,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0019545","count":1},{"id":"GO:0048384","count":1},{"id":"GO:0014032","count":1},{"id":"GO:0060324","count":1},{"id":"GO:0030900","count":1}]},{"hash":"1536178414556915634","title":"Dopaminergic Synaptic Signaling","description":"The top GO terms cluster around nervous system development, dopamine-responsive cellular processes, excitatory synaptic activity (excitatory postsynaptic potentials), and components involved in synapse assembly; together these point to proteins functioning in neuronal signaling with emphasis on dopamine-related modulation of synaptic transmission and synapse organization.","confidence":"Medium","size":15,"edges":14,"triangles":1,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1903206","count":6},{"id":"GO:1903215","count":4},{"id":"GO:0007399","count":4},{"id":"GO:1902499","count":4},{"id":"GO:1903351","count":4}]},{"hash":"1745245365089640865","title":"Telomere Chromatin Regulation","description":"The cluster features several telomere- and DNA structure\u2013related terms (telomeric D-loop disassembly, G-quadruplex DNA formation, and regulation of protein localization to telomere) along with chromatin-related processes (nucleosome assembly, histone H2A deubiquitination) and transcriptional activity (snRNA transcription), pointing to a theme of telomere maintenance intertwined with chromatin state and DNA topology. Some unrelated terms (plant cytokinin signaling, cell wall biogenesis, osmotic stress) are present but do not negate the core telomere/chromatin focus.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0061820","count":5},{"id":"GO:0009736","count":5},{"id":"GO:1901347","count":5},{"id":"GO:0072362","count":5},{"id":"GO:0006334","count":5}]},{"hash":"1012783172134542067","title":"Storage polysaccharide metabolism","description":"The top GO terms cluster around both biosynthesis and catabolism of storage carbohydrates (glycogen, starch/amylopectin, alpha-glucan) and related disaccharides (maltose, trehalose), indicating a cohesive theme of storage polysaccharide metabolism rather than a single specific pathway.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000023","count":1},{"id":"GO:0005978","count":1},{"id":"GO:0030980","count":1},{"id":"GO:0005993","count":1},{"id":"GO:0051692","count":1}]},{"hash":"1905816747005559125","title":"Neuronal endosomal trafficking and receptor recycling","description":"Top GO terms indicate a focus on endosome dynamics and membrane protein processing (receptor recycling, endosome size regulation, membrane ectodomain proteolysis) alongside glutamatergic synaptic transmission, which together suggest roles in neuronal receptor turnover and vesicle trafficking. Some terms appear less directly related or marked obsolete, implying annotation noise or multi-functional proteins, but the core signal points to endosome-mediated regulation of synaptic membrane proteins. Medium","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002003","count":2},{"id":"GO:0006509","count":2},{"id":"GO:0034968","count":2},{"id":"GO:0001881","count":2},{"id":"GO:0006355","count":2}]},{"hash":"1782294615211879765","title":"Unknown","description":"The Top Terms include immune activation (complement activation, T cell activation), cell adhesion, neural and developmental processes, plant chlorophyll biosynthesis, vacuole fusion, and skin gland development, which span disparate biological contexts with no clear shared function. This makes it unlikely there is a single coherent biological role for the cluster. ","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070208","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0042144","count":1},{"id":"GO:0048733","count":1},{"id":"GO:0018230","count":1}]},{"hash":"1811469046330832247","title":"Nuclear gene expression and chromatin regulation","description":"The top GO terms cluster around DNA-templated transcription, mRNA splicing and export, histone methylation, and centromeric chromatin assembly (CENP-A), indicating proteins are mainly involved in regulating gene expression at the chromatin and RNA processing levels. While a few terms touch on microtubule movement or development, the core theme is transcriptional control and chromatin remodeling.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0021510","count":3},{"id":"GO:0051568","count":3},{"id":"GO:0034729","count":3},{"id":"GO:0007018","count":3}]},{"hash":"1425967616554466340","title":"Diverse Aromatic and Lipid Metabolism with Antibiotic Biosynthesis","description":"The top GO terms cluster around metabolic transformations across aromatics (beta-ketoadipate, stilbene degradation), lipids (triglyceride/monoacylglycerol catabolism, phospholipid dephosphorylation), and related oxidation (P450 epoxygenase), with antibiotic biosynthesis as an additional metabolic pathway. This suggests a broad metabolic cluster focused on catabolic and xenobiotic transformation rather than a single specific function, justifying a broad metabolic label.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0017000","count":9},{"id":"GO:0042952","count":8},{"id":"GO:0046272","count":8},{"id":"GO:0055114","count":8},{"id":"GO:0019373","count":8}]},{"hash":"2002297744469116773","title":"Unknown","description":"The GO terms are scattered across immune chemokine production, drug response, ion transport, thermogenesis, apoptotic signaling, and unrelated brain/vascular development processes, with no clear unifying function. The lack of edges and cohesive theme supports labeling this cluster as Unknown.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071642","count":1},{"id":"GO:1901594","count":1},{"id":"GO:0098719","count":1},{"id":"GO:0071651","count":1},{"id":"GO:0002024","count":1}]},{"hash":"626035433602970760","title":"Mitotic Cell Cycle Regulation","description":"The cluster\u2019s top GO terms predominantly describe cell division and mitotic control (cell division; mitotic cell cycle; regulation of metaphase/anaphase transition; APC-dependent catabolic process) and ubiquitin signaling (K11-linked ubiquitination), indicating proteins involved in mitotic progression and targeted degradation during mitosis. Outliers include viral RNA genome replication and autophagy-related terms and translation-related terms, but the core theme centers on mitotic regulation and proteolysis. ","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0039694","count":2},{"id":"GO:0048481","count":1},{"id":"GO:0030071","count":1}]},{"hash":"1928397577227713665","title":"DNA Repair and Developmental Processes","description":"This cluster is characterized by terms related to DNA damage response and homologous recombination (double-strand break repair via HR and replication fork processing) alongside several developmental and germline-related terms (brain development, oocyte maturation, gonad development, meiosis, inner cell mass proliferation, hemopoiesis). The strongest shared signal appears to be DNA repair roles that also contribute to development and reproduction, suggesting these proteins participate in genome maintenance with developmental/germline functions.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000724","count":2},{"id":"GO:0007420","count":2},{"id":"GO:1990426","count":1},{"id":"GO:0033600","count":1},{"id":"GO:0001556","count":1}]},{"hash":"795628729609502491","title":"Cell-cycle and transcription regulation","description":"This cluster is enriched for cell division (GO:0051301) and DNA-templated transcription (GO:0006351), plus related processes like mitotic spindle regulation and protein oligomerization, suggesting roles in cell-cycle control and gene expression. A few tissue-specific terms (mammary gland development/proliferation) appear as noise, but the dominant theme links proliferation with transcriptional regulation.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0019086","count":1},{"id":"GO:0060749","count":1}]},{"hash":"1952040174009690447","title":"Deubiquitinases in DNA damage repair","description":"The top GO terms cluster around protein deubiquitination linked to specific ubiquitin linkages (K48, K63, K11) and DNA repair, including regulation of histone H2A ubiquitination and double-strand break repair. This points to a theme of DUBs modulating chromatin and DNA damage response; peripheral terms about immune signaling or plant development likely reflect unrelated or broad annotations.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071108","count":1},{"id":"GO:0006281","count":1},{"id":"GO:1901315","count":1},{"id":"GO:0071347","count":1},{"id":"GO:0002250","count":1}]},{"hash":"1521742705992118700","title":"Unknown","description":"The proteins span diverse functions (chromatin remodeling and transcription regulation; receptor recycling and endosome size regulation; synaptic transmission; calcium-channel regulation; Rho signaling; telomere disassembly; plant cytokinin signaling), with no clear, single overarching theme. This heterogeneity makes it hard to assign a cohesive, high-level label beyond Unknown.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":2},{"id":"GO:0035249","count":2},{"id":"GO:0001881","count":2},{"id":"GO:0051036","count":2},{"id":"GO:0060316","count":2}]},{"hash":"1599013541133072074","title":"Ribosome Biogenesis and Cytoplasmic Translation","description":"Reasoning: The dominant GO terms are ribosome biogenesis, cytoplasmic translation, and cell cycle, which together point to the protein synthesis machinery and ribosome assembly as the core function of the cluster. These terms have the highest counts (2 each), making them the most representative theme. The other terms appear only once and seem incidental rather than defining the cluster. ","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0099132","count":1},{"id":"GO:0042777","count":1}]},{"hash":"2025652028183816660","title":"Unknown","description":"The top GO terms are scattered across distinct biological areas: plant hormone signaling (cytokinin-activated signaling pathway) and chloroplast-related processes (negative regulation of chlorophyll biosynthetic process) alongside terms like cellular response to interferon-alpha and male sex differentiation, with several obsolete annotations. The lack of a cohesive, single function linking these proteins makes it unclear what unifies the cluster, so I label it Unknown.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0009736","count":6},{"id":"GO:0000278","count":5},{"id":"GO:1902325","count":5},{"id":"GO:1903071","count":5},{"id":"GO:2001162","count":5}]},{"hash":"661776334666286404","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0000462","count":1},{"id":"GO:0042255","count":1},{"id":"GO:0000480","count":1},{"id":"GO:0000461","count":1}]},{"hash":"1321109842690814607","title":"Actin-based membrane remodeling and endomembrane trafficking","description":"GO terms cluster around actin-based protrusions (filopodium, microspike), endomembrane organization (Golgi), and membrane trafficking (pinocytosis), with PI signaling involvement. A TGF-beta signaling term appears but is not core. Overall, the cluster reflects cytoskeleton-driven membrane remodeling and vesicular trafficking processes.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007183","count":1},{"id":"GO:0010256","count":1},{"id":"GO:1904562","count":1},{"id":"GO:0030035","count":1},{"id":"GO:0007179","count":1}]},{"hash":"2014688754041584564","title":"Mitotic spindle assembly and centrosome dynamics","description":"These terms cluster around microtubule organizing centers, spindle assembly during mitosis (and meiosis), centrosome duplication, and microtubule nucleation, plus polarity cues. Together they point to a core function in spindle formation and centrosome dynamics.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045450","count":1},{"id":"GO:0030472","count":1},{"id":"GO:0071963","count":1},{"id":"GO:0090307","count":1},{"id":"GO:0051298","count":1}]},{"hash":"1590662627807318960","title":"Chromatin Regulation and Redox Homeostasis","description":"The GO terms cluster around nuclear functions (DNA-templated transcription, chromatin binding) with indications of chromatin regulation, plus redox-related processes (oxidation-reduction, cellular oxidant detoxification, NAD+ biosynthesis). Although several terms are obsolete, the recurring theme is proteins involved in controlling chromatin states and transcription in the context of cellular redox balance, which points to a cohesive chromatin-regulatory/redox biology cluster rather than distinct unrelated processes.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0016575","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0007369","count":2},{"id":"GO:0008283","count":2}]},{"hash":"380292475163246357","title":"Mitochondrial transport and energy metabolism","description":"The terms cluster around transport across mitochondrial membranes (NAD, deoxynucleotides, thiosulfate) and regulation of mitochondrial permeability, plus energy-related processes (adaptive thermogenesis, liver regeneration). This points to a group of proteins involved in mitochondrial transport and energy homeostasis, with some stress-response connections. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097421","count":4},{"id":"GO:1990845","count":4},{"id":"GO:0060546","count":4},{"id":"GO:0097274","count":4},{"id":"GO:0070542","count":4}]},{"hash":"759229980105008500","title":"cAMP Signaling and Antipsychotic Drug Response","description":"The top GO terms point to cAMP-related signaling (cellular response to cAMP; regulation of PKA activity) and responses to antipsychotic drugs (including clozapine), suggesting the proteins collectively modulate cAMP pathways and pharmacologic drug response. While membrane potential and sodium transport terms appear, the strongest common theme is cAMP-mediated signaling linked to antipsychotic responses.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034638","count":3},{"id":"GO:2000480","count":2},{"id":"GO:0098719","count":2},{"id":"GO:0071320","count":2},{"id":"GO:0097332","count":2}]},{"hash":"24186621639480987","title":"Olfactory GPCR-cAMP Signaling","description":"This cluster is dominated by GO terms for sensory perception of smell, cellular response to cAMP, and regulation of membrane potential, all hallmark features of olfactory receptor signaling via GPCRs that use cAMP as second messenger to drive sodium influx. The presence of terms about responses to clozapine/antipsychotic drugs suggests broader neuronal signaling contexts, but the common thread remains GPCR-mediated cAMP signaling in sensory/neuronal functions.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:2000480","count":3},{"id":"GO:0098719","count":3},{"id":"GO:0071320","count":3},{"id":"GO:0097332","count":3},{"id":"GO:0046827","count":3}]},{"hash":"1240347802069889898","title":"Telomere and chromatin regulation","description":"The listed GO terms cluster around nuclear DNA maintenance and chromatin organization, highlighted by telomere-related processes (telomeric D-loop disassembly, protein localization to telomere, G-quadruplex DNA formation), nucleosome assembly, and histone deubiquitination. While some plant-specific terms appear (cytokinin signaling, secondary cell wall biogenesis), the core signal points to telomere biology and chromatin regulation in the nucleus, rather than a clearly defined cytoplasmic or metabolic pathway.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061820","count":1},{"id":"GO:0009736","count":1},{"id":"GO:1901347","count":1},{"id":"GO:0072362","count":1},{"id":"GO:0006334","count":1}]},{"hash":"720750467347062287","title":"Kinase signaling and cytoskeletal remodeling","description":"Several top GO terms center on protein autophosphorylation and its regulation, plus responses to growth factors (brain-derived neurotrophic factor, prolactin) and calcium-dependent adhesion, suggesting signaling pathways that regulate the cytoskeleton. Terms like myosin II filament disassembly and protein tetramerization reinforce a theme of dynamic cytoskeletal organization and protein complex assembly; peripheral terms such as magnesium ion homeostasis may relate to ATP-dependent kinase activity. Overall, this cluster seems to group proteins involved in phosphorylation-driven signaling interfacing with cytoskeletal remodeling.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046777","count":3},{"id":"GO:0018298","count":2},{"id":"GO:1990416","count":2},{"id":"GO:0010961","count":2},{"id":"GO:0031952","count":2}]},{"hash":"2089378200282570619","title":"Male germline meiosis and spermatogenesis","description":"The GO terms strongly point to male germ cell development and meiotic processes, including male germ-line cyst formation, male meiosis chromosome segregation, spermatocyte division, and male meiosis cytokinesis, along with stem cell population maintenance. A few unrelated terms (viral process, behavioral fear response) appear but do not define the cluster\u2019s main function. Overall, the proteins are best described as involved in spermatogenesis and germline stem cell maintenance.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048136","count":1},{"id":"GO:0007060","count":1},{"id":"GO:0000082","count":1},{"id":"GO:0016032","count":1},{"id":"GO:0048137","count":1}]},{"hash":"1424968069831954638","title":"Telomere maintenance and spindle assembly","description":"This cluster is dominated by terms tied to chromosome/telomere dynamics (localization to telomeres, telomere maintenance, telomerase regulation) and mitotic spindle assembly, with PARP-related ADP-ribosylation activities suggesting chromatin/DNA repair regulation. The convergence of telomere maintenance and spindle assembly points to a nuclear, mitotic chromatin regulatory function rather than cytoskeletal or signaling roles, despite a few unrelated GO terms that may reflect annotation noise.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051225","count":2},{"id":"GO:0070213","count":2},{"id":"GO:0070198","count":2},{"id":"GO:0007205","count":2},{"id":"GO:1904743","count":2}]},{"hash":"51039655298095061","title":"Muscle and Nervous System Development","description":"The strongest signals are skeletal muscle fiber development and skeletal muscle tissue development, with nervous system development and germinal center formation also pointing to developmental processes. The presence of several non-developmental terms (glucosinolate catabolic process, wybutosine biosynthetic process, spindle localization, ubiquitin-dependent proteolysis, swimming) suggests the cluster is heterogeneous but centered on development.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048741","count":3},{"id":"GO:0007399","count":2},{"id":"GO:0007519","count":2},{"id":"GO:0019762","count":2},{"id":"GO:0031591","count":2}]},{"hash":"1942833995875508112","title":"DNA Damage Response and Chromatin Regulation","description":"This cluster centers on genome integrity and chromatin dynamics, with GO terms spanning necroptotic signaling, regulation of kinetochore assembly, chromatin binding regulation, protein desumoylation/deneddylation, and translesion DNA synthesis. Some terms also reference developmental contexts (placental layers, erythrocyte differentiation), which may reflect broader regulatory roles or annotation noise. Overall, the proteins appear to function as regulators of DNA damage response and chromatin state rather than a single cohesive pathway.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070266","count":2},{"id":"GO:0090234","count":1},{"id":"GO:0060711","count":1},{"id":"GO:0016926","count":1},{"id":"GO:1904333","count":1}]},{"hash":"1132312250099697258","title":"Neural development and chromatin regulation","description":"This cluster is enriched for brain development terms (midbrain-hindbrain boundary morphogenesis, third ventricle development) and stem cell differentiation, along with chromatin-related processes (RITS complex localization, histone demethylation). The combination suggests proteins involved in neural development coordinated with epigenetic regulation of gene expression, despite some obsolete GO terms that may reflect annotation history. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":2},{"id":"GO:0021555","count":1},{"id":"GO:0033169","count":1},{"id":"GO:0034630","count":1},{"id":"GO:0060763","count":1}]},{"hash":"1152418198208380447","title":"Insect morphogenesis and ciliogenesis","description":"This cluster is enriched for morphogenesis-related GO terms tied to insect development (face morphogenesis, imaginal disc-derived wing morphogenesis, chaeta morphogenesis) and ciliary biology (intraciliary transport involved in cilium assembly). The presence of spindle orientation and transcription regulation terms suggests roles in cell polarity and gene control during development. Although a few terms are generic (translation, oxidative stress), the strongest signal ties to morphogenesis and ciliogenesis in insects, supporting a label centered on developmental morphology with ciliary processes.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000132","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0090116","count":1},{"id":"GO:0060325","count":1},{"id":"GO:0034599","count":1}]},{"hash":"941579790346195614","title":"Unknown","description":"The GO terms are highly diverse, including immune defense, neural processes, RNA biology, circadian regulation, and development, with no clear shared function linking these proteins (no edges), so there is no coherent theme to name the cluster.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050830","count":2},{"id":"GO:0090328","count":1},{"id":"GO:0002091","count":1},{"id":"GO:0033962","count":1},{"id":"GO:0051823","count":1}]},{"hash":"327230911062813528","title":"Microtubule Cytoskeleton and Neuronal Transport","description":"The top GO terms are dominated by microtubule-related processes (depolymerization, spindle-kinetochore dynamics, cytoskeleton polarity) and neuronal transport/maintenance (anterograde dendritic transport, neuron projection maintenance, Purkinje cell layer organization), suggesting a cohesive theme of microtubule-based cytoskeleton organization and transport in neurons. Some terms touch signaling or growth regulation, which can influence cytoskeletal remodeling, but the core signal is microtubule dynamics and transport.","confidence":"Medium","size":14,"edges":84,"triangles":296,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0010938","count":14},{"id":"GO:0000743","count":14},{"id":"GO:0001560","count":14},{"id":"GO:0032487","count":14},{"id":"GO:0098971","count":14}]},{"hash":"984395207391839033","title":"Ribosome Biogenesis and Translation","description":"The top GO terms cluster around protein synthesis and ribosome assembly: translation, ribosome biogenesis, maturation of SSU-rRNA, and small subunit biogenesis. While there are also proliferation-related terms (DNA replication, G1/S transition) and developmental terms (placenta development, gastrulation), the core signal centers on ribosome assembly and the protein synthesis machinery.","confidence":"High","size":14,"edges":77,"triangles":256,"max_degree":12,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0000082","count":5},{"id":"GO:0001890","count":5},{"id":"GO:0043065","count":5},{"id":"GO:0042254","count":5}]},{"hash":"1644798188760308682","title":"Neural development and signaling","description":"The strongest terms center on cerebellar neural development\u2014Bergmann glial differentiation and cerebellar cortex formation\u2014suggesting a neural-development-focused cluster. Additional terms reflect broad signaling (insulin and T cell receptor pathways) and related processes like endosome transport and cell-cycle regulation, implying a group of proteins involved in signaling linked to neural development rather than a single, narrow pathway.","confidence":"Medium","size":14,"edges":90,"triangles":352,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008286","count":14},{"id":"GO:0060020","count":14},{"id":"GO:0021697","count":14},{"id":"GO:0034501","count":14},{"id":"GO:0045736","count":14}]},{"hash":"1124078163473895220","title":"Fatty acid oxidation and starvation response","description":"The top GO terms cluster around lipid catabolism and energy production: fatty acid beta-oxidation, acetyl-CoA catabolic process, and ketone body metabolism/biosynthesis; glyoxysome organization points to peroxisomal fatty acid processing. Also present is a response to starvation and regulation of mitochondrial membrane permeability in apoptosis, indicating a coordinated metabolic response and cellular protection under nutrient stress. This supports a module focused on fatty acid degradation and energy management during starvation.","confidence":"Medium","size":14,"edges":90,"triangles":352,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006635","count":7},{"id":"GO:0046951","count":4},{"id":"GO:0010111","count":4},{"id":"GO:0046356","count":4},{"id":"GO:0014070","count":4}]},{"hash":"1600487263619173821","title":"Lipid and Vitamin Metabolism","description":"This cluster is driven by lipid-related metabolism: fatty acid biosynthesis and transport, retinol (vitamin A) metabolism, bile acid metabolism, and menaquinone biosynthesis, suggesting a cohesive theme around lipid and vitamin-derived metabolite pathways. Some terms like seed coat development or other catabolic processes are ancillary but do not dilute the primary lipid/metabolite signal.","confidence":"Medium","size":14,"edges":36,"triangles":45,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0010124","count":5},{"id":"GO:0006633","count":5},{"id":"GO:0042572","count":4},{"id":"GO:1902987","count":4},{"id":"GO:0043041","count":4}]},{"hash":"662547725895440215","title":"DNA replication and SOS response","description":"Based on the dominant GO terms, the cluster centers on genome maintenance activities: DNA replication, DNA recombination, transcription regulation related to DNA-templated processes, and the SOS DNA damage response. The viral genome replication term supports a replication-focused theme, while a dendrite morphogenesis term appears as an outlier rather than a unifying function. Overall, a replication/repair-oriented cluster is most representative.","confidence":"High","size":14,"edges":57,"triangles":86,"max_degree":12,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0019079","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0009432","count":4},{"id":"GO:0006310","count":4},{"id":"GO:0045892","count":4}]},{"hash":"1333003913663937522","title":"Neural development and sensory perception","description":"The cluster is dominated by neural-focused GO terms such as axonogenesis, excitatory postsynaptic potential, Schwann cell development, and visual perception, indicating problems related to nervous system development and sensory function. The presence of mitotic cell cycle and G2/M transition terms suggests proliferative neural progenitors, while heart development appears as a broader developmental context; one plant hormone pathway term likely reflects annotation noise rather than a shared function. Overall, the core theme is neural development and sensory maturation.","confidence":"High","size":14,"edges":11,"triangles":2,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060079","count":12},{"id":"GO:0000278","count":12},{"id":"GO:0097011","count":12},{"id":"GO:0006351","count":12},{"id":"GO:0000086","count":11}]},{"hash":"663808412565678123","title":"Developmental signaling and RNA transport","description":"The proteins in this cluster are enriched for various developmental processes (skeletal muscle, skin, blastocyst, substantia nigra development) and for signaling regulation (protein kinase activity, GTPase regulation, autophosphorylation), with mRNA transport also represented. This pattern suggests a theme of development-associated signaling and RNA trafficking, though the diverse GO terms indicate broader regulatory roles. ","confidence":"Medium","size":14,"edges":5,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0048741","count":5},{"id":"GO:0021762","count":5},{"id":"GO:0071456","count":4},{"id":"GO:0051028","count":4},{"id":"GO:0071902","count":4}]},{"hash":"1532020170580878805","title":"Neuronal development and signaling","description":"This cluster is enriched for neural-focused processes, including CNS projection neuron axonogenesis and dopaminergic synaptic transmission, plus regulation of neural patterning. While several terms reflect broader cellular trafficking or signaling (endosome transport, nuclear export, p53 signaling, immune differentiation, pseudohyphal growth), the neural development/signaling theme is the strongest connection, giving a moderate level of confidence.","confidence":"Medium","size":14,"edges":34,"triangles":40,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046827","count":12},{"id":"GO:2000641","count":11},{"id":"GO:0007124","count":11},{"id":"GO:1901621","count":11},{"id":"GO:1904637","count":11}]},{"hash":"113326336672407576","title":"mRNA Splicing and Post-Transcriptional Regulation","description":"The GO terms are dominated by spliceosome-mediated mRNA processing (cis splicing, polyadenylation, snoRNA splicing) and regulatory ncRNA\u2013mediated gene silencing, plus controls on translation, pointing to a cohesive post-transcriptional regulatory function. A few terms hint at signaling or immune context, but the core theme remains RNA processing and splicing.","confidence":"High","size":14,"edges":16,"triangles":3,"max_degree":13,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":7},{"id":"GO:0006378","count":7},{"id":"GO:0031047","count":4},{"id":"GO:0048026","count":4},{"id":"GO:2000766","count":4}]},{"hash":"784417995957376224","title":"Protein Targeting and Folding Under Stress","description":"This cluster is dominated by terms related to targeting nascent proteins to membranes (SRP- and post-translational targeting) and responses to unfolded proteins or heat, i.e., protein maturation and quality control under stress. While there are a few outliers (DNA replication, iron-sulfur cluster assembly, and karyogamy), the shared theme centers on protein targeting and stress-related folding/quality control.","confidence":"Medium","size":14,"edges":46,"triangles":66,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0016925","count":3},{"id":"GO:0090084","count":2},{"id":"GO:0016226","count":2},{"id":"GO:0034620","count":2}]},{"hash":"1717911433615321453","title":"Mitotic cycle regulation and APC/C proteolysis","description":"This cluster is anchored by strong mitosis-related terms: mitotic cell cycle, cell division, and an APC/C-dependent catabolic process, suggesting coordinated control of chromosome segregation and proteolysis during mitosis. While there are additional signals (DNA-templated transcription, ribosomal rRNA maturation, and signaling regulators) that are more general or developmental, the core theme centers on mitotic progression and regulated protein turnover via the APC/C. Confidence: Medium","confidence":"","size":14,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0071276","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0031145","count":4},{"id":"GO:0051301","count":4}]},{"hash":"365397680537193394","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:0031047","count":4},{"id":"GO:0048026","count":4},{"id":"GO:0000398","count":3},{"id":"GO:0006283","count":3},{"id":"GO:0071031","count":3}]},{"hash":"570130051645103342","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0000209","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0019079","count":2},{"id":"GO:0006260","count":2}]},{"hash":"2138653618952319851","title":"Ubiquitin-dependent proteolysis and signaling regulation","description":"This cluster centers on ubiquitin-mediated protein degradation (ERAD, autoubiquitination, general proteolysis) and its influence on signaling pathways (Wnt receptor turnover, JNK cascade, TNF signaling) as well as growth regulation. The inclusion of histone turnover and negative growth regulation supports a theme of ubiquitin-driven control of proteostasis and signaling, tying the proteins together.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0030433","count":11},{"id":"GO:0046621","count":8},{"id":"GO:0033151","count":8},{"id":"GO:0038018","count":8},{"id":"GO:0051865","count":8}]},{"hash":"436929748998340355","title":"Neural development and signaling","description":"The cluster is dominated by neural-related terms: CNS projection neuron axonogenesis, dopaminergic synaptic transmission, and neural tube patterning, with other terms touching signaling regulation (p53 mediator signaling, hedgehog pathway-related) and receptor trafficking (endosome transport). This suggests a cohesive theme around neural development and neuronal signaling, with endosomal transport supporting signaling dynamics. Some non-neural terms may reflect broader developmental processes or annotation noise, but the neural theme is the strongest signal.","confidence":"Medium","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":14},{"id":"GO:0007124","count":14},{"id":"GO:1901621","count":14},{"id":"GO:1904637","count":14},{"id":"GO:0001963","count":14}]},{"hash":"435804158066806270","title":"Embryonic Neural and Skeletal Development","description":"The top GO terms are dominated by developmental processes: neural tube closure, forebrain development, skeletal system development, and multicellular organism development, supported by general transcription and cell cycle activity (DNA-templated transcription and mitotic cell cycle). While there are ancillary stress and immune responses (cadmium response, defense against Gram-positive bacteria), the strongest signal points to embryonic/neuronal and skeletal developmental programs acting together, with common regulatory activity. ","confidence":"Medium","size":14,"edges":63,"triangles":144,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001843","count":14},{"id":"GO:0071276","count":14},{"id":"GO:0001501","count":14},{"id":"GO:0007275","count":14},{"id":"GO:0050830","count":14}]},{"hash":"235616615832103146","title":"Neural development and signaling","description":"Based on the enriched GO terms, the cluster is driven by neural development and neuronal signaling processes, including axonogenesis of CNS neurons, dopaminergic synaptic transmission, and neural tube patterning regulation, with endosome transport highlighting signaling receptor trafficking. While there are outliers related to other tissues (immune, cartilage, fungal growth), the dominant signal centers on neural development and communication.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":14},{"id":"GO:0007124","count":14},{"id":"GO:1901621","count":14},{"id":"GO:1904637","count":14},{"id":"GO:0001963","count":14}]},{"hash":"1963405020803599466","title":"Spliceosome-Driven mRNA Processing and Translation Control","description":"The cluster is dominated by GO terms for mRNA splicing via the spliceosome (including positive/negative regulation and cis splicing) and processes related to translation initiation/reinitiation, along with miRNA-mediated silencing and stress-related mRNA stability regulation, suggesting a cohesive module linking mRNA maturation to translation control.","confidence":"High","size":14,"edges":44,"triangles":60,"max_degree":13,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000398","count":5},{"id":"GO:0010610","count":5},{"id":"GO:0031047","count":4},{"id":"GO:0048026","count":4},{"id":"GO:0045292","count":4}]},{"hash":"839658014276764200","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":32,"triangles":22,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0000466","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0007064","count":2}]},{"hash":"1580716963135467314","title":"Cytoskeleton-driven migration, division, and trafficking","description":"The top GO terms repeatedly point to actin- and microtubule-dependent processes: ameboidal cell migration, cell spreading, spindle/kinetochore dynamics, and cleavage furrow ingression, all reflecting cytoskeletal remodeling during movement and division. Also present are vesicle trafficking and signaling events\u2014phagosome maturation, T cell degranulation, and Wnt signalosome assembly\u2014that depend on cytoskeletal dynamics and membrane trafficking. A couple terms (copper homeostasis, oligodendrocyte differentiation) are broader context but do not contradict the main theme. Overall, the cluster centers on cytoskeleton-driven movement, division, and trafficking.","confidence":"Medium","size":14,"edges":51,"triangles":69,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1903215","count":14},{"id":"GO:0001667","count":14},{"id":"GO:0006878","count":14},{"id":"GO:0043316","count":14},{"id":"GO:1900026","count":14}]},{"hash":"223036219150198907","title":"Germline Stem Cell Maintenance and Meiosis","description":"This cluster centers on germline biology, with terms for female germ-line stem cell population maintenance and meiosis I, plus stem cell differentiation. Supporting signals include ubiquitin-dependent protein catabolic processes and transcription regulation, which are key in developmental control and proteostasis during germline development. The presence of translation initiation factor complex assembly also suggests coordinated translational control in these contexts, reinforcing a germline development/meiosis-focused theme.","confidence":"Medium","size":14,"edges":70,"triangles":186,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0032436","count":5},{"id":"GO:0000122","count":4},{"id":"GO:0007127","count":3},{"id":"GO:0048863","count":3},{"id":"GO:0006511","count":3}]},{"hash":"1279417547717395520","title":"Meiosis chromosome condensation and synaptonemal complex assembly","description":"The top terms are strongly centered on meiotic processes: chromosome condensation, synaptonemal complex assembly, meiotic chromosome separation, and regulation of meiotic DSBs, with supporting signals from microsporogenesis and general cell division. While a couple terms touch on broader nuclear/plastid aspects, the dominant theme is meiosis-related chromosomal dynamics and pairing. ","confidence":"High","size":14,"edges":86,"triangles":314,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0030466","count":1},{"id":"GO:0051307","count":1},{"id":"GO:0007076","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0043007","count":1}]},{"hash":"1129274526137137811","title":"Ubiquitin-Dependent Protein Degradation","description":"The cluster\u2019s top GO terms are dominated by ubiquitination and ubiquitin-dependent degradation processes (protein ubiquitination, ubiquitin-dependent protein catabolic process, autoubiquitination, ubiquitin-dependent ERAD). Additional terms indicate broader protein turnover and signaling regulation that can be controlled by ubiquitin tagging (histone catabolic process, Wnt receptor catabolic process, TNF signaling, RIG-I pathway regulation, negative regulation of organ growth). Together, these terms point to a cohesive theme of ubiquitin-mediated proteolysis and turnover.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046621","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0038018","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0033151","count":2}]},{"hash":"1058550737797232120","title":"Sugar transport and osmotic stress response","description":"This cluster centers on transmembrane transport of sugars (glucose, galactose, fructose) and related nutrient uptake, plus osmotic/osmoregulatory responses and associated metabolic processes. The presence of sodium and xenobiotic transport terms broadens the transport theme but still supports a core function as sugar/nutrient transporters involved in osmotic stress adaptation. The quorum-sensing term is peripheral and not key to the main theme.","confidence":"High","size":14,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0052106","count":3},{"id":"GO:0006970","count":3},{"id":"GO:1904659","count":3},{"id":"GO:0015757","count":3},{"id":"GO:1990539","count":3}]},{"hash":"1554392228577121125","title":"Chromatin remodeling and transcription control","description":"The cluster\u2019s top terms cluster around nuclear processes: nucleosome assembly and disassembly, DNA-templated transcription, and cell-cycle regulation at the G1/S transition, all pointing to chromatin dynamics governing transcription and replication. A few terms touch on protein transport or microtubule dynamics, but the dominant theme is chromatin remodeling intertwined with transcriptional control, consistent with a nucleus-centric functional group. Confidence in this label is Medium.","confidence":"Medium","size":14,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0032869","count":2},{"id":"GO:0000002","count":2},{"id":"GO:0043666","count":1},{"id":"GO:0000082","count":1}]},{"hash":"271835760927876553","title":"Telomere maintenance and chromatin regulation","description":"These proteins cluster around genome stability in the nucleus, with several GO terms pointing to telomere dynamics (telomeric D-loop disassembly, regulation of protein localization to telomeres), chromatin assembly/remodeling (nucleosome assembly, histone H2A deubiquitination), and DNA topology (G-quadruplex DNA). A few terms relate to transcription and stress responses, but the dominant theme is chromatin regulation and telomere maintenance, suggesting a role in genomic integrity rather than cytosolic signaling.","confidence":"Medium","size":14,"edges":2,"triangles":0,"max_degree":2,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0061820","count":3},{"id":"GO:0009736","count":3},{"id":"GO:1901347","count":3},{"id":"GO:0072362","count":3},{"id":"GO:0006334","count":3}]},{"hash":"1757476604391819477","title":"Neuronal Signaling and Synaptic Vesicle Cycling","description":"Top GO terms indicate endocytosis, regulated exocytosis, excitatory postsynaptic potentials, dopamine response, and ephrin signaling, all central to neuronal communication and synaptic vesicle trafficking. Additional terms on axon extension and focal adhesion hint at neurite outgrowth and synaptic connectivity. The cluster appears to group proteins involved in neuronal signaling and vesicle dynamics, though its sparse connectivity suggests a looser association, yielding a Medium confidence. ","confidence":"Medium","size":14,"edges":2,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006897","count":3},{"id":"GO:0070374","count":3},{"id":"GO:0045956","count":3},{"id":"GO:0051893","count":3},{"id":"GO:0060079","count":3}]},{"hash":"899863735673928245","title":"Vertebrate Development and Organogenesis","description":"The top GO terms cluster around vertebrate development and organ formation, including neural tube closure, forebrain and skeletal system development, placenta development, and general multicellular organism development. The presence of a DNA-templated transcription term suggests regulatory roles during development, while a few immune/stress terms may reflect broader annotation rather than a unifying function for the entire cluster.","confidence":"Medium","size":14,"edges":10,"triangles":2,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0009636","count":3},{"id":"GO:0001843","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0001501","count":3},{"id":"GO:0007275","count":3}]},{"hash":"606088125916041114","title":"Starch, glycogen, and trehalose metabolism","description":"These proteins mainly map to carbohydrate metabolism involving alpha-glucans, including starch and glycogen biosynthesis and breakdown, as well as trehalose and related disaccharide pathways. The GO terms cluster around both biosynthetic and catabolic processes for starch/glycogen and trehalose, indicating a coherent alpha-glucan turnover function.","confidence":"High","size":14,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000023","count":4},{"id":"GO:0005978","count":4},{"id":"GO:0030980","count":4},{"id":"GO:0005993","count":4},{"id":"GO:0051692","count":4}]},{"hash":"487721468727944718","title":"Autophagy-Linked Carbohydrate Metabolism","description":"The cluster games revolve around autophagy-related processes (glycophagy and positive regulation of macroautophagy) along with various carbohydrate catabolic pathways (maltose, starch, glucosinolate) and associated carbon utilization regulation. This suggests a functional module where autophagy intersects with carbohydrate metabolism, despite some peripheral developmental terms. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000025","count":1},{"id":"GO:0043609","count":1},{"id":"GO:0046959","count":1},{"id":"GO:0061723","count":1},{"id":"GO:0046475","count":1}]},{"hash":"348840407475935644","title":"Unknown","description":"Top terms are heterogeneous, spanning metabolic pathways (glyoxylate, terpenoid, xylulose, glycolysis, acetyl-CoA regulation) and neural development (pyramidal neuron development, olfactory bulb mitral cell layer development). With no edges or cohesion among terms, there is no clear shared function linking these proteins. Therefore, a precise label cannot be assigned.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046487","count":1},{"id":"GO:0016114","count":1},{"id":"GO:0052865","count":1},{"id":"GO:0061732","count":1},{"id":"GO:0005999","count":1}]},{"hash":"1011664008023157397","title":"Unknown","description":"The GO terms cover diverse processes across different systems (nuclear export, endosome transport, fungal pseudohyphal growth, hedgehog signaling, calcium signaling, dopaminergic synaptic transmission, p53 signaling, NK T cell differentiation, neuron axonogenesis, and an obsolete stress-aging term), with no clear single theme linking them.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046827","count":14},{"id":"GO:2000641","count":13},{"id":"GO:0007124","count":13},{"id":"GO:1901621","count":13},{"id":"GO:1904637","count":13}]},{"hash":"2142461800578703434","title":"Cytoskeleton remodeling and cellular signaling","description":"The top GO terms point to dynamic actin organization, cell movement (chemotaxis), and membrane trafficking (endosome transport), suggesting a core theme of cytoskeletal remodeling driving signaling and trafficking. While other terms touch on metabolism, growth, and transcription, the most representative cluster signal is actin/cytoskeleton\u2013mediated processes that underpin movement and vesicular transport, with metabolic and transcriptional notes providing broader context. This makes a cytoskeleton-centric label appropriate, with secondary themes acknowledged.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030866","count":4},{"id":"GO:0045793","count":4},{"id":"GO:0034198","count":4},{"id":"GO:0001890","count":4},{"id":"GO:0006006","count":4}]},{"hash":"320795023405611877","title":"Neural development and dopaminergic signaling","description":"The dominant GO terms point to nervous system development and neuronal signaling, including nervous system development, dopaminergic synaptic transmission, and regulation of neural patterning via Hedgehog-related pathways. Endosomal trafficking and calcium signaling (ionomycin response) fit with neuronal transport and synaptic activity, while some terms (pseudohyphal growth, parathyroid hormone response, spindle checkpoint) appear as noise or cross-species annotations. Overall, the cluster is best described by a neural development and signaling theme, with dopaminergic transmission as a prominent facet.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071374","count":3},{"id":"GO:0007124","count":3},{"id":"GO:2000641","count":3},{"id":"GO:0000187","count":3},{"id":"GO:0007094","count":3}]},{"hash":"1038510211340743197","title":"Lipid metabolism and lipoprotein regulation","description":"Top terms point to triglyceride synthesis, cholesterol efflux, plasma lipoprotein particle regulation, and macrophage foam cell differentiation, suggesting a cohesive focus on lipid handling and atherosclerosis-related processes. Other terms (palmitoylation, APP biosynthesis, and Hedgehog signaling) appear secondary or incidental to this main theme. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090116","count":1},{"id":"GO:0060262","count":1},{"id":"GO:0042986","count":1},{"id":"GO:0018191","count":1},{"id":"GO:0019432","count":1}]},{"hash":"267781377950343202","title":"Cell Growth Signaling and Gene Regulation","description":"These proteins cluster around insulin signaling, adipogenesis, and muscle-stimulated responses, coupled with chromatin remodeling and mRNA processing, pointing to a module that coordinates cell growth and differentiation through signaling and transcriptional control. Telomere maintenance terms appear supplementary, reflecting proliferative context rather than core function.","confidence":"Medium","size":14,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000186","count":2},{"id":"GO:0045815","count":2},{"id":"GO:0008286","count":2},{"id":"GO:0032212","count":2},{"id":"GO:0045736","count":2}]},{"hash":"1341830210578086417","title":"Embryonic Development and Gene Regulation","description":"The terms center on embryogenesis (placenta development, neural tube closure, multicellular development) and gene expression control (DNA-templated transcription, regulation of cell size), with other entries reflecting metabolism or stress responses. The dominant signal points to developmental programs and transcriptional regulation, suggesting these proteins function in embryonic development and gene control.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045793","count":9},{"id":"GO:0001890","count":9},{"id":"GO:0006006","count":9},{"id":"GO:0006351","count":9},{"id":"GO:0033160","count":9}]},{"hash":"1708366039591691553","title":"Nuclear transcription regulation and chromatin remodeling","description":"The top terms cluster around transcriptional control (regulation of DNA-templated transcription, DNA-templated transcription) and chromatin dynamics (nucleosome assembly/disassembly), plus associated nuclear processes like protein transport. While some terms (ethylene signaling, chemotaxis, secondary growth) are more distant or plant-specific, the dominant signal is regulation of gene expression through transcription and chromatin remodeling. Medium","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":4},{"id":"GO:0010105","count":2},{"id":"GO:0006935","count":2},{"id":"GO:0000160","count":2},{"id":"GO:0080117","count":2}]},{"hash":"325313241079498772","title":"Cell Division and Intracellular Transport","description":"The top terms include both mitotic processes (cell division, sister chromatid cohesion, meiotic division regulation, mitotic DNA replication) and intracellular trafficking/transport (Golgi to endosome transport, nuclear pore localization, actin remodeling), suggesting a cluster of proteins involved in essential cell-cycle functions together with components of vesicular trafficking and nuclear transport, rather than a single specific pathway.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006895","count":2},{"id":"GO:0014902","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0090344","count":2},{"id":"GO:0031081","count":2}]},{"hash":"2050728212032493179","title":"Immune and Apoptotic Signaling","description":"These proteins show GO terms spanning apoptotic signaling in response to DNA damage by p53, cellular and TNF-mediated immune signaling, NF-kappaB regulation, and antigen processing/presentation via MHC class II. The collection hints at a broad immune/inflammatory and apoptotic theme, but the terms are diverse and only sparsely connected, indicating a loose association rather than a tightly cohesive function. ","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042771","count":1},{"id":"GO:0071222","count":1},{"id":"GO:0033209","count":1},{"id":"GO:0034051","count":1},{"id":"GO:0042347","count":1}]},{"hash":"389937885034339159","title":"Ion Transport and Membrane Potential Regulation","description":"This cluster centers on proteins associated with transporting ions and maintaining calcium/metal ion homeostasis and membrane potential (sodium, potassium, calcium, copper; membrane repolarization). While there are some outlier terms like lipopolysaccharide biosynthesis, stilbene catabolic process, epoxygenase P450 pathway, and testosterone response, the dominant signal is ion transport and membrane potential regulation.","confidence":"Medium","size":14,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0086009","count":4},{"id":"GO:0009103","count":4},{"id":"GO:0002028","count":4},{"id":"GO:0046272","count":4},{"id":"GO:0099132","count":4}]},{"hash":"714080673995856224","title":"Neuronal Development and Growth Signaling","description":"The top terms include spinal cord development and neuron projection development, indicating a clear neuronal development theme. Additional terms for TORC1 signaling and ribosome biogenesis suggest linked Growth/Metabolic regulation, while stress-response terms are present but do not override the neural-development signal.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071480","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0031175","count":2}]},{"hash":"288550328902468664","title":"mRNA Processing and Decay","description":"The top GO terms cluster around mRNA maturation and turnover\u2014splicing (mRNA cis splicing via spliceosome, snoRNA splicing), polyadenylation, and decay (deadenylation-independent decay)\u2014as well as regulation of translation. This strongly points to proteins involved in RNA processing and mRNA stability, with some regulatory signaling connections (e.g., p38MAPK, glucocorticoid response) that are secondary. Therefore, a concise label is mRNA Processing and Decay.","confidence":"High","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006378","count":6},{"id":"GO:0045292","count":6},{"id":"GO:0034247","count":5},{"id":"GO:0098789","count":5},{"id":"GO:2000766","count":4}]},{"hash":"626148331777775153","title":"Neuronal synaptic plasticity and social behavior","description":"The Top Terms center on dendritic spine morphogenesis, long-term synaptic plasticity, and structural/functional regulation of excitatory synapses, plus sensory perception of sound and vocalization/social behavior. This points to proteins involved in neural circuit remodeling and communication, with ubiquitin-related processes suggesting regulation of synaptic protein turnover. Therefore, the cluster likely reflects neuronal synaptic plasticity linked to social and vocal behaviors.","confidence":"High","size":14,"edges":8,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0060997","count":3},{"id":"GO:0070535","count":3},{"id":"GO:0007605","count":3},{"id":"GO:0035176","count":3},{"id":"GO:0060292","count":3}]},{"hash":"415456061641252916","title":"Mitochondrial lipid transport and cardiolipin metabolism","description":"The top GO terms cluster around mitochondria: regulation of mitochondrial membrane potential and cytochrome c release (linked to apoptosis), together with phospholipid transport, cardiolipin metabolism, and phosphatidylcholine biosynthesis, plus positive regulation of cellular respiration. This points to a cohesive module focused on mitochondrial lipid handling and energy metabolism, with apoptosis as a related process; the outlier germarium-derived oocyte differentiation term is likely incidental noise in this set.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010917","count":1},{"id":"GO:0090201","count":1},{"id":"GO:0045332","count":1},{"id":"GO:0015871","count":1},{"id":"GO:0030706","count":1}]},{"hash":"2148388256740570769","title":"Stem Cell Maintenance and Differentiation","description":"The list includes somatic stem cell population maintenance, hematopoietic stem cell differentiation, and skeletal muscle satellite cell maintenance, indicating a theme of stem cell maintenance across tissues. The presence of transcriptional regulation and Wnt signaling terms supports coordinated control of stem cell fate.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014834","count":2},{"id":"GO:0043433","count":2},{"id":"GO:0006351","count":2},{"id":"GO:1903204","count":1},{"id":"GO:2000052","count":1}]},{"hash":"1867257292833446467","title":"Lipid Catabolism and Signaling","description":"GO terms are dominated by lipid-related catabolic processes (triglyceride, diacylglycerol, monoacylglycerol, phosphatidylserine catabolism) and lipid signaling (regulation of endocannabinoid signaling). The presence of plant-specific terms (cellulose, chlorophyll catabolism) and detoxification/oxidation hints at broader metabolism, but the core theme links lipid breakdown with lipid-derived signaling.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0019433","count":6},{"id":"GO:0030245","count":6},{"id":"GO:2000124","count":6},{"id":"GO:0098869","count":6},{"id":"GO:0015996","count":6}]},{"hash":"752126746723549454","title":"Unknown","description":"The top GO terms show a broad and inconsistent mix across development, metabolism, lipid modification, cell wall, and signaling. With no edges and many obsolete terms, there is no clear shared function linking these proteins, so a concise, representative label cannot be assigned.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019878","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0033512","count":1},{"id":"GO:0006507","count":1},{"id":"GO:0048076","count":1}]},{"hash":"809195593919258740","title":"Cardiac development and mitochondrial fatty acid oxidation","description":"Proteins in this cluster show heart development and cardiac muscle differentiation terms, along with mitochondrial dynamics and lipid metabolism processes (mitochondrial fission; long-chain fatty acid catabolism; beta-oxidation with acyl-CoA dehydrogenase; carnitine biosynthesis; leucine catabolism). This combination suggests a link between cardiac development/differentiation and mitochondrial energy metabolism, particularly fatty acid oxidation, justifying the label. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":2},{"id":"GO:0007018","count":2},{"id":"GO:0000266","count":2},{"id":"GO:0006111","count":1},{"id":"GO:0006693","count":1}]},{"hash":"543821314111630504","title":"Unknown","description":"The GO terms are highly diverse, covering neurotrophic signaling, hormonal responses, ion homeostasis, phosphorylation, adhesion, cytoskeleton remodeling, and necroptosis, with no single dominant process. The lack of edges also suggests no tight functional coupling among these proteins, so there isn\u2019t a clear cohesive theme to name a specific function cluster.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990416","count":1},{"id":"GO:0010961","count":1},{"id":"GO:0031952","count":1},{"id":"GO:0071454","count":1},{"id":"GO:1990637","count":1}]},{"hash":"1256811480390679993","title":"Unknown","description":"The proteins listed show a mix of functions across apoptosis (DNA damage response), immune signaling (lipopolysaccharide response, TNF signaling, NF-kappaB), development (epithelium morphogenesis), neural signaling (GABAergic synaptic transmission), hormone response (estrogen), and plant immunity (hypersensitive response regulation). With no cohesive biological process tying these terms together and no network connections (edges/triangles = 0), there isn\u2019t a clear shared function to name the cluster.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042771","count":2},{"id":"GO:0071222","count":2},{"id":"GO:0033209","count":2},{"id":"GO:0034051","count":2},{"id":"GO:0042347","count":2}]},{"hash":"262048263248267554","title":"Kinase signaling regulation and cell cycle control","description":"This cluster centers on regulation of protein serine/threonine kinase activity (positive and negative), autophosphorylation, and GTPase activity, pointing to broader signal transduction control; the presence of mitotic cell cycle and cell proliferation terms supports a theme of cell-cycle regulation. Hypoxia response and mRNA transport are related processes but secondary to the core theme of signaling modulation tied to proliferation.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":2},{"id":"GO:0071456","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0071902","count":2},{"id":"GO:0043547","count":2}]},{"hash":"1739869916732222865","title":"Unknown","description":"This cluster shows a highly diverse set of GO terms ranging from protein oligomerization, cell division and centromere assembly to ribosome biogenesis, RNA splicing/export under stress, ubiquitin ligase activity, aging, and inflammatory cytokine production, with no clear shared function or interaction pattern (no edges/triangles). Therefore, there isn\u2019t a coherent, identifiable theme tying the proteins together.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0000747","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0042254","count":2}]},{"hash":"1848811111348681711","title":"Ubiquitin-dependent innate immune signaling regulators","description":"The top GO terms point to ubiquitination processes (autoubiquitination, ubiquitin-dependent protein degradation, K48-linked ubiquitination, ERAD) alongside innate immune and inflammatory signaling (innate immune response, NF-kappaB activation, TNF signaling). This suggests the cluster comprises proteins that regulate immune signaling through ubiquitin-mediated proteolysis and pathway modulation, including effects on necroptosis and antiviral trafficking. Even without direct connections among proteins, the shared function centers on ubiquitin-driven control of innate immunity.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":7},{"id":"GO:0042787","count":7},{"id":"GO:0030433","count":6},{"id":"GO:0070936","count":5},{"id":"GO:0060546","count":5}]},{"hash":"1673522168001572832","title":"Ubiquitin-regulated signaling and mitosis","description":"This cluster is dominated by GO terms tied to ubiquitination (protein polyubiquitination; ubiquitin-dependent ERAD pathway; histone ubiquitination), with additional terms pointing to regulation of signaling pathways (GTPase activity, Rap signaling) and the mitotic cell cycle. Although there are a few outlier terms related to plant hormone biosynthesis, neural structure, and cholangiocyte proliferation, the strongest common theme is ubiquitin-mediated regulation of signaling and cell division.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000209","count":5},{"id":"GO:0043547","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0009688","count":3}]},{"hash":"1795870163837498265","title":"Copper Ion Transport and Homeostasis","description":"Most of the terms point to copper handling: intracellular copper ion homeostasis, regulation of copper ion transmembrane transport, and copper import across membranes. The xenobiotic transmembrane transport and cellular response to cisplatin support a transporter-associated copper/homeostasis module, with possible links to metal-trafficking through the ER-Golgi pathway. While a few terms touch on broader stress responses, the dominant theme is copper transport and homeostasis.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":1},{"id":"GO:0072719","count":1},{"id":"GO:0006855","count":1},{"id":"GO:0015680","count":1},{"id":"GO:1902311","count":1}]},{"hash":"1433683849628196948","title":"Zinc and Cadmium Ion Transport","description":"The top GO terms indicate zinc and cadmium transmembrane transport, suggesting the cluster is enriched for membrane transport proteins that move metal ions. Other single-annotation terms (peptide catabolism, antigen processing, symbiont entry, etc.) are weaker signals and do not form a cohesive alternative theme.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071577","count":2},{"id":"GO:0070574","count":2},{"id":"GO:0043171","count":1},{"id":"GO:0030154","count":1},{"id":"GO:0002003","count":1}]},{"hash":"580849226379653575","title":"Ribosome Biogenesis and Translation","description":"This cluster is enriched for ribosome-related processes, including ribosome biogenesis (both small and large subunits), ribosomal subunit export from nucleus, cytoplasmic translation, and tRNA modification, indicating a cohesive group of factors central to ribosome assembly and protein synthesis. Additional terms for cell cycle/division reflect growth-linked coordination but do not redefine the primary ribosome-focused theme.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061732","count":2},{"id":"GO:0002181","count":1},{"id":"GO:1901001","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0042274","count":1}]},{"hash":"1275722129481737435","title":"Cell cycle regulation and DNA repair","description":"This cluster emphasizes core processes of cell proliferation and genome maintenance, as seen in GO terms for DNA-templated transcription, G1/S and G2/M transitions, re-entry into the mitotic cell cycle, mitotic spindle dynamics, and DNA repair. While there are additional terms related to development and signaling (cerebellum and mammary gland proliferation, dopamine response), the strongest and most frequent signals center on controlling the cell cycle and maintaining DNA integrity, suggesting a cohesive theme around cell cycle regulation and DNA damage response.","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0007118","count":2},{"id":"GO:0010696","count":2},{"id":"GO:1903351","count":2},{"id":"GO:0000086","count":2}]},{"hash":"1595635680831612133","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0045292","count":4},{"id":"GO:0001731","count":4},{"id":"GO:0071456","count":4},{"id":"GO:0061158","count":4},{"id":"GO:0006378","count":4}]},{"hash":"1845386368351819463","title":"Cell Division and Transcription","description":"The top GO terms cluster around mitosis and cell cycle (cell division, mitotic cell cycle) and DNA-templated transcription, suggesting proteins involved in coordinating cell division with transcriptional regulation. Some noise terms (viral transcription, mammary gland development) exist, but the core pattern supports a cell-cycle\u2013transcription functional theme.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0019086","count":1},{"id":"GO:0060749","count":1}]},{"hash":"2169468317545087414","title":"TLR-driven innate immune signaling","description":"The proteins appear to cluster around Toll-like receptor pathways (TLR2/3/4), innate immune response, and regulation of dendritic cell cytokine production, indicating a cohesive module of innate immune recognition and activation. A few non-immune terms (bone formation, brassinosteroid stimulus, axis specification) may be irrelevant annotations, but the dominant signal is TLR-mediated immune signaling.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0002730","count":3},{"id":"GO:0002322","count":3},{"id":"GO:0034142","count":3},{"id":"GO:1900155","count":3},{"id":"GO:0051770","count":3}]},{"hash":"1489869209536491349","title":"Neuronal signaling and olfactory perception","description":"The top GO terms point to neural signaling processes, especially sensory perception of smell, cellular responses to cAMP and cGMP, and regulation of membrane potential, which are hallmark features of neuronal activity and olfactory pathways. The mention of antipsychotic drug response further supports a neurotransmission-related theme. Some terms (transcription-related) are more general, but the strongest cohesive signal is neuronal signaling and olfaction, giving a Medium confidence.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0010754","count":3},{"id":"GO:0007608","count":3},{"id":"GO:0071321","count":3},{"id":"GO:0006351","count":3},{"id":"GO:2000480","count":2}]},{"hash":"1777129296812586404","title":"Ciliary Axoneme Assembly and Motility","description":"The enriched GO terms cluster around cilium/axoneme biology, microtubule regulation, and tubulin post-translational modifications (polyglutamylation, polyglycylation), including sperm axoneme assembly, epithelial cilium movement, and microtubule severing. This pattern strongly points to a module involved in ciliogenesis and ciliary/microtubule-based motility rather than other processes.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051607","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0046827","count":2},{"id":"GO:0003353","count":1},{"id":"GO:0030516","count":1}]},{"hash":"1311949998565312273","title":"Regulatory signaling and development processes","description":"The top GO terms show a cluster of proteins involved in regulation and signaling across multiple processes: autophosphorylation, transcription, cell cycle control (CDK activity), ubiquitination/deubiquitination, and development (face and vasculature) as well as immune-related regulation (B cell homeostasis, leukocyte migration) and telomere maintenance. This pattern suggests a set of regulatory proteins that influence signaling networks governing transcription, cell cycle, and developmental pathways, rather than a single, cohesive pathway. Confidence: Medium","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031954","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0000019","count":1},{"id":"GO:0060324","count":1},{"id":"GO:0002686","count":1}]},{"hash":"98549995095549898","title":"Unknown","description":"The top terms span mitochondrial lipid biosynthesis, viral transcription and host interaction, mammary gland development, and cell cycle regulation, with no single cohesive function connecting all proteins. Given the lack of a unifying theme and the zero edges, there is no clear representative label. ","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032049","count":1},{"id":"GO:0016024","count":1},{"id":"GO:0019086","count":1},{"id":"GO:0060749","count":1},{"id":"GO:0010696","count":1}]},{"hash":"1761924162717612431","title":"Bacterial cell wall biosynthesis and antibiotic response","description":"The dominant terms (peptidoglycan biosynthesis, beta-lactam antibiotic response, and cell wall organization) point to bacterial cell wall metabolism and antibiotic interaction; the remaining terms appear less central, suggesting a primary theme around cell envelope remodeling with some auxiliary stress-related processes.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":1},{"id":"GO:0030655","count":1},{"id":"GO:0006508","count":1},{"id":"GO:0009252","count":1},{"id":"GO:0071555","count":1}]},{"hash":"323929204701324996","title":"Telomere maintenance and telomerase activity","description":"The listed GO terms cluster around telomere biology\u2014telomere maintenance via telomerase, telomere assembly/capping, D-loop disassembly, and localization to telomeres\u2014consistent with proteins involved in telomere maintenance and telomerase RNP assembly/localization.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061820","count":1},{"id":"GO:0071166","count":1},{"id":"GO:1905776","count":1},{"id":"GO:0032212","count":1},{"id":"GO:0070200","count":1}]},{"hash":"783344555515976134","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0048015","count":3},{"id":"GO:0006413","count":2},{"id":"GO:0035914","count":2},{"id":"GO:0042254","count":2}]},{"hash":"707892930395371037","title":"Unknown","description":"The terms cover disparate processes across transcriptional/post-transcriptional control, ubiquitin-related regulation, neuronal development, immune signaling, and apoptosis. With no shared pathway or functional module and no network connectivity, there isn\u2019t a coherent theme to bind these proteins into a single functional cluster.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000728","count":1},{"id":"GO:1904668","count":1},{"id":"GO:0050773","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0061641","count":1}]},{"hash":"1800032130180207559","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000637","count":2},{"id":"GO:0061157","count":2},{"id":"GO:0001308","count":2},{"id":"GO:1902416","count":2},{"id":"GO:0000056","count":2}]},{"hash":"1529280365485840181","title":"Innate Antiviral Immune Signaling","description":"This cluster is driven by antiviral and innate immune functions, with terms like defense response to virus, innate immune response, and regulation of interferon production, plus NF-kappaB signaling and ubiquitination-related processes that link protein quality control to immune signaling. A few terms (skin development, muscle contraction) appear as outliers, but the dominant theme centers on antiviral innate immunity and associated signaling pathways.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051607","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0000209","count":2},{"id":"GO:0043123","count":1},{"id":"GO:0043588","count":1}]},{"hash":"2223617028056527731","title":"Chromatin Organization and Spindle Assembly","description":"The terms point to chromatin-related processes (nucleosome assembly and histone modification) and mitotic spindle assembly, suggesting a cluster of proteins involved in genome organization and cell division, with some development-related signals. Despite some obsolete GO terms, the recurring themes of chromatin remodeling and spindle formation support this label.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051225","count":2},{"id":"GO:0070562","count":1},{"id":"GO:0051569","count":1},{"id":"GO:0097536","count":1},{"id":"GO:1901674","count":1}]},{"hash":"1851878362097860518","title":"Membrane Transport and Ion Homeostasis","description":"The top GO terms cluster around transport of ions and osmolytes (glycine betaine, taurine, cobalt, monoatomic anions), lipid movement (ceramide translocation), and ion-channel\u2013related activities and membrane potential regulation. The SOS/antibiotic response and cytochrome complex assembly further point to membrane-associated stress responses and energy metabolism. Together, these suggest a membrane-centric group focused on transport and ionic balance, especially under stress.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0031460","count":3},{"id":"GO:0099133","count":3},{"id":"GO:0006824","count":3},{"id":"GO:0099040","count":3}]},{"hash":"2255132664101640038","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071276","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0071560","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0006351","count":2}]},{"hash":"105304794449650753","title":"Mitochondrial Redox and Iron Homeostasis","description":"These terms converge on mitochondrial function and cellular redox/iron balance, including import into the intermembrane space, oxidative stress response, redox/homeostasis, and iron homeostasis. Autophagy and necroptosis regulation also fit stress/metabolic control. Some tissue/metabolic terms (liver regeneration, adaptive thermogenesis) reflect mitochondria-driven energy metabolism.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045041","count":1},{"id":"GO:0034599","count":1},{"id":"GO:0016242","count":1},{"id":"GO:0045454","count":1},{"id":"GO:0006879","count":1}]},{"hash":"53553821561861140","title":"Cardiac contraction and calcium signaling","description":"The top GO terms cluster around heart-related functions: regulation of heart rate, cardiac muscle contraction, cardiac myofibril assembly, and regulation of release of sequestered calcium into the cytosol, all pointing to cardiac muscle physiology and calcium handling. Some other terms (memory, certain development processes) appear less connected and may reflect annotation noise, but the predominant theme is cardiac function. ","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002027","count":3},{"id":"GO:0007616","count":3},{"id":"GO:0060048","count":3},{"id":"GO:0055003","count":2},{"id":"GO:0097274","count":2}]},{"hash":"2216263049307033022","title":"Cell polarity and cytoskeletal organization","description":"These GO terms cluster around cellular architecture and trafficking: establishment of epithelial cell polarity, actin filament bundle assembly, spindle assembly, and protein localization to the plasma membrane; together with protein auto-ADP-ribosylation and chromosome telomere localization, they point to regulation of cell shape, polarity, and intracellular transport. A few inflammation/cardiac signaling terms appear, but they do not dominate the theme, so the label reflects the core pattern of cell polarity and cytoskeletal organization.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0071642","count":4},{"id":"GO:1901594","count":4},{"id":"GO:0086070","count":4},{"id":"GO:0090162","count":4},{"id":"GO:0071651","count":4}]},{"hash":"1071022626801194320","title":"Centrosome and microtubule dynamics","description":"The cluster's GO terms center on microtubule nucleation and polymerization, centrosome/centriole regulation, spindle pole body duplication, and motile cilium assembly, pointing to a shared theme of microtubule organization at the centrosome and cilia. Some items (cone photoresponse recovery, neuroblast proliferation) fit broader cellular contexts but do not override the core microtubule-centric signal.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043488","count":2},{"id":"GO:0010968","count":1},{"id":"GO:0031115","count":1},{"id":"GO:0036368","count":1},{"id":"GO:0007405","count":1}]},{"hash":"1598746769842211071","title":"Mitotic control and cell cycle checkpoints","description":"The cluster is dominated by terms tied to mitosis and cell cycle control: kinetochore localization, negative regulation of CDK activity, mitotic cytokinesis checkpoint signaling, and the general cell cycle term. While a few terms pertain to synaptic processes, the strongest and most frequent annotations point to chromosome segregation and mitotic regulation, suggesting a coherent role in cell division control.","confidence":"High","size":13,"edges":41,"triangles":81,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0034501","count":11},{"id":"GO:0045736","count":11},{"id":"GO:0097107","count":8},{"id":"GO:0051898","count":8},{"id":"GO:0051895","count":8}]},{"hash":"1853468522579025124","title":"Negative Regulators of Signaling and Synaptic Organization","description":"This cluster is dominated by GO terms for negative regulation of signaling pathways (T cell receptor signaling, ERK cascade, PI3K/AKT), plus terms tied to synaptic processes (postsynaptic density assembly, synaptic vesicle clustering) and immune/apoptotic signaling (JAK-STAT suppression, TRAIL signaling) and adhesion regulation. The common thread is proteins that dampen or modulate signaling and influence synaptic architecture, suggesting a function as negative regulators of signaling with a synaptic/immune regulatory scope.","confidence":"High","size":13,"edges":77,"triangles":275,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0050860","count":12},{"id":"GO:0000200","count":12},{"id":"GO:0070373","count":12},{"id":"GO:0097107","count":11},{"id":"GO:0051898","count":11}]},{"hash":"1307319021040304111","title":"Steroid and alkaloid metabolism","description":"The top GO terms point to metabolism of diverse small molecules and steroids, including brassinosteroid biosynthesis, testosterone and androgen metabolism, isoquinoline alkaloid metabolism, and xenobiotic catabolic processes (carbazole, camphor). A few terms relate to development and cell-cycle regulation, but the strongest signal is secondary metabolite/hormone metabolism rather than a single developmental pathway. Therefore the label Steroid and alkaloid metabolism captures the central theme of the cluster.","confidence":"Medium","size":13,"edges":24,"triangles":23,"max_degree":10,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0046232","count":7},{"id":"GO:0019383","count":7},{"id":"GO:0008209","count":6},{"id":"GO:1900087","count":6},{"id":"GO:0016132","count":6}]},{"hash":"2274305217809280477","title":"Neuronal microtubule dynamics and projections","description":"These proteins cluster around microtubule cytoskeleton dynamics and neuron-specific processes. The top GO terms include microtubule depolymerization, spindle/kinetochore interactions, cytoskeleton polarity, and anterograde dendritic transport, along with neuron projection maintenance and cerebellar layer organization, all pointing to microtubule-guided transport and maintenance in neuronal contexts. A plant-related movement term appears but the dominant signal is microtubule dynamics in neural projections.","confidence":"High","size":13,"edges":65,"triangles":176,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0010938","count":13},{"id":"GO:0000743","count":13},{"id":"GO:0001560","count":13},{"id":"GO:0032487","count":13},{"id":"GO:0098971","count":13}]},{"hash":"1335437394627372889","title":"Ubiquitin-Mediated Regulation and Degradation","description":"The terms cluster around ubiquitination processes (protein ubiquitination, K48-linked ubiquitination, autoubiquitination, ubiquitin-dependent ERAD) and ubiquitin-driven regulation of signaling (TNF-mediated signaling, necroptosis regulation) as well as chromatin-related ubiquitination (histone catabolic processes). This points to a cohesive theme of ubiquitin-dependent control of protein turnover, signaling, and chromatin dynamics, with additional links to growth regulation. ","confidence":"High","size":13,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0060546","count":3},{"id":"GO:0046621","count":3},{"id":"GO:0051865","count":3}]},{"hash":"1850756328230570199","title":"Neural development and dopaminergic signaling","description":"The top terms cluster around neural development and synaptic activity, including CNS projection neuron axonogenesis and dopaminergic synaptic transmission, with supporting links to endosome transport and neuronal signaling regulation. While a few terms appear unrelated (pseudohyphal growth, NK T cell differentiation, cartilage condensation), the neural development/synaptic theme is the most coherent explanation for the cluster.","confidence":"Medium","size":13,"edges":33,"triangles":19,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":13},{"id":"GO:0007124","count":13},{"id":"GO:1901621","count":13},{"id":"GO:1904637","count":13},{"id":"GO:0001963","count":13}]},{"hash":"1328230587434718612","title":"Plant Signaling and Phosphorylation Regulation","description":"The GO terms cluster around signaling and phosphorylation control, including cellular response to growth-factor-like signals (TGF-beta), negative regulation of TGF-beta receptor signaling, and multiple dephosphorylation processes, with a plant development cue (maintenance of meristem identity). Although some terms are obsolete or outliers (e.g., photosystem stoichiometry adjustment), the dominant theme is plant signaling and post-translational modification.","confidence":"Medium","size":13,"edges":11,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0071560","count":1},{"id":"GO:0080005","count":1},{"id":"GO:0061191","count":1},{"id":"GO:0010991","count":1},{"id":"GO:0010074","count":1}]},{"hash":"2300707995448491543","title":"Chromosome replication and mitotic chromatin assembly","description":"The cluster is enriched for terms tied to cell division, DNA replication, and centromere/chromatin assembly (e.g., CENP-A chromatin assembly) as well as microtubule severing, all of which point to chromosome maintenance and mitosis. While there are a few peripheral terms related to transcription regulation and ER proteostasis, the dominant signal is nuclear processes governing chromosome replication and segregation.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0001649","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0030433","count":2}]},{"hash":"241411507241876866","title":"Organogenesis and mitosis","description":"This cluster blends organ development terms (kidney, brain, liver, neural tube patterning) with mitotic processes (mitotic spindle assembly, mitotic cell cycle) and vesicle trafficking (COPII budding) plus growth signaling (TORC1, GTPase regulation). The proteins likely coordinate developmental patterning with cell division and trafficking, supporting a cohesive theme of organogenesis linked to proliferation.","confidence":"Medium","size":13,"edges":71,"triangles":220,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0090114","count":3},{"id":"GO:0043547","count":2},{"id":"GO:1904263","count":2},{"id":"GO:0001822","count":2},{"id":"GO:0051301","count":2}]},{"hash":"1280510991753224254","title":"Ribosome biogenesis and translation","description":"The top GO terms are centered on maturation of SSU and LSU rRNA (including 5.8S) and translation, indicating core involvement in ribosome assembly and protein synthesis. Additional terms reflect RNA processing/regulation (ncRNA silencing, spliceosome-associated regulation) and RNA localization to Cajal bodies, which are consistent with nucleolar ribosome biogenesis. A few context-specific terms (ischemia response, ROS regulation) appear ancillary. Overall, the cluster is best described as ribosome biogenesis and translation.","confidence":"High","size":13,"edges":67,"triangles":189,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0031047","count":2}]},{"hash":"936045618984267102","title":"Neural development and cell cycle regulation","description":"Contains clear neural development signals (forebrain development, neuron development, dendrite morphogenesis) alongside cell cycle/DNA replication terms (mitotic cell cycle, DNA replication, cell division). Other terms reflect stress/defense responses but do not dominate. Thus the cluster appears centered on neural development with concurrent proliferation regulation.","confidence":"Medium","size":13,"edges":76,"triangles":265,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0001843","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0048813","count":3}]},{"hash":"852872745220006279","title":"Neuronal development with ER stress and secretory trafficking","description":"The cluster includes neural development terms (neural tube closure, forebrain development) alongside ER-Golgi transport and ER-stress\u2013related apoptotic signaling, plus broader stress responses like cadmium exposure. This points to a theme where neural development processes intersect with ER function and secretory trafficking, making the label a reasonable representation of the cluster\u2019s functions.","confidence":"Medium","size":13,"edges":16,"triangles":2,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001843","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0050830","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0006888","count":2}]},{"hash":"2149398624390972903","title":"Nuclear gene expression and chromatin regulation","description":"The cluster features several nuclear-level functions: DNA-templated transcription, mRNA splicing, and CENP-A\u2013containing chromatin assembly, along with regulation of mRNA export and protein ubiquitination. While a few terms (gonad development, dendrite development, inflammatory cytokine production) are less central, the dominant signals point to transcriptional/post-transcriptional control and chromatin organization, with ubiquitin-related regulation often tied to protein turnover in these processes.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0008584","count":2},{"id":"GO:0055114","count":2},{"id":"GO:2000728","count":1},{"id":"GO:1904668","count":1}]},{"hash":"491749882878421961","title":"Unknown","description":"The top GO terms span immune signaling, transcriptional regulation, vesicle trafficking, fungal development, neural development, calcium signaling, neurotransmission, p53 signaling, and immune differentiation, across diverse organisms. This lack of a cohesive, single-function theme means no reliable, specific label can be assigned to the cluster.","confidence":"","size":13,"edges":59,"triangles":125,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0097011","count":13},{"id":"GO:0006351","count":13},{"id":"GO:2000641","count":12},{"id":"GO:0007124","count":12},{"id":"GO:1901621","count":12}]},{"hash":"20572831256040981","title":"Developmental Regulation and Cell Cycle","description":"The cluster is dominated by embryonic/organ development terms (neural tube closure, forebrain development, skeletal system development, multicellular organism development) along with DNA-templated transcription and mitotic cell cycle, suggesting proteins that coordinate development with basic gene expression and cell division. Some other terms (defense response, cadmium ion response) appear ancillary or pleiotropic, but the central theme remains developmental regulation.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001843","count":7},{"id":"GO:0071276","count":7},{"id":"GO:0001501","count":7},{"id":"GO:0007275","count":7},{"id":"GO:0050830","count":7}]},{"hash":"2094676094878547588","title":"Neural development and signaling cluster","description":"This cluster centers on neural development and signaling, with terms like axonogenesis, dopaminergic synaptic transmission, and neural tube patterning; other terms reflect differentiation and trafficking, suggesting a broader developmental signaling theme.","confidence":"Medium","size":13,"edges":64,"triangles":163,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":13},{"id":"GO:0007124","count":13},{"id":"GO:1901621","count":13},{"id":"GO:1904637","count":13},{"id":"GO:0001963","count":13}]},{"hash":"115804974384448142","title":"Neural development and signaling regulators","description":"The cluster shows enrichment in neural development and signaling-related GO terms (axonogenesis, dopaminergic synaptic transmission, Hedgehog-related pathway regulation, neural tube patterning) along with related cellular signaling (ionomycin response, p53 mediator signaling) and connections to endosomal transport. This combination suggests a group of proteins that coordinate neural development and synaptic signaling, with trafficking components possibly supporting endocytic trafficking relevant to signaling.","confidence":"Medium","size":13,"edges":76,"triangles":265,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":13},{"id":"GO:0007124","count":13},{"id":"GO:1901621","count":13},{"id":"GO:1904637","count":13},{"id":"GO:0001963","count":13}]},{"hash":"465732464848312216","title":"Nuclear transport and cell-cycle signaling","description":"The cluster\u2019s GO terms cluster around nuclear processes (mitotic nuclear membrane reassembly; NLS-bearing protein import into nucleus), cell growth signaling (TORC1 signaling; positive regulation of kinase activity), transcriptional regulation (positive regulation of transcription by RNA polymerase III), and developmental/apoptotic contexts (apoptotic morphogenesis; extrinsic apoptotic signaling pathway in absence of ligand). While diverse, these terms collectively point to regulation of nuclear transport, cell growth, and division, rather than a single tightly defined pathway, suggesting a cohesive theme of nuclear transport coupled with cell-cycle signaling. ","confidence":"Medium","size":13,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007084","count":3},{"id":"GO:0045945","count":3},{"id":"GO:0097711","count":3},{"id":"GO:0001938","count":3},{"id":"GO:0060561","count":3}]},{"hash":"1258394492664653525","title":"ER-Golgi vesicle trafficking and cell division","description":"The cluster is enriched for ER-Golgi vesicle transport terms (COPII budding; Golgi-ER and ER-Golgi trafficking) and for mitotic processes (spindle assembly, mitosis, proliferation), suggesting proteins that couple membrane trafficking with cell division during development.","confidence":"Medium","size":13,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:0006890","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0008283","count":2}]},{"hash":"175342741191887557","title":"Developmental transcription and metabolic regulation","description":"This cluster centers on DNA-templated transcription and key developmental processes (placenta development, neural tube closure, multicellular organism development), with metabolic context (glucose metabolic process) and regulatory activities. While some terms reflect stress or movement responses, the strongest shared signal is transcriptional control linked to embryonic/developmental programs, complemented by metabolism. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0045793","count":4},{"id":"GO:0001890","count":4},{"id":"GO:0006006","count":4},{"id":"GO:0033160","count":4}]},{"hash":"910422295953085354","title":"Unknown","description":"The terms cover endocrine signaling, GTPase signaling, sensory transduction, cell cycle, muscle and cuticle development, tissue remodeling, kidney development, and nuclear transport\u2014no single unifying function stands out for this cluster.","confidence":"","size":13,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035774","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0007602","count":3},{"id":"GO:0007601","count":3},{"id":"GO:1903087","count":3}]},{"hash":"1418447219866308682","title":"Post-transcriptional mRNA processing and translation control","description":"The terms cluster around mRNA processing and post-transcriptional regulation\u2014splicing (canonical and alternative), mRNA modification and stability, and ncRNA/miRNA-mediated silencing, plus involvement in translation initiation (eIF4F complex assembly). This suggests proteins in this cluster coordinate post-transcriptional gene expression control rather than a single enzymatic activity.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":2},{"id":"GO:0048025","count":2},{"id":"GO:0035278","count":2},{"id":"GO:0010610","count":2},{"id":"GO:0016556","count":2}]},{"hash":"1598356605317697154","title":"Unknown","description":"The top GO terms span stress-related mRNA processing, ubiquitin signaling, neural development, chromatin assembly, inflammatory cytokine production, cell cycle control, glial apoptosis, and GPCR signaling, with no single cohesive function emerging for the cluster.","confidence":"","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2000728","count":1},{"id":"GO:1904668","count":1},{"id":"GO:0050773","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0061641","count":1}]},{"hash":"688161149574139278","title":"MAPK signaling with glial/immune regulation","description":"This cluster centers on signaling pathways, especially MAPK cascades (p38MAPK, ERK5), and their roles in regulating glial cell behavior and immune outputs (glial proliferation, IL-10 production). Additional terms touching cell polarity and various developmental processes suggest broader tissue-patterning roles, but the recurring emphasis on MAPK signaling and immune-glial modulation provides the strongest cohesive theme.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060252","count":2},{"id":"GO:0007502","count":2},{"id":"GO:0034351","count":2},{"id":"GO:2001181","count":2},{"id":"GO:1900745","count":2}]},{"hash":"586116577439756239","title":"Cell Division and Chromosome Dynamics","description":"The top GO terms are dominated by cell cycle processes: cell division (GO:0051301), mitotic chromosome condensation (GO:0007076), and meiotic chromosome separation (GO:0051307). There are also related chromosomal maintenance processes (maintenance of rDNA) and some vesicle transport activities that can accompany mitosis. A few terms like melanosome organization or microsporogenesis are less central, but overall the cluster centers on cell division and chromosome dynamics.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0006888","count":2},{"id":"GO:0035617","count":2},{"id":"GO:0051307","count":1},{"id":"GO:0007076","count":1}]},{"hash":"177215897935599850","title":"Mitotic spindle and cytoskeleton dynamics","description":"The top GO terms cluster around mitosis and cytoskeletal remodeling\u2014mitotic spindle assembly, mitotic cell cycle, microtubule-based movement, APC-dependent proteolysis, actin depolymerization and crosslinking, and regulation of GTPase activity\u2014indicating a cohesive group involved in coordinating spindle function and cytoskeletal changes during cell division.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030042","count":2},{"id":"GO:0043087","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0070979","count":2}]},{"hash":"142338249237294996","title":"Histone demethylation and chromatin regulation","description":"Most represented GO terms point to histone demethylation (H3K9, H3K4, H3K27) and chromatin-related processes (RITS complex localization), suggesting a core theme of chromatin modification and gene silencing. While several development-related terms appear, they appear less consistently, making chromatin regulation the most coherent shared function among the cluster\u2019s proteins.","confidence":"Medium","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0021555","count":3},{"id":"GO:0033169","count":3},{"id":"GO:0034630","count":3},{"id":"GO:0060763","count":3},{"id":"GO:0060275","count":3}]},{"hash":"239930919784632885","title":"Nuclear RNA processing and chromatin regulation","description":"This cluster shows GO terms centered on RNA metabolism and transcriptional/chromatin control, including deadenylation-dependent decapping, spliceosomal assembly, P-body formation, histone mRNA metabolism, and termination of RNA Pol II transcription, with additional links to DNA-binding regulation and heterochromatin formation. The convergence on nuclear RNA processing and chromatin maintenance suggests a cohesive theme around coordinated RNA processing and chromatin state rather than disparate pathways.","confidence":"Medium","size":13,"edges":28,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0042981","count":1},{"id":"GO:0016579","count":1},{"id":"GO:0043392","count":1},{"id":"GO:0008334","count":1},{"id":"GO:0000245","count":1}]},{"hash":"1342927469105246866","title":"Cytoplasmic Translation Machinery","description":"The Top Terms are dominated by translation-related GO terms: translation (cytoplasmic translation, initiation, termination), and selenocysteine incorporation, with additional support from positive regulation of cytoplasmic translation and translational elongation. This strongly points to components of the cytoplasmic protein synthesis apparatus and its regulation. The presence of deadenylation-dependent mRNA decay suggests a link between translation and mRNA turnover, reinforcing the overall theme. A few terms (glial cell proliferation, response to antibiotic) appear peripheral to the core translation function.","confidence":"High","size":13,"edges":76,"triangles":265,"max_degree":12,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":10},{"id":"GO:0046677","count":6},{"id":"GO:0002181","count":4},{"id":"GO:0014009","count":3},{"id":"GO:2000767","count":3}]},{"hash":"1527074328391131724","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":66,"triangles":179,"max_degree":12,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0000470","count":2},{"id":"GO:0046330","count":2},{"id":"GO:0007338","count":2}]},{"hash":"1162431362977842107","title":"Sugar and isoprenoid metabolism with cGMP signaling","description":"This cluster centers on diverse metabolic processes, including galactose-derived glycolysis, D-galacturonate metabolism, the mevalonate pathway producing IPP and FPP, cholesterol biosynthesis, and GDP-L-fucose salvage. In addition, it includes signaling-related terms such as cellular response to cGMP and negative regulation of receptor guanylyl cyclase signaling, and sensory perception of smell, which may reflect cGMP-linked signaling in sensory pathways. Overall, the dominant theme is metabolic biosynthesis, with a secondary connection to signaling contexts.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010754","count":2},{"id":"GO:0007608","count":2},{"id":"GO:0071321","count":2},{"id":"GO:0061623","count":1},{"id":"GO:0006695","count":1}]},{"hash":"401102783665815895","title":"Cellular stress and apoptosis response","description":"The cluster contains GO terms emphasizing responses to external stimuli (peptide hormones, toxins, cocaine) and apoptotic processes, pointing to a shared theme of cellular stress and regulation of cell fate. Additional terms related to the centrosome cycle and metabolism may reflect contextual roles in cell growth and division. Overall, the dominant pattern is signaling and survival/death decisions in stress conditions.","confidence":"Medium","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071375","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0007098","count":2},{"id":"GO:0045793","count":2}]},{"hash":"1749931080905592506","title":"Immune cell differentiation and signaling","description":"The top GO terms are strongly immune-related, including NK T cell differentiation, B cell affinity maturation, dendritic cell cytokine production, Fc receptor signaling, and regulation of leukocyte chemotaxis, which together point to processes involved in the development and activation of immune cells and their signaling networks. While a few terms (neural development, pH response, vitamin D metabolism) are not obviously tied to immunity, the prevailing theme is immune cell differentiation and signaling, justifying this label for the cluster.","confidence":"Medium","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001865","count":12},{"id":"GO:0021952","count":12},{"id":"GO:0042523","count":12},{"id":"GO:0002344","count":12},{"id":"GO:0071469","count":12}]},{"hash":"1084370652210575892","title":"Neurodevelopment and Stress-Responsive Regulation","description":"The cluster is enriched for neural development terms (neural tube closure, forebrain development, multicellular organism development) alongside general transcription and cell cycle processes, and stress-related pathways (ER stress\u2013induced apoptosis, cadmium response, defense to Gram-positive bacteria). These together point to a theme of developmental regulation coupled with cellular stress responses and transcriptional control, hence the label.","confidence":"Medium","size":13,"edges":66,"triangles":184,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001843","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0050830","count":4},{"id":"GO:0030900","count":4}]},{"hash":"1341491859840472040","title":"Ribosome Biogenesis and Translation Machinery","description":"The dominant GO terms are about translation and ribosome assembly (translation, cytoplasmic translation, ribosomal large subunit assembly, ribosome biogenesis) and SRP-dependent cotranslational targeting to membranes, indicating a core role in protein synthesis and ribosome function. Interleukin-4 response and antibiotic response appear as ancillary signals, suggesting these are secondary associations rather than defining features of the cluster.","confidence":"High","size":13,"edges":16,"triangles":14,"max_degree":7,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0002181","count":4},{"id":"GO:0000027","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0006614","count":2}]},{"hash":"575083844254123258","title":"Plant pollen development and nuclear RNA processing","description":"Proteins in this cluster are enriched for plant-specific pollen sperm cell differentiation, cytokinin signaling, and several nuclear/RNA processing activities (snoRNA processing, RNase MRP-dependent mRNA decay, chromosome condensation, DNA replication, telomerase assembly), suggesting a cohesive theme of reproductive development coordinated with nuclear RNA metabolism and genome maintenance in plants. Some terms reflect general stress responses, but the dominant signal supports a plant reproductive/nuclear function.","confidence":"Medium","size":13,"edges":14,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0030261","count":3},{"id":"GO:0000294","count":3},{"id":"GO:0034965","count":3},{"id":"GO:0048235","count":3},{"id":"GO:0006261","count":2}]},{"hash":"872977283015298096","title":"Hepatic amino acid metabolism and glucagon response","description":"This set features amino acid metabolism and nitrogen-related responses (glutamine, ammonium, amines) and fasting-related signaling (starvation). The inclusion of hepatocyte differentiation and glucagon stimulus suggests a liver-centric metabolic/hormonal response module.","confidence":"Medium","size":13,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":1},{"id":"GO:0008153","count":1},{"id":"GO:1903718","count":1},{"id":"GO:0043200","count":1},{"id":"GO:0071377","count":1}]},{"hash":"309037157226090339","title":"Unknown","description":"Top terms are spread across translation, endocytic recycling, membrane remodeling, mitotic cycle, ECM disassembly, cytokinesis, sporulation membrane formation, eye development, lipid biosynthesis, and osteoblast fate. The lack of a coherent, shared function or pathway linking these terms makes it difficult to assign a single, meaningful label beyond Unknown.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:1990126","count":1},{"id":"GO:0097320","count":1},{"id":"GO:0000278","count":1},{"id":"GO:0022617","count":1}]},{"hash":"1420623721865187149","title":"Telomere-associated chromatin regulation","description":"The top GO terms cluster around chromatin organization (nucleosome assembly, transcription regulation) and telomere biology (telomeric D-loops, telomere protein localization), with mentions of G-quadruplex DNA, suggesting a theme of chromatin dynamics tied to telomere maintenance. Some terms appear as noise (plant signaling, cell wall processes), but the core signal points to telomere-related chromatin regulation.","confidence":"Medium","size":13,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0061820","count":2},{"id":"GO:0009736","count":2},{"id":"GO:1901347","count":2},{"id":"GO:0072362","count":2}]},{"hash":"1838253568094613889","title":"Cell Cycle Regulation and Chromatin Remodeling","description":"This cluster is dominated by G2/M transition and broader cell cycle regulation, along with chromatin remodeling, indicating coordination of cell division with chromatin dynamics. The presence of cytokinin-activated signaling and kinase activity terms suggests plant growth signaling and phosphorylation-based control, while metabolic and xenobiotic response terms (nitrogen utilization, gluconeogenesis regulation, cellular response to xenobiotic stimulus, vacuole fusion) may reflect broader growth-stress integration linking metabolism and cell cycle.","confidence":"High","size":13,"edges":9,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0042144","count":2},{"id":"GO:0019740","count":2},{"id":"GO:0090526","count":2},{"id":"GO:0071157","count":2},{"id":"GO:0035690","count":2}]},{"hash":"112382365146915249","title":"Ubiquitin-Driven Regulation of Cell Cycle and Immunity","description":"The top terms are dominated by various ubiquitination processes (autoubiquitination, polyubiquitination, histone ubiquitination), indicating regulation of protein turnover and chromatin. Additional terms touch on cell division, apoptosis, and cell proliferation, plus ER-Golgi transport and immune-related processes like V(D)J recombination and TNF signaling. This suggests a cluster of proteins linked by ubiquitin-mediated control across both cell cycle and immune signaling pathways.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070535","count":6},{"id":"GO:0051865","count":6},{"id":"GO:0051301","count":5},{"id":"GO:0000209","count":5},{"id":"GO:0008283","count":4}]},{"hash":"196565623574560388","title":"Nociception and Innate Immunity","description":"The cluster is dominated by GO terms related to pain perception and thermosensory behavior, plus innate immune responses and inflammatory mediator production, suggesting a functional group centered on nociceptive/temperature sensing linked to immune signaling. Development and transcription terms appear less central but may reflect broader cellular priming or regulation.","confidence":"High","size":13,"edges":25,"triangles":18,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019233","count":7},{"id":"GO:0007275","count":7},{"id":"GO:0046827","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0045087","count":4}]},{"hash":"213918742401846022","title":"Ubiquitin-Dependent Protein Degradation","description":"The top GO terms are dominated by ubiquitin-related processes: ubiquitin-dependent protein catabolic process, K48-linked ubiquitination, and ERAD, indicating a core theme of tagging proteins for degradation. Additional terms such as Wnt receptor catabolic process and peroxisomal protein import (which can involve ubiquitination for trafficking) further support a focus on ubiquitin-mediated turnover and quality control. Some terms related to X chromosome inactivation and V(D)J recombination may reflect broader regulatory roles of ubiquitination in chromatin and signaling, but the predominant pattern is ubiquitin-proteasome\u2013driven degradation and turnover. Confidence reflects this strong, cohesive theme across most terms.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0046621","count":11},{"id":"GO:0038018","count":11},{"id":"GO:0051865","count":11},{"id":"GO:0030433","count":11},{"id":"GO:0042787","count":11}]},{"hash":"2053706527234653765","title":"Mitotic sister chromatid cohesion and cell division","description":"Based on the dominant GO terms, the cluster centers on mitosis-related processes: mitotic sister chromatid cohesion, its establishment, and general cell division. While some terms appear obsolete or noisy, the cohesive theme is cohesion of sister chromatids during mitosis and progression through cell division.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":2},{"id":"GO:0061587","count":2},{"id":"GO:0009405","count":2},{"id":"GO:0034087","count":1},{"id":"GO:1990022","count":1}]},{"hash":"1519534249806799704","title":"Neural stress response with RNA processing and ubiquitination","description":"Top GO terms indicate heat-stress\u2013driven regulation of mRNA export, splicing, and chromatin assembly, plus protein ubiquitination and cell-cycle control, with additional signals related to glial apoptosis, brain development, inflammatory cytokine production, and GPCR signaling. This suggests a neural context where stress triggers RNA processing and proteostasis via ubiquitination, linked to neural development and neuroinflammation, justifying a label centered on neural stress, RNA processing, and ubiquitin regulation.","confidence":"Medium","size":13,"edges":47,"triangles":55,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000728","count":4},{"id":"GO:1904668","count":4},{"id":"GO:0000398","count":4},{"id":"GO:0061641","count":4},{"id":"GO:0002534","count":4}]},{"hash":"1655029817478740807","title":"Unknown","description":"The top GO terms span several distinct themes, including cell cycle regulation, membrane processes, ion transport, metabolism, and development, with no single unifying function evident for the entire cluster. This lack of a cohesive theme makes it inappropriate to assign a specific, representative label other than Unknown.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000082","count":2},{"id":"GO:0086009","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0002028","count":2},{"id":"GO:0046272","count":2}]},{"hash":"2059154713917583286","title":"ER-Golgi-Endosome Transport","description":"Top GO terms point to vesicle trafficking within the secretory and endocytic pathways, including ER-to-Golgi (COPII), Golgi-to-endosome, endosome-to-Golgi, and recycling routes, with Rab signaling regulation. This makes \"ER-Golgi-Endosome Transport\" a coherent, representative label.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048227","count":3},{"id":"GO:0051534","count":3},{"id":"GO:0071955","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0035526","count":2}]},{"hash":"1181302023614714075","title":"Unknown","description":"The GO terms are highly diverse, spanning RNA processing and translation (initiation, reinitiation, splicing, mRNA export), protein ubiquitination, chromatin assembly (CENP-A), and programs like dendrite development and inflammatory cytokine production. With no edges connecting proteins and no clear shared pathway, there is no cohesive functional theme to identify a specific cluster name. ","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2},{"id":"GO:1901407","count":2},{"id":"GO:2000728","count":1},{"id":"GO:1904668","count":1}]},{"hash":"166924137050797804","title":"Unknown","description":"The terms span very different areas: animal development (midbrain-hindbrain boundary morphogenesis, mammary duct growth, third ventricle development) and metabolism/sporulation (acetoin catabolic process, sporulation), plus chromatin-related localization and obsolete demethylation terms. There isn't a single dominant function or pathway tying the proteins together, so a coherent label cannot be assigned. Confidence None","confidence":"","size":13,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0045150","count":2},{"id":"GO:0030435","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0021555","count":1},{"id":"GO:0033169","count":1}]},{"hash":"1094399658670580772","title":"Developmental Vesicle Trafficking in Secretory Pathway","description":"These proteins cluster around developmental processes (skin, brain, bone formation, multicellular development) and vesicle trafficking between the ER and Golgi (COPII budding, ER-Golgi transport, Golgi-ER transport). This suggests a theme where development is linked to secretory pathway dynamics, even though the network edges are zero.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043588","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0043931","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0007420","count":2}]},{"hash":"1165414777241721051","title":"Mitochondrial import and membrane regulation","description":"Top GO terms show a clear mitochondrial theme, notably regulation of mitochondrial membrane permeability and protein import into the mitochondrial matrix. Additional terms point to associated lipid metabolism (triglyceride biosynthesis) and some unrelated or obsolete signals, but they do not override the mitochondrial-centric pattern. Therefore, the cluster is best described as focused on mitochondrial function and metabolism.","confidence":"High","size":13,"edges":48,"triangles":77,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":12},{"id":"GO:2000134","count":12},{"id":"GO:0070940","count":12},{"id":"GO:1903740","count":12},{"id":"GO:0010867","count":12}]},{"hash":"2128831223751099449","title":"Neuronal signaling and Golgi-to-plasma membrane trafficking","description":"Based on the top GO terms, there is a clear emphasis on neuronal processes (positive regulation of neuron apoptotic process; regulation of long-term neuronal synaptic plasticity) and membrane trafficking from the Golgi to the plasma membrane, suggesting a role in synaptic signaling and surface protein delivery. While some terms are more general or unrelated (e.g., autophagy, copper homeostasis, immune degranulation), the dominant signal points to neuronal regulation linked to protein trafficking to the membrane. Confidence: Medium.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0046909","count":2},{"id":"GO:0043525","count":2},{"id":"GO:0048169","count":2},{"id":"GO:0043001","count":2}]},{"hash":"2274901832979788841","title":"Neuronal vesicle trafficking and development","description":"The terms converge on neural development and neuronal vesicle trafficking: spinal cord development and adult locomotory behavior point to neural function, while ER-Golgi transport and synaptic vesicle budding, plus microtubule-based movement, indicate cellular machinery for vesicle trafficking and transport. Some entries like pigmentation and DNA-templated transcription are less central but may reflect broader cellular functions or annotation noise; overall the cluster seems best described by neuron-specific trafficking and development.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021510","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0043473","count":2}]},{"hash":"1351214788409437517","title":"Autophagy and vesicle trafficking","description":"This cluster is dominated by autophagy-related processes, including CVT (cytoplasm-to-vacuole targeting), piecemeal microautophagy of the nucleus, and mitochondrion autophagy, along with ER-to-Golgi vesicle transport and C-terminal lipidation, suggesting a cohesive theme of autophagy-associated vesicle dynamics and turnover. Some transcription-related terms appear, but they are not central to the main theme. ","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0032258","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0042220","count":3}]},{"hash":"1623118222937224835","title":"Innate Antiviral Immune Response","description":"This cluster is dominated by GO terms tied to antiviral immunity and dsRNA sensing: cellular response to type I interferon, cellular response to exogenous dsRNA, innate immune response, and defense response to virus by host. These indicate functions in recognizing viral components and triggering interferon-mediated defenses. Some terms about plant hormone signaling and chlorophyll biosynthesis are likely noise or cross-species annotations, but the core theme supports antiviral innate immunity.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071357","count":11},{"id":"GO:0050689","count":11},{"id":"GO:0009938","count":11},{"id":"GO:0051301","count":11},{"id":"GO:0071360","count":11}]},{"hash":"1262512497227325427","title":"Nervous system development and signaling","description":"The top GO terms point to neural development and communication, notably CNS projection neuron axonogenesis and dopaminergic synaptic transmission, with supporting terms on neural patterning and calcium-related signaling. While a few terms reference general cellular processes (endosome transport, ionomycin response), the strongest theme is nervous system development and neuronal signaling, justifying this label.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000641","count":1},{"id":"GO:0007124","count":1},{"id":"GO:1901621","count":1},{"id":"GO:1904637","count":1},{"id":"GO:0001963","count":1}]},{"hash":"221400129757944968","title":"Unknown","description":"The terms span a wide range of disparate processes (immune recombination, NF-kB signaling, ubiquitination, Wnt catabolism, NOS regulation, necroptosis, synaptic vesicle transport) with no clear single function or pathway dominating, and there are no interactions among proteins in the cluster. This lack of cohesive theme warrants an Unknown label.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043123","count":1},{"id":"GO:0046621","count":1},{"id":"GO:0033151","count":1},{"id":"GO:0016567","count":1},{"id":"GO:0038018","count":1}]},{"hash":"350866121648350740","title":"Unknown","description":"This cluster's GO terms are highly heterogeneous, spanning glucose stimulus response, fibrinolysis, heat response, angiotensin regulation, ECM secretion, hepatocyte proliferation, deglutamylation, and Purkinje cell differentiation. Only a minority touch on a shared pathway (fibrinolysis/coagulation), while many terms point to unrelated processes, giving no clear, cohesive function to label the cluster beyond Unknown.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071333","count":2},{"id":"GO:0010757","count":1},{"id":"GO:0009408","count":1},{"id":"GO:0002002","count":1},{"id":"GO:0003331","count":1}]},{"hash":"240854341319857603","title":"Nuclear RNA Processing and Ubiquitin Signaling","description":"The terms cluster around nuclear RNA processing and export (splicing, mRNA export, translation initiation) together with ubiquitin-related regulation (polyubiquitination, regulation of ubiquitin ligase activity), plus related processes such as chromatin assembly and cell cycle control. This suggests a theme of nuclear RNA metabolism linked to ubiquitin-mediated protein regulation, with ancillary connections to chromatin dynamics and inflammation. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1904668","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0032933","count":5},{"id":"GO:0046784","count":4},{"id":"GO:2000728","count":4}]},{"hash":"1980781096596467337","title":"Unknown","description":"The top GO terms are diverse, spanning immune regulation, neural signaling, cardiac and epithelial contexts, and tissue development, with no single predominant process tying the proteins together. There are no edges or shared pathways to define a cohesive functional theme, so a specific label isn\u2019t justifiable.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002730","count":1},{"id":"GO:0071642","count":1},{"id":"GO:1903215","count":1},{"id":"GO:1901594","count":1},{"id":"GO:1902499","count":1}]},{"hash":"414845633698788848","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning animal development (nervous system and skeletal muscle development, germinal center formation), plant signaling and metabolism (brassinosteroid signaling, glucosinolate catabolic process), and general cellular processes (Wybutosine biosynthesis, ubiquitin-dependent protein catabolic process, spindle midzone localization, swimming). There isn\u2019t a clear, single unifying function or pathway linking these terms, suggesting the cluster does not reflect a cohesive biological theme.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":1},{"id":"GO:0007519","count":1},{"id":"GO:0019762","count":1},{"id":"GO:0031591","count":1},{"id":"GO:0035853","count":1}]},{"hash":"950226414156056072","title":"Actin Cytoskeleton Regulation and Cell Motility","description":"Most top GO terms cluster around actin cytoskeleton organization and its regulation, including Rac signaling, cell spreading, and cytoskeleton-driven motility. Additional terms touch on cell movement in microglia and locomotion, as well as morphogenesis, suggesting a shared theme of cytoskeletal control of movement and shape rather than a single organ-specific function. This makes \"Actin Cytoskeleton Regulation and Cell Motility\" a representative, specific label for the cluster.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032956","count":1},{"id":"GO:1904140","count":1},{"id":"GO:0031999","count":1},{"id":"GO:1904693","count":1},{"id":"GO:0001865","count":1}]},{"hash":"916506016055307344","title":"Ceramide and glycosphingolipid transport","description":"The Top Terms are dominated by lipid transport and sphingolipid metabolism: glycolipid transport, ceramide transport, glycosphingolipid metabolic process, and ER to Golgi ceramide transport, pointing to a membrane trafficking role for sphingolipids. Other transport terms (ammonium, polyol, organic cation) suggest general transporter activity, while defense-related terms may reflect plant signaling crosstalk with sphingolipid pathways; the histone deubiquitination term appears as an outlier. Overall, a sphingolipid transport/metabolism theme best fits the cluster.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046836","count":1},{"id":"GO:1902389","count":1},{"id":"GO:0006687","count":1},{"id":"GO:0035621","count":1},{"id":"GO:0072488","count":1}]},{"hash":"172795385069801642","title":"Muscle, vascular, and nervous system development","description":"The top GO terms pull from developmental processes across several tissues: sarcomere organization and smooth muscle development (muscle), endothelial tube lumen extension (vasculature), and sympathetic nervous system development (nervous system), plus broader morphogenesis signals like Rho/GTPase signaling. While there isn\u2019t a single tight function, the common theme is developmental morphogenesis across muscle, blood vessels, and neural tissues, with shared signaling pathways guiding remodeling. Confidence: Medium","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070212","count":2},{"id":"GO:0045762","count":2},{"id":"GO:0007264","count":2},{"id":"GO:0045214","count":2},{"id":"GO:0097498","count":2}]},{"hash":"1245215512911896924","title":"Cell division and membrane remodeling","description":"The cluster\u2019s top GO terms cluster around mitotic processes (mitotic cell cycle, cleavage furrow formation) and membrane dynamics (chloride transport, endocytic recycling, plasma membrane tubulation, phosphatidic acid biosynthesis), suggesting proteins involved in cytokinesis and membrane trafficking rather than a single specialized pathway. Some terms (eye development, prospore membrane formation) reflect broader membrane-related processes across contexts, but the dominant signal is division coupled with membrane remodeling.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902476","count":2},{"id":"GO:0051301","count":2},{"id":"GO:1990126","count":1},{"id":"GO:0097320","count":1},{"id":"GO:0000278","count":1}]},{"hash":"2204624956951133923","title":"Innate immune signaling and inflammasome regulation","description":"The cluster centers on immune-regulatory processes, notably canonical NF-kappaB signaling, interferon production regulation, and negative regulation of the NLRP3 inflammasome, with supporting terms related to stress granule localization and protein quality control (ERAD). While some terms (skin development, muscle contraction, host-symbiont interactions) seem peripheral, the dominant Theme is innate immune signaling and cellular stress responses, suggesting a cohesive cluster around immune regulation rather than a single specific pathway.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043123","count":1},{"id":"GO:0043588","count":1},{"id":"GO:0030433","count":1},{"id":"GO:1901896","count":1},{"id":"GO:0006936","count":1}]},{"hash":"563249187643815601","title":"Unknown","description":"There is no enriched GO signal or network connection among the proteins (no edges or triangles, no top terms). Without a common function or process to anchor a label, a meaningful cluster name cannot be assigned.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"975340751684970383","title":"Plant Nuclear Chromatin and Telomere Regulation","description":"The terms cluster around chromatin dynamics and telomere biology (nucleosome assembly, telomeric D-loop disassembly, G-quadruplex DNA formation, H2A deubiquitination), with supporting hints of transcriptional control and osmotic stress responses in plants. Although some GO terms point to cytokinin signaling and cell wall biogenesis, the shared theme is nuclear chromatin maintenance and telomere-related processes in plant cells.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061820","count":2},{"id":"GO:0009736","count":2},{"id":"GO:1901347","count":2},{"id":"GO:0072362","count":2},{"id":"GO:0006334","count":2}]},{"hash":"1356549374575617041","title":"Plant telomere and chromatin regulation","description":"The proteins cluster around nuclear chromatin and telomere-associated processes, including telomeric D-loop disassembly, nucleosome assembly, and G-quadruplex DNA formation, with supporting signals from histone modification/demodification and plant-specific pathways like cytokinin signaling and osmotic stress response. Although the terms span multiple related processes and there are no dense interactions, the overarching theme appears to be plant chromatin maintenance and telomere biology. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061820","count":1},{"id":"GO:0009736","count":1},{"id":"GO:1901347","count":1},{"id":"GO:0072362","count":1},{"id":"GO:0006334","count":1}]},{"hash":"1095308211955476051","title":"Mitotic Regulation via Phosphorylation","description":"The term set centers on cell division control, including mitotic cytokinesis checkpoint signaling, actomyosin contractile ring maturation, and kinetochore localization, as well as modulation of kinase/phosphatase activity (protein dephosphorylation and negative regulation of kinases). These together suggest a core theme of coordinating mitosis and chromosome segregation through phosphorylation dynamics, with a few outliers (immune signaling and habituation) that are less central. ","confidence":"High","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006470","count":7},{"id":"GO:0014850","count":7},{"id":"GO:0039563","count":6},{"id":"GO:0044878","count":6},{"id":"GO:1902406","count":6}]},{"hash":"1967808436341408455","title":"DNA replication and mitotic chromatin assembly","description":"This cluster is dominated by core nuclear processes: DNA replication, CENP-A\u2013containing chromatin assembly, and cell division, along with microtubule severing, all pointing to chromosome maintenance and mitosis. A few terms related to RNA processing or trafficking appear as outliers, which may reflect multifunctional proteins or dataset noise, but the central theme remains genome duplication and chromosome segregation.","confidence":"Medium","size":12,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0035617","count":3},{"id":"GO:0000184","count":3},{"id":"GO:0048568","count":3},{"id":"GO:0061641","count":3}]},{"hash":"1495225059813945977","title":"Neural development and synaptic signaling","description":"The cluster shows strongest enrichment for nervous system development and synaptic functions, with terms like substantia nigra development, excitatory postsynaptic potential, and regulation of synaptic vesicle exocytosis. While there are also general development and cell cycle terms present, the neuronal and synaptic signals dominate, supporting a neural development/synaptic function theme.","confidence":"Medium","size":12,"edges":10,"triangles":3,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0021762","count":4},{"id":"GO:0043931","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0010628","count":3}]},{"hash":"1432344313347694631","title":"LPS Core and ADP-heptose Biosynthesis","description":"The cluster is dominated by GO terms for ADP-L-glycero-beta-D-manno-heptose biosynthesis and lipopolysaccharide biosynthetic processes, pointing to bacterial LPS core assembly; other terms (development, actin, ATP response, phosphorylation) appear as noise but do not change the core LPS signal.","confidence":"Medium","size":12,"edges":27,"triangles":22,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0097171","count":3},{"id":"GO:0048741","count":2},{"id":"GO:0021762","count":2},{"id":"GO:0071318","count":2},{"id":"GO:0016311","count":2}]},{"hash":"1334475992427280916","title":"Mitotic spindle assembly and microtubule nucleation","description":"The top GO terms are dominated by mitosis and microtubule organization (spindle pole body duplication, microtubule nucleation, mitotic cell cycle), indicating a core function in spindle dynamics during cell division. Additional signals include regulation of kinases and GTPases, supporting mitotic control. Some terms touch on other processes, but the central theme remains microtubule-driven mitosis.","confidence":"High","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1903087","count":5},{"id":"GO:0007020","count":5},{"id":"GO:0071456","count":5},{"id":"GO:0051028","count":5},{"id":"GO:0071902","count":5}]},{"hash":"383049204863433724","title":"Neuronal cytoskeleton remodeling and vesicle trafficking","description":"This cluster centers on actin-driven processes like filopodium assembly and substrate adhesion-dependent spreading, driven by small GTPase signaling, which points to cytoskeletal remodeling in neurons. The inclusion of brain development and GABAergic synaptic transmission suggests neuronal differentiation and synaptic function. The vesicle trafficking terms (COPII coating regulation and multivesicular body size) alongside mitochondrial fission reinforce a theme of intracellular transport and organelle dynamics relevant to neurite growth and synaptic activity.","confidence":"High","size":12,"edges":9,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1900026","count":8},{"id":"GO:0051489","count":8},{"id":"GO:0045792","count":8},{"id":"GO:0046847","count":8},{"id":"GO:0051932","count":8}]},{"hash":"1361255165808581653","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0071374","count":7},{"id":"GO:0090084","count":7},{"id":"GO:1901621","count":7},{"id":"GO:0006458","count":7},{"id":"GO:0070843","count":7}]},{"hash":"2199099179304799982","title":"Developmental morphogenesis and apoptotic signaling regulators","description":"This cluster centers on developmental processes (spinal cord, adrenal gland, eye morphogenesis) and regulation of signaling and apoptosis (GTPase activity, extrinsic apoptotic pathways). The mix suggests proteins that modulate development and cell fate through signaling and adhesion dynamics, rather than a single, narrow function. ","confidence":"Medium","size":12,"edges":11,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0021510","count":2},{"id":"GO:0007584","count":2},{"id":"GO:0043547","count":2},{"id":"GO:2000212","count":1},{"id":"GO:0030325","count":1}]},{"hash":"669985022152692349","title":"Unknown","description":"The cluster shows a mix of GO terms spanning membrane transport (sodium and proton), lipid biosynthesis, translation, hormone signaling, and plant/animal development, with no single cohesive function or pathway uniting the terms. Because the terms are heterogeneous and some are even obsolete, there isn\u2019t a clear, representative label that captures a common theme for this group.","confidence":"","size":12,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0035725","count":1},{"id":"GO:0015992","count":1},{"id":"GO:0001576","count":1},{"id":"GO:0002181","count":1},{"id":"GO:0042921","count":1}]},{"hash":"1717265084287238235","title":"Lipids and small-molecule biosynthesis","description":"This cluster is dominated by GO terms for biosynthesis of various small molecules, especially lipids and related cofactors (fatty acid, retinol, fructose, menaquinone biosynthesis) and proteins involved in activating substrates for nonribosomal peptide biosynthesis, suggesting a broad role in lipid and metabolite production rather than a single unified pathway. Some terms like seed coat development or obsolete GO entries may be incidental, but the prevailing theme is lipid and small-molecule biosynthesis. ","confidence":"Medium","size":12,"edges":59,"triangles":158,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006633","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0042572","count":5},{"id":"GO:0046370","count":4},{"id":"GO:1902987","count":3}]},{"hash":"1417363210829915244","title":"Unknown","description":"Top GO terms cover disparate processes, from bone resorption and copper homeostasis to phagosome maturation, Wnt signaling, and oligodendrocyte differentiation, with no clear shared function dominating the cluster. The lack of edges and triangles (edges: 0, triangles: 0) further suggests these proteins do not form a cohesive functional module in this dataset. Because there is no unifying theme, Unknown best represents the cluster.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045453","count":2},{"id":"GO:1903215","count":1},{"id":"GO:0001667","count":1},{"id":"GO:0006878","count":1},{"id":"GO:0043316","count":1}]},{"hash":"1705553837723388020","title":"Neural development and signaling","description":"The cluster includes strong neural-specific terms such as central nervous system projection neuron axonogenesis and dopaminergic synaptic transmission, suggesting roles in neuronal development and synaptic signaling. Endosome transport regulation could further relate to neuronal trafficking, though several non-neural terms appear as well, so the connection is present but not exclusive. Medium","confidence":"Medium","size":12,"edges":35,"triangles":39,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":12},{"id":"GO:0007124","count":12},{"id":"GO:1901621","count":12},{"id":"GO:1904637","count":12},{"id":"GO:0001963","count":12}]},{"hash":"2246220737946804994","title":"Unknown","description":"The terms are highly diverse, including mitotic cell cycle, cell morphogenesis, cadmium response, innate immune response, several biosynthetic and regulatory processes, and even calcium signaling, with no clear shared pathway or cohesive function across the proteins. The absence of edges further suggests the proteins do not cluster around a single identifiable function, so a specific label isn\u2019t supported.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0000902","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0016311","count":1}]},{"hash":"42244343037684797","title":"Ribosome biogenesis and translation","description":"The cluster is dominated by GO terms related to ribosome production and function (translation, ribosome biogenesis, ribosomal subunit biogenesis, rRNA methylation, and RNA processing), indicating a cohesive module for ribosome assembly and protein synthesis. Additional terms addressing the cell cycle and Golgi retention fit with broader links between growth, ribosome production, and trafficking, reinforcing a central theme around ribosome biogenesis and translation.","confidence":"High","size":12,"edges":27,"triangles":40,"max_degree":7,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0042254","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0051260","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1250060357898991806","title":"Mitotic and DNA Damage Response","description":"Based on the top GO terms, the dominant signals point to mitosis (mitotic cell cycle, protein localization to kinetochore, mitotic intra-S DNA damage checkpoint signaling) and DNA repair (DNA double-strand break processing via SDSA). There are also signals of broader stress-related pathways (glucocorticoid signaling, connective tissue regulation, EMT). The core cluster appears to center on cell cycle progression and DNA damage response, with secondary ties to stress signaling. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":1},{"id":"GO:0016311","count":1},{"id":"GO:0010719","count":1},{"id":"GO:0034501","count":1},{"id":"GO:0046086","count":1}]},{"hash":"452043091654648064","title":"Stress-Responsive Signaling and Cell Cycle Regulation","description":"Top GO terms indicate several ligand- and stress-responsive pathways (responses to morphine, glucocorticoid signaling, innate immune response, unfolded protein response, and metal ion response) together with mitotic control mechanisms (APC-dependent catabolic process and metaphase/anaphase transition). This points to a cluster of proteins involved in stress- and signaling responses that interface with cell cycle regulation, rather than a single cohesive pathway.","confidence":"Medium","size":12,"edges":12,"triangles":1,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043278","count":11},{"id":"GO:0006463","count":10},{"id":"GO:2000324","count":10},{"id":"GO:0045087","count":10},{"id":"GO:1903546","count":10}]},{"hash":"1837197596668781958","title":"Post-transcriptional mRNA regulation and stress granules","description":"The top GO terms point to processes that manage mRNA after transcription: splicing regulation, mRNA stability and decay, translation inhibition by miRNA, and localization to cytoplasmic stress granules. These collectively suggest a cluster centered on post-transcriptional control and RNA granule dynamics, with a few development-related terms that may reflect broader roles in maturation and differentiation. ","confidence":"Medium","size":12,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":1},{"id":"GO:0048025","count":1},{"id":"GO:0035278","count":1},{"id":"GO:0001556","count":1},{"id":"GO:0010610","count":1}]},{"hash":"606586175435108220","title":"Chromatin and Telomere Regulation","description":"The top GO terms cluster around chromatin organization (nucleosome assembly, histone deubiquitination) and transcription-related processes (snRNA transcription, G-quadruplex DNA), plus telomere biology (telomere disassembly, protein localization to telomere), suggesting a core theme of chromatin architecture and telomere maintenance. A few terms (mitochondrial translation, plant signaling) appear as outliers or noise, but overall the group points to DNA/RNA metabolism and chromatin regulation.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032543","count":2},{"id":"GO:0061820","count":1},{"id":"GO:0009736","count":1},{"id":"GO:1901347","count":1},{"id":"GO:0072362","count":1}]},{"hash":"545409885667673260","title":"Ribosome Biogenesis and RNA Processing","description":"Based on the GO terms, the cluster is dominated by ribosome biogenesis (GO:0042254 with 3 hits) and accompanying RNA metabolism activities such as RNase MRP-dependent mRNA catabolic process and intronic snoRNA processing. While other terms touch on plant-specific differentiation and various metabolic pathways, the strongest shared function relates to production of ribosomes and processing of RNA in the nucleus/nucleolus, suggesting a nucleolar RNA-processing hub.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0032147","count":2},{"id":"GO:0030261","count":1},{"id":"GO:0000294","count":1},{"id":"GO:0034965","count":1}]},{"hash":"1497061149761458974","title":"RNA processing and translation regulation","description":"Top GO terms cluster around post-transcriptional control: mRNA splicing, polyadenylation, stability, and modification, plus translation initiation and RNA-silencing pathways, indicating involvement in RNA maturation and translation regulation rather than transcriptional control.","confidence":"High","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1900363","count":4},{"id":"GO:0048025","count":4},{"id":"GO:0035278","count":4},{"id":"GO:0010610","count":4},{"id":"GO:0016556","count":4}]},{"hash":"166649578135052261","title":"DNA maintenance and tRNA modification cluster","description":"The terms show primary emphasis on DNA replication, repair, and recombination, with additional signals for translation-related processes and tRNA wobble modification, plus telomere localization and mitotic checkpoint hints. The mix suggests a nuclear maintenance module that couples genome stability with RNA modification/translation readiness. ","confidence":"Medium","size":12,"edges":15,"triangles":10,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0006310","count":1},{"id":"GO:0002101","count":1},{"id":"GO:0072581","count":1},{"id":"GO:0006281","count":1}]},{"hash":"369208530826427155","title":"Cell cycle progression and division","description":"The top GO terms cluster around cell division and cell cycle control, including mitotic phase transitions, meiosis I, proliferation, and regulation of CDK activity, with some transcriptional regulation links. Redox homeostasis and morphogenesis terms appear but do not override the core signal of cell-cycle\u2013related processes. This suggests a coherent theme of growth through division and cycle progression.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0008283","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0045737","count":1},{"id":"GO:0007127","count":1}]},{"hash":"629335558473355345","title":"Mitochondrial energy metabolism and apoptosis in development","description":"The cluster centers on mitochondrial electron transport and apoptotic processes, with additional developmental terms (circulatory and reproductive systems) suggesting a theme of mitochondria-associated energy metabolism and programmed cell death connected to development.","confidence":"Medium","size":12,"edges":39,"triangles":72,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0070584","count":2},{"id":"GO:0072358","count":2},{"id":"GO:0061458","count":2},{"id":"GO:0010259","count":2}]},{"hash":"1421343572838461642","title":"ER-Golgi Trafficking & Wnt Secretion","description":"The cluster is enriched for GO terms related to the secretory pathway, especially ER exit, COPI-coated vesicles, ER lumen retention, and ER-to-Golgi transport, plus positive regulation of Wnt protein secretion. Developmental phenotypes such as axis specification and egg-laying behavior are consistent with Wnt signaling and secretory pathway involvement, making a cohesive theme around ER-Golgi trafficking and protein secretion.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048042","count":2},{"id":"GO:0061357","count":2},{"id":"GO:0002121","count":2},{"id":"GO:0007311","count":2},{"id":"GO:0070863","count":2}]},{"hash":"1375769317755512187","title":"Neurotransmitter biosynthesis and neural signaling","description":"This cluster is driven by terms for monoaminergic neurotransmitter production (norepinephrine, octopamine) and signaling (amphetamine response), along with CNS-associated processes such as myelin maintenance, sodium transport, and glucose homeostasis. Additional broad cellular processes like DNA-templated transcription and nitric oxide catabolism appear but do not outweigh the neural signaling/metabolic theme, suggesting the proteins collectively participate in nervous system signaling and associated metabolism.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046210","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0042421","count":1},{"id":"GO:0071927","count":1},{"id":"GO:0014740","count":1}]},{"hash":"982892781017600988","title":"RNA Processing and Translation Regulation","description":"This cluster centers on gene expression control at multiple RNA-related stages: transcription (DNA-templated transcription), RNA processing and splicing (alternative splicing, regulation of splicing), mRNA stability and modification, miRNA-mediated silencing, and translation initiation/regulation (eIF4F assembly, translation termination-reinitiation). The combination of transcriptional and post-transcriptional mechanisms suggests a cohesive theme of RNA-level regulation of gene expression.","confidence":"High","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:1900363","count":2},{"id":"GO:0048025","count":2},{"id":"GO:0035278","count":2},{"id":"GO:0010610","count":2}]},{"hash":"2230116999069119039","title":"Unknown","description":"The GO terms are a broad mix (mechanical stimulus response, chromatin remodeling, immune signaling, cardiac cell communication, polarity, spindle assembly, protein localization, etc.) with no clear shared function or interaction among the proteins, and the cluster has no edges, suggesting no cohesive biological theme. ","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":3},{"id":"GO:0043044","count":2},{"id":"GO:0071642","count":2},{"id":"GO:1901594","count":2},{"id":"GO:0086070","count":2}]},{"hash":"1210147855861373228","title":"Ubiquitin-Dependent Protein Degradation","description":"This cluster centers on ubiquitin-related protein turnover, including ubiquitin-dependent protein catabolic process, K48- and K6-linked ubiquitination, autoubiquitination, histone degradation, ERAD, and Wnt receptor catabolism, indicating a concerted role in tagging substrates for ubiquitin-proteasome\u2013mediated degradation.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:0051865","count":6},{"id":"GO:0070936","count":6},{"id":"GO:0036205","count":5},{"id":"GO:1903265","count":5}]},{"hash":"2123172298025762007","title":"Potassium-Driven Membrane Potential Regulation","description":"These proteins cluster around the regulation and stabilization of membrane potential, particularly via potassium ion transport and K+ homeostasis, which underlie membrane excitability in neurons and cardiac tissue. The presence of mechanosensory and repolarization terms supports a common theme of ion-channel/transport\u2013driven excitability, with a few outlier terms likely due to broad or pleiotropic annotations. ","confidence":"High","size":12,"edges":40,"triangles":58,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0030322","count":3},{"id":"GO:0060075","count":3},{"id":"GO:0050976","count":3},{"id":"GO:0071805","count":3},{"id":"GO:0098914","count":3}]},{"hash":"320577390420179667","title":"Pain and Thermosensation Ion Channel Pathway","description":"The cluster is enriched for GO terms linked to sensory pain perception and thermosensory behavior, plus ion transport across membranes and a caspazepine-related response, pointing to involvement of ion channels (likely TRP family) in nociception and heat sensing. The presence of cytokine/chemokine production terms suggests additional immune signaling ties in, while development and metabolism terms reflect broader physiological roles. Overall, the dominant theme is pain/thermal sensing mediated by ion channel activity.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019233","count":4},{"id":"GO:1990573","count":4},{"id":"GO:0097623","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0071642","count":3}]},{"hash":"355484765175597523","title":"Mitotic progression and ubiquitin signaling","description":"Cluster centers on cell division and ubiquitin-mediated regulation: GO terms include cell division, APC/C-dependent catabolic process, CENP-A chromatin assembly, regulation of cell cycle checkpoint, and protein polyubiquitination/positive regulation of ubiquitin ligase activity. Minor associations to mRNA processing and heat-stress responses suggest nuclear regulation but do not outweigh the core mitotic theme.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0031145","count":3},{"id":"GO:2000728","count":2},{"id":"GO:1904668","count":2},{"id":"GO:0000398","count":2}]},{"hash":"1537670702306303488","title":"Unknown","description":"The GO terms span steroid hormone receptor signaling, immune response, photoreceptor localization, metal ion response, protein modification regulation, and cell cycle/mitotic transitions, with no single clear mechanism tying all proteins together. Therefore there isn\u2019t a confident, representative label for this cluster.","confidence":"","size":12,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006463","count":8},{"id":"GO:2000324","count":8},{"id":"GO:0045087","count":8},{"id":"GO:1903546","count":8},{"id":"GO:0031400","count":8}]},{"hash":"672101934240821269","title":"Antibiotic and steroid-lipid-pigment biosynthesis","description":"Top GO terms show biosynthesis of antibiotics, steroid hormones (androgen, testosterone), sphingolipids, phylloquinone, and melanin, with an additional transcription regulation term. This pattern points to a cluster enriched for diverse metabolite biosynthesis rather than a single, cohesive function, spanning antibiotic, steroid/lipid, and pigment pathways. The label reflects the broad biosynthetic theme tying these terms together, though the specific enzymes may participate in multiple pathways. ","confidence":"Medium","size":12,"edges":3,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0008207","count":3},{"id":"GO:0042376","count":3}]},{"hash":"2156452690888898572","title":"ECM Remodeling and Tissue Morphogenesis","description":"These terms center on extracellular matrix remodeling and tissue morphogenesis: collagen and basement membrane degradation, bone resorption and ossification, and branching or decidualization processes, with related catalytic regulation and immune interactions. Together they point to ECM-driven remodeling guiding development and tissue remodeling.","confidence":"High","size":12,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0010813","count":8},{"id":"GO:0045453","count":8},{"id":"GO:0001957","count":8},{"id":"GO:0030574","count":8},{"id":"GO:0046697","count":8}]},{"hash":"679898090248981079","title":"Unknown","description":"The top GO terms span diverse processes (ERK cascade regulation, apoptosis, vision, glutamatergic transmission, endosome transport, and even pseudohyphal growth), with no single unifying function apparent. The absence of edges/triangles also suggests these proteins do not form a cohesive functional module, so there is no clear, representative label beyond Unknown.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070374","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0007601","count":3},{"id":"GO:0035249","count":3},{"id":"GO:0032092","count":3}]},{"hash":"1037301963329122554","title":"Ubiquitin-Dependent Signaling and Death Regulation","description":"The cluster centers on ubiquitin-related regulations (protein autoubiquitination and K48-linked ubiquitination) and TNF signaling with necroptosis regulation, pointing to a module of proteins that modulate signaling and cell fate via ubiquitin pathways. A few terms about histone catabolic process and growth regulation may reflect broader chromatin and growth-control roles tied to ubiquitin signaling. Therefore, a concise label capturing ubiquitin-mediated signaling and survival control fits best.","confidence":"Medium","size":12,"edges":32,"triangles":28,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0009395","count":2},{"id":"GO:0046621","count":1},{"id":"GO:0051865","count":1},{"id":"GO:0060546","count":1},{"id":"GO:0048078","count":1}]},{"hash":"2139030816383304428","title":"Mitochondrial redox stress response and antioxidant biosynthesis","description":"The cluster\u2019s GO terms point to mitochondrial stress regulation (mitochondrial depolarization, apoptotic mitochondrial changes) and antioxidant systems (glutathione biosynthesis/transport, L-ascorbic acid metabolism) along with detox responses to metals (cadmium, phytochelatin). This pattern suggests a cohesive theme of maintaining redox homeostasis and protecting mitochondria under stress, rather than a single, narrow function.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051900","count":1},{"id":"GO:0071372","count":1},{"id":"GO:0046938","count":1},{"id":"GO:0046686","count":1},{"id":"GO:0019852","count":1}]},{"hash":"2121904922082550506","title":"Energy metabolism and vacuolar function","description":"The top GO terms cluster around energy production and vacuolar processes: proton transmembrane transport, proton motive force-driven ATP synthesis, and vacuolar acidification, plus catabolic steps for NAD+, CoA, and dADP. This points to a cohesive theme of cellular energy metabolism and vacuolar function. A couple of terms (notochord vacuolation, caudal fin development) are developmental contexts that may reflect tissue-specific roles or annotation noise, but do not override the dominant metabolic signal.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060036","count":1},{"id":"GO:0015991","count":1},{"id":"GO:0007035","count":1},{"id":"GO:0033336","count":1},{"id":"GO:0042777","count":1}]},{"hash":"1859338667395243206","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":2},{"id":"GO:0000027","count":1},{"id":"GO:1990417","count":1},{"id":"GO:0010501","count":1},{"id":"GO:1902626","count":1}]},{"hash":"1313254539427771184","title":"Sperm flagellum axoneme formation and motility","description":"The top GO terms cluster around cilium/axoneme formation, sperm-specific motility, and tubulin modifications (polyglycylation, polyglutamylation) with microtubule severing. This combination points to proteins involved in assembling and powering the sperm flagellum/axoneme, rather than general ciliary functions, justifying a focused label on flagellum formation and motility.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003353","count":2},{"id":"GO:0030516","count":2},{"id":"GO:0018094","count":2},{"id":"GO:0018095","count":2},{"id":"GO:0007288","count":2}]},{"hash":"171178160082677449","title":"Xenobiotic and oxidative stress response","description":"Based on the prominent GO terms, the cluster is enriched for responses to various xenobiotics (curcumin, catechin, mercury) and for oxidant detoxification, suggesting a chemical-stress and detoxification function. A few terms (ER protein folding, cell adhesion) are less central and may be incidental, but the dominant signature points to chemical stress response. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904643","count":2},{"id":"GO:0007155","count":2},{"id":"GO:0046689","count":2},{"id":"GO:1902168","count":2},{"id":"GO:1903206","count":1}]},{"hash":"2119513096941970690","title":"Nuclear RNA processing and cell cycle machinery","description":"The top GO terms cluster around nuclear functions: mRNA splicing, mRNA export, ribosome biogenesis, and CENP-A\u2013mediated chromatin assembly, all linked to cell division. While there are some stress-response notes ( ER stress\u2013related apoptosis, ubiquitin ligase regulation), the dominant theme is nuclear gene expression and cell cycle regulation, suggesting these proteins function together in coordinating transcriptional/RNA processing with chromatin dynamics during division.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051260","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0070059","count":4},{"id":"GO:0000747","count":4},{"id":"GO:0050679","count":4}]},{"hash":"943343181128713178","title":"Telomere-Chromatin Regulation","description":"The top GO terms cluster around telomere biology (telomeric D-loop disassembly; establishment of protein localization to telomere) and chromatin organization (nucleosome assembly, histone H2A deubiquitination) with DNA structure elements (G-quadruplex formation) and transcription-related processes (snRNA transcription). Plant-specific signals (cytokinin signaling) and osmotic stress response may reflect regulation of gene expression via chromatin changes in stress conditions. Overall, the cluster seems best described by chromatin remodeling and telomere maintenance themes rather than a single linear pathway.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061820","count":2},{"id":"GO:0009736","count":2},{"id":"GO:1901347","count":2},{"id":"GO:0072362","count":2},{"id":"GO:0006334","count":2}]},{"hash":"1147325465823456726","title":"Plant hormone signaling and stress response","description":"This cluster centers on plant signaling and development, with multiple terms for ethylene and cytokinin signaling, secondary growth, and regulation of transcription, plus stress-related responses like xenobiotic stimulus and proteolysis. While some terms (chemotaxis, response to cocaine) are less plant-specific and could reflect annotation noise, the core pattern points to plant hormone signaling driving growth and defense.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006508","count":4},{"id":"GO:0035690","count":4},{"id":"GO:0010105","count":3},{"id":"GO:0006935","count":3},{"id":"GO:0000160","count":3}]},{"hash":"1610237549474643701","title":"Mitochondrial Function and Neuromuscular Processes","description":"The top GO terms point to mitochondrial biology (cristae formation, mitochondrial membrane protein insertion, and regulation of mitochondrial translation, plus mitochondrial morphogenesis and lipid metabolism) and neuromuscular/musculoskeletal movement, suggesting the proteins function in mitochondria to support muscle/nerve activity. A couple of terms are obsolete or unrelated (e.g., regulation of buoyancy), likely annotation noise. Overall, the cluster appears centered on mitochondrial roles tied to neuromuscular function.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050881","count":1},{"id":"GO:0070584","count":1},{"id":"GO:0031413","count":1},{"id":"GO:0019216","count":1},{"id":"GO:0050905","count":1}]},{"hash":"518372389453142497","title":"Hepatic remodeling and fibrinolysis","description":"Based on the top GO terms, there is a hepatic signal in the cluster: liver regeneration and regulation of hepatocyte proliferation, coupled with fibrinolysis and regulation of ECM secretion, suggesting liver tissue remodeling and coagulation-related processes. However, several terms (deglutamylation and Purkinje cell differentiation) are unrelated to liver biology, so the connection is imperfect and the overall theme is only moderately supported.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097421","count":2},{"id":"GO:0010757","count":1},{"id":"GO:0009408","count":1},{"id":"GO:0002002","count":1},{"id":"GO:0003331","count":1}]},{"hash":"484502010500108460","title":"Cytokine and NO-mediated signaling","description":"Top GO terms cluster around cytokine production (IL-6, IL-8), nitric oxide signaling and related post-translational modifications, and hormonal responses (FSH stimulus), with additional metabolic terms. This suggests a shared theme of signal transduction across immune, hormonal, and neuronal NO pathways, justifying a label focused on cytokine and NO signaling as representative of the cluster\u2019s function.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014740","count":4},{"id":"GO:0072604","count":4},{"id":"GO:0006814","count":4},{"id":"GO:0071372","count":4},{"id":"GO:0010124","count":4}]},{"hash":"2104670794663702410","title":"ER-Golgi trafficking and developmental fate specification","description":"The top terms point to ER-to-Golgi vesicle transport, unfolded protein response, and maturation/localization of proteins, suggesting a core of trafficking and protein processing functions. Additional terms about wing/eye cell fate specification and epithelial-mesenchymal transition regulation hint at regulatory roles in development. Together, the cluster seems to combine ER-Golgi transport with developmental differentiation themes.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0042676","count":1},{"id":"GO:0034620","count":1},{"id":"GO:0032815","count":1},{"id":"GO:0038005","count":1}]},{"hash":"506834481902286202","title":"Regulation of apoptosis, necroptosis, and immune signaling","description":"Top GO terms point to suppression/control of apoptotic and necroptotic pathways, ubiquitination, and modulation of TLR signaling, with notes on transcriptional and cell-cycle regulation. Together these terms suggest a cluster of regulatory proteins balancing cell death and innate immune responses.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060544","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0043066","count":1},{"id":"GO:0000209","count":1},{"id":"GO:0034121","count":1}]},{"hash":"1334898181858043928","title":"Golgi\u2013endosome vesicle transport","description":"This cluster centers on intracellular vesicle trafficking, especially routes between the plasma membrane, endosomes, and the Golgi (recycling/retrograde transport and COPII cargo loading). While there are a couple of regulatory terms (Rab/Rap signaling and a cell-cycle/kinase activity term), the dominant signal is vesicle transport within the Golgi\u2013endosome network.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048227","count":1},{"id":"GO:0071955","count":1},{"id":"GO:0006886","count":1},{"id":"GO:0035526","count":1},{"id":"GO:0034499","count":1}]},{"hash":"2094724264839096909","title":"Centrosome and Cilium Organization","description":"The GO terms point to centrosome/ciliary functions\u2014centrosome cycle, microtubule anchoring at spindle pole bodies, and intraciliary transport for cilium assembly\u2014suggesting a common theme of centrosomal and ciliary microtubule organization, despite no observed protein connections in this cluster.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990810","count":1},{"id":"GO:0007098","count":1},{"id":"GO:0035020","count":1},{"id":"GO:0035735","count":1}]},{"hash":"380631374050442767","title":"Drosophila Neuroblast Development and Spindle Localization","description":"Most terms point to neural and germline development with a focus on cell division machinery: neuroblast division and proliferation, germarium oocyte differentiation, astral microtubule nucleation, and spindle localization. The cluster appears to group proteins involved in microtubule-based processes and developmental regulation in Drosophila, hence this label.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021873","count":1},{"id":"GO:0030706","count":1},{"id":"GO:0030954","count":1},{"id":"GO:0070972","count":1},{"id":"GO:0006987","count":1}]},{"hash":"1597862823278465221","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033615","count":1},{"id":"GO:0000294","count":1},{"id":"GO:0001682","count":1},{"id":"GO:0034965","count":1},{"id":"GO:0000447","count":1}]},{"hash":"27154330301834430","title":"ECM Remodeling and Adhesion Signaling","description":"The cluster's top GO terms cluster around extracellular matrix disassembly, regulation of adhesion molecule production, and PKC signaling, indicating a shared theme of ECM remodeling and cell\u2013matrix/adhesion signaling. Other terms (podocyte development, ERAD) are less tightly connected, adding noise but not overriding the core ECM/adhesion theme. Confidence is moderate given partial cohesion across terms.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045541","count":2},{"id":"GO:0052547","count":2},{"id":"GO:0070528","count":2},{"id":"GO:0022617","count":2},{"id":"GO:0060355","count":2}]},{"hash":"1362539488157056889","title":"Heart calcium signaling and nephron development","description":"The top terms point to two cohesive themes: calcium handling and contraction in cardiac muscle (positive regulation of release of sequestered calcium into cytosol; positive regulation of the force of heart contraction; cardiac myofibril assembly) and development of renal structures (metanephric connecting tubule, collecting duct, and distal convoluted tubule development). Together, they suggest a cluster of proteins involved in organ-specific calcium signaling and development, spanning heart function and kidney nephrogenesis.","confidence":"Medium","size":11,"edges":35,"triangles":54,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0055003","count":6},{"id":"GO:0072286","count":6},{"id":"GO:0051281","count":6},{"id":"GO:0042994","count":6},{"id":"GO:0042554","count":6}]},{"hash":"945833742469256918","title":"ER Protein Folding and Quality Control","description":"Most top GO terms point to endoplasmic reticulum (ER) processes involved in protein folding and quality control, including protein folding in the ER, ER-associated degradation (ubiquitin-dependent ERAD), response to unfolded protein, and chaperone-assisted refolding. Additional terms related to translocation into membranes and redox homeostasis in the ER support a cohesive theme of ER protein maturation and surveillance. A distant term (DNA replication) may be incidental noise rather than representative of the cluster.","confidence":"High","size":11,"edges":6,"triangles":1,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0090084","count":4},{"id":"GO:0031204","count":4},{"id":"GO:1900035","count":4},{"id":"GO:0070389","count":4}]},{"hash":"1553161318664950583","title":"Multisystem developmental signaling","description":"The GO terms point to regulation of signaling and developmental processes across multiple tissues, including neural development (axonogenesis, neural tube patterning), neurotransmission (dopaminergic synapse), immune differentiation (NK T cells), cartilage formation, and regulation of key signaling pathways (p53-mediated signaling, calcium-related responses). The common thread is coordination of signaling and differentiation across diverse cell types rather than a single tissue-specific function.","confidence":"Medium","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":11},{"id":"GO:0007124","count":11},{"id":"GO:1901621","count":11},{"id":"GO:1904637","count":11},{"id":"GO:0001963","count":11}]},{"hash":"2205422509826070441","title":"Unknown","description":"The GO terms span disparate processes (nuclear export, visual perception, mitotic cell cycle, endosome transport, fungal growth, Hedgehog pathway regulation, calcium response, dopaminergic synaptic transmission, p53 signaling, and NK T cell differentiation), with no single unifying function tying the cluster together.","confidence":"","size":11,"edges":39,"triangles":69,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046827","count":10},{"id":"GO:0007601","count":9},{"id":"GO:0000278","count":9},{"id":"GO:2000641","count":8},{"id":"GO:0007124","count":8}]},{"hash":"2065337015929978290","title":"Germ cell differentiation and vesicle exocytosis regulation","description":"This cluster is dominated by germ cell development terms (spermatid nucleus differentiation; negative regulation of male germ cell proliferation) and vesicle trafficking/exocytosis terms (positive regulation of calcium-dependent exocytosis; synaptic vesicle budding), suggesting a cohesive theme around germ cell maturation coupled with vesicle trafficking. The redox and polarity terms are present but less central, so the core idea centers on differentiation paired with vesicle processes.","confidence":"Medium","size":11,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007289","count":3},{"id":"GO:2000255","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0002674","count":2}]},{"hash":"695168875825046263","title":"Calcium-dependent signaling and vesicle trafficking","description":"The top GO terms highlight calcium ion response, neurotransmitter secretion, and regulation of synaptic vesicle exocytosis, all of which point to calcium-driven signaling and vesicle trafficking. Additional terms such as phosphatidylinositol signaling and long-term potentiation reinforce this membrane- and signaling-centric theme. Some terms (myoblast fusion, VEGF signaling, abscisic acid signaling) reflect broader or cross-species annotations, but the core pattern favors calcium-mediated signaling and vesicle handling as the unifying function of this cluster.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071277","count":2},{"id":"GO:0007520","count":2},{"id":"GO:0007269","count":2},{"id":"GO:0036324","count":2},{"id":"GO:0009738","count":2}]},{"hash":"890144255419065671","title":"Unknown","description":"The terms span DNA repair regulation, metal stress responses (cadmium, arsenite), transcription, cell-cycle checkpoints, and unrelated processes like pseudohyphal growth and endosome transport, with no clear shared function linking all proteins; thus a cohesive label is not evident. ","confidence":"","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:2001033","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0006351","count":3},{"id":"GO:1903936","count":3},{"id":"GO:0071374","count":2}]},{"hash":"2012965668594233951","title":"Unknown","description":"The terms are a heterogeneous mix, including plant-specific cytokinin signaling and chlorophyll biosynthesis, along with animal-related interferon response and many obsolete GO terms, providing no single coherent functional theme for the cluster. Edge structure also shows very little connectivity, supporting an Unknown label.","confidence":"","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0009736","count":5},{"id":"GO:0000278","count":5},{"id":"GO:1902325","count":5},{"id":"GO:1903071","count":5},{"id":"GO:2001162","count":5}]},{"hash":"1176428776436094262","title":"Nutrient-Sensing Growth Regulation","description":"The cluster centers on cellular responses to metabolic status, with enrichment for transcription, glucose metabolism, and amino acid starvation, along with regulation of TORC1 signaling, cell size, and apoptosis. This points to coordinated growth control and metabolic adaptation under nutrient stress; a few terms (e.g., placenta development) may reflect annotation noise rather than core function. ","confidence":"Medium","size":11,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0046827","count":7},{"id":"GO:0045793","count":7},{"id":"GO:0034198","count":7},{"id":"GO:0001890","count":7}]},{"hash":"1177328256676911676","title":"Actin-driven morphogenesis and cytoskeletal remodeling","description":"Top GO terms point to actin dynamics (actin sequestration, formin-nucleated cables, thin filament assembly) and developmental morphogenesis (histoblast morphogenesis, neural tube closure, salivary gland morphogenesis), suggesting a shared function in actin-mediated tissue shaping during development. While transcription regulation terms appear, the dominant signal is cytoskeletal remodeling during morphogenesis.","confidence":"High","size":11,"edges":7,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0045944","count":3},{"id":"GO:0048709","count":3},{"id":"GO:0007488","count":2},{"id":"GO:0071689","count":2},{"id":"GO:0042989","count":2}]},{"hash":"2289240839219871873","title":"Translation initiation and Golgi vesicle trafficking","description":"The cluster is strongly enriched for translation initiation terms, including formation of the translation preinitiation complex, translational initiation, and regulation of translational initiation, suggesting a core role in starting protein synthesis. It also includes Golgi-centered trafficking terms (Golgi organization, intra-Golgi vesicle-mediated transport) and general protein transport, indicating a link to intracellular trafficking alongside translation-related functions. Some dsRNA transport and viral translation reinitiation terms may reflect broader RNA handling contexts, but the dominant signal points to initiation of translation with associated trafficking processes.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0010569","count":1},{"id":"GO:2000002","count":1},{"id":"GO:0006446","count":1},{"id":"GO:0006413","count":1}]},{"hash":"673652868969115559","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000154","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0016126","count":2},{"id":"GO:0032120","count":2},{"id":"GO:0000244","count":1}]},{"hash":"355181639464589371","title":"Ribosome Biogenesis and RNA Processing","description":"The strongest signals are SSU rRNA maturation and ribosome biogenesis, with additional RNA processing activities (mRNA splicing and export) and chromatin assembly, suggesting a nuclear/nucleolar cluster focused on ribosome production and RNA metabolism. Secondary terms related to ubiquitin signaling, cell cycle regulation, and stress responses may reflect regulatory layers, but the core theme centers on ribosome biogenesis and RNA processing.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000462","count":3},{"id":"GO:0042254","count":3},{"id":"GO:2000728","count":2},{"id":"GO:1904668","count":2},{"id":"GO:0000398","count":2}]},{"hash":"731890001555904193","title":"Developmental signaling and calcium regulation","description":"The top GO terms suggest involvement in signaling and development across different tissues (cardiac muscle structure, cuticle development, metanephric tubule development) alongside general signaling activities (calcium ion release regulation, protein kinase activity regulation, nuclear import) and ROS generation. Although several terms are organism- or process-specific or obsolete, the common thread appears to be signaling and developmental regulation, with calcium signaling and kinase modulation as central themes. This makes a label centered on developmental signaling with calcium regulation a reasonable, cohesive summary of the cluster.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055003","count":2},{"id":"GO:0097274","count":2},{"id":"GO:0008365","count":2},{"id":"GO:1905205","count":2},{"id":"GO:0072286","count":2}]},{"hash":"1818073388581685825","title":"Unknown","description":"The top GO terms span diverse organisms and processes (plant hormone signaling and development; animal neuroblast polarity, hypoxia response, and lung development; and even a glucocorticoid signaling term), with only a single edge and no clear shared function. This suggests the proteins do not form a cohesive functional cluster, so the label Unknown is appropriate. ","confidence":"","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042921","count":1},{"id":"GO:0045201","count":1},{"id":"GO:2000012","count":1},{"id":"GO:0043947","count":1},{"id":"GO:2000299","count":1}]},{"hash":"1309965708791286489","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by GO terms for rRNA maturation (SSU/LSU/5.8S), ribosomal large subunit biogenesis, and core translation processes (translation, initiation, termination), pointing to proteins involved in assembling and functioning of the ribosome and protein synthesis. A couple of mRNA decay terms linked to translation further support a link to translation-associated quality control. ","confidence":"High","size":11,"edges":46,"triangles":104,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0000463","count":6},{"id":"GO:0000466","count":5},{"id":"GO:0000462","count":5},{"id":"GO:0042273","count":4}]},{"hash":"986793319947292733","title":"Ubiquitin-dependent proteostasis and mRNA processing","description":"This cluster shows a clear enrichment for ubiquitin-related functions (ubiquitin-dependent proteolysis, deubiquitination, and related processes) and RNA processing events (mRNA processing and cytoplasmic processing body assembly). While some terms touch on stress responses (ERAD, necroptosis-related assembly), the dominant theme ties protein turnover via ubiquitin pathways with RNA regulation, supporting a cohesive label around ubiquitin-mediated proteostasis and RNA processing.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070537","count":1},{"id":"GO:0006397","count":1},{"id":"GO:0008583","count":1},{"id":"GO:1900425","count":1},{"id":"GO:0035871","count":1}]},{"hash":"770759270550917828","title":"Oxidative Stress and Metabolic Response","description":"The terms include cellular responses to antioxidants (vitamin E, ascorbic acid), fatty acids, growth factor stimuli, and apoptosis, along with pathways related to aerobic respiration and hemoglobin metabolism. Together they suggest a general oxidative stress\u2013related metabolic response rather than a single specific function.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071363","count":3},{"id":"GO:0033197","count":3},{"id":"GO:0051092","count":3},{"id":"GO:0006915","count":2},{"id":"GO:0009060","count":2}]},{"hash":"1451980968426728399","title":"Redox Metabolism and Nitrosative Stress","description":"The cluster is enriched for oxidation-reduction processes, nitrosative stress response, and related metabolic activities (retinol and prostaglandin metabolism, NADH-related oxidation, and peptidyl-cysteine S-nitrosylation). The recurring signals of redox chemistry and nitrosative signaling, alongside a mix of metabolism terms, suggest a cohesive theme around redox regulation and stress response. Some terms are obsolete, but the core connection remains redox/nitrosative biology.","confidence":"Medium","size":11,"edges":35,"triangles":59,"max_degree":8,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0042572","count":5},{"id":"GO:0019595","count":3},{"id":"GO:0006693","count":3},{"id":"GO:0046688","count":3}]},{"hash":"1714296537893445631","title":"Steroid hormone biosynthesis and metabolism","description":"This cluster is dominated by GO terms related to steroid hormone production and processing, including C21-steroid hormone metabolic process, androgen metabolic process, testosterone biosynthetic process, and estrogen biosynthetic process. While other biosynthetic terms (melanin, sphingolipid) appear, the strongest and most coherent theme is steroid hormone biosynthesis and metabolism, suggesting the proteins share involvement in steroid-related lipid metabolism. Confidence: High","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0008207","count":3},{"id":"GO:0042376","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0008209","count":3},{"id":"GO:0061370","count":3}]},{"hash":"819733262253624707","title":"Ribosome Biogenesis and Translation","description":"The top GO terms cluster around translation (cytoplasmic translation), ribosome biogenesis and subunit assembly, and rRNA maturation, indicating proteins involved in ribosome production and function; an antibiotic response term adds a minor reflection of ribosome-targeting stress, reinforcing the ribosome-centric theme.","confidence":"High","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0042254","count":4},{"id":"GO:0002181","count":3},{"id":"GO:0042274","count":3},{"id":"GO:0046677","count":3}]},{"hash":"207166222072030357","title":"Unknown","description":"The terms span RNA processing (tRNA modification, ribosomal subunit export) and various trafficking/development processes (synaptic vesicle budding, endosome/lysosome transport, Golgi transport, epithelial polarity, spermatid differentiation), with little overlap and no connecting edges among proteins. Because there isn\u2019t a single coherent function tying the cluster together, a specific label cannot be reliably assigned.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006400","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0045956","count":1},{"id":"GO:0090162","count":1},{"id":"GO:0070142","count":1}]},{"hash":"1420453805064710749","title":"Telomere-Chromatin Regulation","description":"The cluster\u2019s terms cluster around telomere biology (telomeric D-loop disassembly, telomere protein localization), nucleosome assembly, and chromatin-associated processes (G-quadruplex DNA, histone ubiquitination/deubiquitination) plus transcription-related activity, suggesting a core theme of telomere maintenance and chromatin regulation. Some plant-specific signals (cytokinin signaling, secondary cell wall biogenesis) and osmotic stress appear as auxiliary signals that can influence transcription/chromatin dynamics, but they are weaker in this set. Overall, the dominant theme is telomere- and chromatin-related regulation with a stress-response overlay.","confidence":"Medium","size":11,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0061820","count":1},{"id":"GO:0009736","count":1},{"id":"GO:1901347","count":1},{"id":"GO:0072362","count":1},{"id":"GO:0006334","count":1}]},{"hash":"1844109934903422382","title":"Regulated excitatory synaptic transmission and vesicle trafficking","description":"The cluster centers on synaptic function, with terms for excitatory postsynaptic potential regulation, synaptic vesicle docking, spontaneous neurotransmitter secretion, and receptor localization to synapse, plus Golgi-associated trafficking, indicating a cohesive theme around neurotransmission and vesicle/membrane trafficking at the synapse. Some outlier terms (immune signaling, sphingolipid metabolism) exist but do not override the dominant neuronal theme.","confidence":"High","size":11,"edges":26,"triangles":25,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:2000463","count":5},{"id":"GO:0010811","count":5},{"id":"GO:0016081","count":5},{"id":"GO:0061669","count":5},{"id":"GO:0006896","count":5}]},{"hash":"1503032172373725579","title":"Plant Hormone Signaling and Transcription","description":"Top GO terms indicate plant hormone signaling (cytokinin-activated pathway; ABA response) together with transcription-related activities (DNA-templated transcription, snRNA transcription) and chromatin dynamics (nucleosome assembly, G-quadruplex DNA formation). This suggests a cluster of proteins involved in hormone-responsive transcription and chromatin regulation. Some terms like liver regeneration and telomeric D-loop disassembly are broad or cross-species annotations and do not undermine the apparent theme.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009736","count":4},{"id":"GO:0009737","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0097421","count":3},{"id":"GO:0061820","count":3}]},{"hash":"816995235469674452","title":"Cell cycle and chromatin regulation","description":"The GO terms center on regulation of CDK activity, nucleosome assembly/disassembly, and histone acetylation, combined with transcriptional control and stem cell division, indicating a theme of coordinating chromatin state with cell-cycle\u2013linked gene expression.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045737","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0015031","count":1},{"id":"GO:0006337","count":1},{"id":"GO:0006334","count":1}]},{"hash":"113814955557439246","title":"Chromatin Remodeling and Transcription Regulation","description":"The top GO terms cluster around chromatin remodeling (GO:0043044), regulation of transcription via RNA Pol II (GO:0010880, GO:0006369), histone modification (GO:0036124), and DNA methylation regulation (GO:0044030), with supporting signals for transcription start site selection. This points to a shared function in regulating chromatin state and transcription. A few terms (olfactory nerve development, growth hormone secretion, gamma radiation response) appear less connected and may be broader or indirect associations, but the dominant theme is chromatin and transcription control.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0043044","count":8},{"id":"GO:0010880","count":5},{"id":"GO:0001178","count":5},{"id":"GO:0021553","count":5},{"id":"GO:2001229","count":5}]},{"hash":"63377890521444286","title":"ER Proteostasis and Stress Response","description":"The cluster is enriched for endoplasmic reticulum\u2013associated proteostasis processes (unfolded protein response, ERAD, aggresome assembly, ubiquitin-related pathways, protein homooligomerization) and intersects with transcriptional regulation and stress responses (DNA-templated transcription, transcription elongation, gamma radiation response). This combination suggests a module centered on ER proteostasis coupled to stress-induced transcriptional changes. ","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0030968","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0071480","count":2}]},{"hash":"1405787866402107476","title":"Membrane Potential Regulation and Ion Transport","description":"Most terms refer to ion movement and membrane potential: potassium and sodium transport, resting potential regulation, and membrane repolarization. The touch sensation term suggests mechanosensitive ion channels, while cAMP/cGMP responses relate to channel regulation. Together, they define a cluster of ion transporters and channels governing membrane excitability.","confidence":"High","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030322","count":11},{"id":"GO:0060075","count":11},{"id":"GO:0050976","count":11},{"id":"GO:0071805","count":11},{"id":"GO:0098914","count":11}]},{"hash":"1207000456244835350","title":"Unknown","description":"The top GO terms are broad and scattered across development, cell cycle, transcription, signaling, and trafficking with no clear common function. With zero edges and no cohesive theme, there isn\u2019t a single representative label for this cluster.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007507","count":3},{"id":"GO:0051298","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006397","count":3},{"id":"GO:0050853","count":3}]},{"hash":"1898630177605894488","title":"Nuclear RNA processing and export","description":"This cluster is best described by RNA processing and export: spliceosome-related conformational changes, nuclear envelope organization, and mRNA export dominate the GO terms, suggesting a role in RNA maturation and transport across the nucleus, with lipid-related terms likely reflecting membrane-associated functions that accompany these processes.","confidence":"High","size":11,"edges":30,"triangles":35,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0000388","count":2},{"id":"GO:0006998","count":2},{"id":"GO:0055088","count":2},{"id":"GO:0006406","count":2},{"id":"GO:0031642","count":1}]},{"hash":"636169732861806920","title":"Mitotic spindle assembly and centrosome dynamics","description":"The cluster is enriched for GO terms related to spindle and microtubule dynamics, including mitotic spindle organization, spindle assembly, centrosome duplication, astral microtubule anchoring, and microtubule nucleation, as well as the meiotic cell cycle. These collectively point to a core function in spindle formation and centrosome regulation during cell division. A couple of terms about transcription or mRNA localization appear less central but do not override the dominant theme. ","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0045450","count":1},{"id":"GO:0030472","count":1},{"id":"GO:0071963","count":1},{"id":"GO:0090307","count":1}]},{"hash":"1114794300422766022","title":"Ribosome biogenesis and cell cycle machinery","description":"The top GO terms cluster around ribosome biogenesis and assembly, pre-replicative complex assembly for DNA replication, and mitotic nuclear membrane reassembly, pointing to core cell growth and division processes. While there are a few developmental or regulatory terms (Pol III transcription, phosphorylation, docking, endothelial proliferation, morphogenesis), the dominant theme is basic biosynthetic and cell-cycle machinery, justifying a label centered on ribosome biogenesis and cell cycle functions.","confidence":"Medium","size":11,"edges":10,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000027","count":1},{"id":"GO:0006267","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0010197","count":1},{"id":"GO:0006468","count":1}]},{"hash":"1509947337053992240","title":"Ubiquitin-Mediated Regulation in Immune Signaling","description":"This cluster centers on ubiquitination-related processes (ubiquitin transferase activity, autoubiquitination, free ubiquitin chains, and K29-linked ubiquitination) and immune signaling pathways (TRIF-dependent TLR and T cell receptor signaling), suggesting a coordinated role in regulating signaling and protein turnover via ubiquitination in immune contexts. Some terms touch DNA repair and neuronal development, but the ubiquitination-immune axis is the most coherent shared theme.","confidence":"High","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035666","count":11},{"id":"GO:0070911","count":11},{"id":"GO:0051443","count":11},{"id":"GO:0051865","count":11},{"id":"GO:0050852","count":11}]},{"hash":"124662775524886150","title":"Signaling regulation and ubiquitination","description":"This cluster centers on regulation of signaling pathways (NF-kappaB activation, Wnt receptor turnover, necroptosis) and protein modification (autoubiquitination), with immune-related processes (V(D)J recombination) and NOS activity also represented. The common theme is regulatory control of signaling and protein modification across diverse pathways, rather than a single dedicated function.","confidence":"Medium","size":11,"edges":21,"triangles":17,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0043123","count":2},{"id":"GO:0046621","count":2},{"id":"GO:0033151","count":2},{"id":"GO:0038018","count":2},{"id":"GO:0051865","count":2}]},{"hash":"1145643361460317814","title":"Immune secretory vesicle trafficking and degranulation","description":"This cluster centers on secretory and trafficking processes in immune cells: degranulation of NK cells and neutrophils, histamine release from mast cells, vesicle targeting and Golgi trafficking, and related regulation of protein targeting and receptor recycling. The overlap of secretory/granule exocytosis terms with vesicle trafficking and immune effector processes supports a cohesive theme of immune cell secretory function.","confidence":"High","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1903595","count":2},{"id":"GO:0001921","count":1},{"id":"GO:0043320","count":1},{"id":"GO:0043312","count":1},{"id":"GO:0006903","count":1}]},{"hash":"1975060640201041525","title":"APC/C-Driven Mitotic Protein Degradation","description":"The top GO terms cluster around cell division, the mitotic cell cycle, and especially APC/C-dependent protein catabolic processes, including K11-linked ubiquitination. This points to ubiquitin-mediated proteolysis timed to mitosis as the core function, with supporting ubiquitin-dependent degradation pathways. Some plant-specific signaling terms appear but do not dominate; overall, the theme is APC/C-driven mitotic regulation.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0070979","count":4},{"id":"GO:0031145","count":4},{"id":"GO:0030433","count":3},{"id":"GO:0042787","count":3}]},{"hash":"694583497560802054","title":"Unknown","description":"The top GO terms are very diverse and do not converge on a single function or pathway: cadmium ion response, angiogenesis, mitotic cell cycle, cytokinin-activated signaling, chlorophyll biosynthesis regulation, histone dephosphorylation (obsolete), ER-associated ubiquitin-dependent degradation (obsolete), male sex differentiation, and several obsolete regulations. The absence of edges and the inclusion of species- or context-specific terms suggest no coherent cluster theme. Therefore, Unknown with no clear representative function.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071276","count":3},{"id":"GO:0001525","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0009736","count":2},{"id":"GO:1902325","count":2}]},{"hash":"1259804933827606329","title":"Neuromuscular development and signaling","description":"The terms show a clear neuromuscular theme: musculoskeletal movement, neuromuscular process controlling balance, and spinal cord motor neuron differentiation, with IGF receptor signaling reinforcing muscle/neuronal growth and signaling. While other terms touch on metabolism and RNA regulation, the strongest shared function among the cluster members is neuromuscular development and signaling, so the label emphasizes that core pattern.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006740","count":1},{"id":"GO:0015992","count":1},{"id":"GO:0050881","count":1},{"id":"GO:0050885","count":1},{"id":"GO:0031571","count":1}]},{"hash":"156135883044229014","title":"Mitochondrial tRNA charging and translation","description":"The strongest signals are mitochondrial tRNA aminoacylation (aspartyl, lysyl, and asparaginyl) and overall translation, with a related tRNA wobble modification term. DNA replication/repair terms are present but appear secondary, suggesting a primary function in mitochondrial protein synthesis and RNA modification rather than DNA maintenance.","confidence":"Medium","size":11,"edges":17,"triangles":8,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0072581","count":6},{"id":"GO:0071915","count":6},{"id":"GO:0006412","count":6},{"id":"GO:0070146","count":6},{"id":"GO:0070154","count":6}]},{"hash":"2268822493361134289","title":"Ubiquitin-Mediated Regulation in Immune Signaling","description":"Top terms emphasize ubiquitination processes (ubiquitin-protein transferase activity, autoubiquitination, free ubiquitin chains, K29-linked ubiquitination) and immune signaling pathways (TRIF-dependent TLR signaling, T cell receptor signaling), with additional links to ERAD-related transport and DNA repair via ubiquitin modification. This points to a cohesive theme where ubiquitin-driven regulation modulates both immune signaling and protein quality control/DNA damage responses, making the label a concise reflection of the cluster\u2019s function.","confidence":"High","size":11,"edges":42,"triangles":73,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035666","count":4},{"id":"GO:0070911","count":4},{"id":"GO:0051443","count":4},{"id":"GO:0051865","count":4},{"id":"GO:0050852","count":4}]},{"hash":"564001379534392070","title":"Ubiquitin-regulated TNF/NF-kB signaling","description":"This cluster centers on ubiquitin-related processes (autoubiquitination, ubiquitin-dependent protein degradation) and signaling pathways like TNF, NF-kB, JNK, and I-kappaB regulation, suggesting a theme of ubiquitin-mediated control of inflammatory signaling. A few terms (V(D)J recombination, histone and dosage compensation) are less directly linked but do not overturn the main theme. ","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":2},{"id":"GO:0033151","count":2},{"id":"GO:0033209","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0036205","count":2}]},{"hash":"1140414961002525049","title":"Mitochondrial membrane permeability and protein import","description":"The Top Terms show a clear mitochondrial focus, with dominant signals for regulation of mitochondrial membrane permeability and protein import into the mitochondrial matrix, plus redox/homeostasis and lipid metabolism tied to mitochondrial function. Some low-count terms (photoreceptor maintenance, nonphotochemical quenching) seem unrelated or noisy. Overall, the cluster appears centered on mitochondrial processes.","confidence":"High","size":11,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":9},{"id":"GO:2000134","count":9},{"id":"GO:0070940","count":9},{"id":"GO:1903740","count":9},{"id":"GO:0010867","count":9}]},{"hash":"2276343950013351830","title":"Unknown","description":"The top GO terms span very diverse processes (Golgi localization, DNA replication, plant hormone signaling, xenobiotic response, telomerase assembly, IL-4 signaling, bacterial motility, hypoxia detection, ethylene signaling) with no clear common function or dominant pathway tying the proteins together, and the cluster has no edges or higher connectivity\u2014thus no coherent biological role can be assigned. ","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000042","count":1},{"id":"GO:0006261","count":1},{"id":"GO:0009736","count":1},{"id":"GO:0033160","count":1},{"id":"GO:0035690","count":1}]},{"hash":"620800782344152145","title":"Unknown","description":"The top GO terms span steroid/receptor signaling, innate immunity, photoreceptor localization, metal ion response, unfolded protein response, and cell cycle transitions, with little cohesive overlap across the cluster. There isn\u2019t a single clear biological function or pathway that ties these proteins together, so a concise, representative label isn\u2019t defensible. ","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006463","count":6},{"id":"GO:2000324","count":6},{"id":"GO:0045087","count":6},{"id":"GO:1903546","count":6},{"id":"GO:0031400","count":6}]},{"hash":"1838345555263227486","title":"Nucleotide Biosynthesis and Chromatin Regulation","description":"The cluster\u2019s top GO terms include several nucleotide biosynthetic processes (UTP, CTP, GTP) and chromatin/epigenetic processes (histone H3-K4 methylation, subtelomeric heterochromatin formation, dosage compensation), suggesting a shared theme around nucleotide metabolism coupled with chromatin regulation. There are also development-related terms, but they are less central to the core signal. ","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003351","count":3},{"id":"GO:0042464","count":2},{"id":"GO:0051568","count":2},{"id":"GO:1902176","count":2},{"id":"GO:0021591","count":2}]},{"hash":"1716445109758256392","title":"Ubiquitin-Dependent Protein Degradation","description":"This cluster is dominated by GO terms for ubiquitination and ubiquitin\u2011dependent protein catabolism (including autoubiquitination, K48-linked ubiquitination, and ERAD) as well as general protein ubiquitination and degradation, pointing to proteins involved in tagging substrates for proteasomal turnover and receptor turnover such as Wnt receptors.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":6},{"id":"GO:0030433","count":5},{"id":"GO:0042787","count":5},{"id":"GO:0070936","count":5},{"id":"GO:1901253","count":5}]},{"hash":"486024139553894808","title":"Ubiquitin-Dependent Protein Degradation","description":"Top GO terms are dominated by ubiquitination and proteasomal degradation, including ubiquitin-dependent protein catabolic process, K48-linked ubiquitination, and ERAD. This suggests a cohesive role in tagging and removing proteins via the ubiquitin-proteasome system; other terms (growth regulation, Wnt receptor turnover, peroxisome matrix import) appear as broader or less-fitting annotations.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046621","count":6},{"id":"GO:0038018","count":6},{"id":"GO:0051865","count":6},{"id":"GO:0042787","count":6},{"id":"GO:1900095","count":6}]},{"hash":"1594754754532525601","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000001","count":1},{"id":"GO:0042128","count":1},{"id":"GO:0006809","count":1},{"id":"GO:0001949","count":1},{"id":"GO:0032286","count":1}]},{"hash":"1091615601460885634","title":"Unknown","description":"The terms span nitric oxide metabolism, immune signaling, cuticle development, ion transport, and various metabolic processes, with no single cohesive function binding the cluster. While a couple of GO terms relate to nitric oxide biology, the diversity prevents a precise, representative label.","confidence":"","size":11,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046210","count":3},{"id":"GO:0014740","count":2},{"id":"GO:0072604","count":2},{"id":"GO:0008365","count":2},{"id":"GO:0072592","count":2}]},{"hash":"2275293158177340798","title":"Transmembrane Transporters for Small Molecules","description":"Proteins in this cluster are strongly linked to transmembrane transport of a broad range of substrates, including xenobiotics, vitamins, sugars (galactose), ions (sodium, phosphate), nitrite, nitrate, and related metabolites. This convergence on transmembrane transport GO terms suggests they function as membrane transporters or solute carriers mediating uptake and efflux of diverse small molecules.","confidence":"High","size":11,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":11},{"id":"GO:0042891","count":11},{"id":"GO:0035461","count":11},{"id":"GO:0015757","count":8},{"id":"GO:0035725","count":8}]},{"hash":"552921239304791060","title":"Telomere-Chromatin Regulation","description":"The top terms cluster around telomere biology (telomeric D-loop disassembly, regulation of telomere localization) and chromatin/nucleosome processes (nucleosome assembly, G-quadruplex DNA formation), suggesting a theme of chromatin structure and telomere maintenance, with some peripheral stress-related terms as noise.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006950","count":1},{"id":"GO:0061820","count":1},{"id":"GO:0009736","count":1},{"id":"GO:1901347","count":1},{"id":"GO:0072362","count":1}]},{"hash":"1828591277845963238","title":"DNA Damage Response and Transcription Regulation","description":"Based on the top GO terms, the proteins cluster around DNA metabolism\u2014DNA-templated transcription, replication, repair, and the SOS response\u2014indicating a nucleus-associated DNA damage response and transcription regulation theme. Some terms are obsolete or peripheral, but the core signal is genome maintenance and transcription control in response to DNA stress.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000746","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0045892","count":1},{"id":"GO:0006281","count":1}]},{"hash":"2305066922014850029","title":"Glutamatergic synaptic recycling and endocytic trafficking","description":"The cluster centers on membrane trafficking at excitatory synapses, with multiple terms for endocytic and receptor recycling and glutamatergic synaptic transmission, supported by related lipid biosynthesis processes; a few nuclear regulation terms may reflect multifunctional proteins.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0034968","count":3},{"id":"GO:0001881","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0051036","count":3},{"id":"GO:0035023","count":3}]},{"hash":"1699673093714508614","title":"Unknown","description":"No shared GO terms or connectivity are evident for this set; with edges and triangles both zero and Top Terms empty, there is no clear common function. The note about six proteins re-added by ReCIPE does not provide a unifying functional signal. ","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1778715994823035793","title":"Lens and Eye Development","description":"The cluster\u2019s top GO terms are dominated by lens-related and visual perception functions (lens development in camera-type eye, lens fiber cell development, camera-type eye development, and visual perception), indicating proteins likely involved in lens/eye formation and light perception. A few unrelated biosynthetic terms appear but do not define the core theme.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009246","count":1},{"id":"GO:0043085","count":1},{"id":"GO:0046938","count":1},{"id":"GO:1904715","count":1},{"id":"GO:0006508","count":1}]},{"hash":"1951178538075012508","title":"Neuronal signaling and endosomal trafficking","description":"The set centers on glutamatergic synaptic transmission, receptor recycling, and regulation of endosome size, pointing to neuronal signaling with endosomal trafficking and receptor cycling. Supporting signals include Rho-mediated signaling, which ties to cytoskeletal dynamics essential for trafficking and synaptic architecture. A few terms about transcription regulation and histone methylation are present but appear less central to the dominant theme of synaptic/endosomal function. Therefore the label captures the most coherent shared function of the cluster.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034968","count":2},{"id":"GO:0001881","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0051036","count":2},{"id":"GO:0035023","count":2}]},{"hash":"187609910083509130","title":"Muscle development and Calcineurin-NFAT signaling","description":"This cluster centers on muscle biology, with terms for skeletal muscle fiber development, fast/slow fiber transitions, and cardiac muscle hypertrophy in response to stress, all connected through the calcineurin-NFAT signaling cascade. This calcium-dependent pathway is a classic driver of muscle differentiation and hypertrophy, supporting a cohesive theme of muscle development and hypertrophic signaling, despite a few tangential terms related to tissue remodeling.","confidence":"High","size":10,"edges":18,"triangles":9,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1905205","count":6},{"id":"GO:0014898","count":6},{"id":"GO:0051531","count":6},{"id":"GO:0033173","count":6},{"id":"GO:0060487","count":6}]},{"hash":"122796217551862854","title":"Regulated Trafficking and Signaling in Eukaryotes","description":"The top GO terms cluster around regulation of transport and signaling processes (nuclear export, endosome transport, kinetochore localization, kinase activity regulation, and various signal-transduction pathways), suggesting these proteins act as general regulators of intracellular trafficking and signaling across different contexts (cell cycle, development, immune differentiation, and neurotransmission). Confidence: Medium","confidence":"Medium","size":10,"edges":32,"triangles":60,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046827","count":9},{"id":"GO:0034501","count":9},{"id":"GO:0045736","count":9},{"id":"GO:2000641","count":8},{"id":"GO:0007124","count":8}]},{"hash":"1523855826013300829","title":"Cerebellar cortex development and Bergmann glia differentiation","description":"The cluster shows strong representation of cerebellar-specific terms, notably Bergmann glial cell differentiation and cerebellar cortex formation, pointing to a cerebellar development theme. While there are broader terms like mitotic cell cycle and various signaling pathways that are less tissue-specific, the cerebellar-related terms provide a clear, dominant thread for naming. ","confidence":"Medium","size":10,"edges":16,"triangles":9,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":8},{"id":"GO:0034501","count":7},{"id":"GO:0045736","count":7},{"id":"GO:0050852","count":7},{"id":"GO:0007601","count":7}]},{"hash":"1200047682520719705","title":"Pollen wall formation and anther dehiscence","description":"The Top Terms include pollen exine formation and anther dehiscence, which strongly point to plant pollen development and maturation. While other terms reflect general cellular metabolism and processes, the pollen-related terms provide the most coherent theme for this cluster. Confidence reflects this primary signal amid noisy terms.","confidence":"Medium","size":10,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007100","count":2},{"id":"GO:0006487","count":1},{"id":"GO:0006798","count":1},{"id":"GO:0046032","count":1},{"id":"GO:0009901","count":1}]},{"hash":"550115469555154518","title":"Amino acid metabolism and hormone-responsive signaling","description":"These terms collectively point to amino acid and nitrogen metabolism (glutamine, ammonium, amino acid, folate-related processes) and to regulation by hormones (insulin, glucagon) and stressors (ethanol, zinc), with some protein turnover (proteolysis). The label highlights the central theme of metabolic processing of amino acids with hormone-driven nutrient signaling.","confidence":"Medium","size":10,"edges":44,"triangles":112,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":4},{"id":"GO:0045471","count":3},{"id":"GO:0006508","count":3},{"id":"GO:0010043","count":3},{"id":"GO:0032868","count":3}]},{"hash":"1512554096359249175","title":"Cell Cycle and Translational Regulation","description":"This cluster is dominated by GO terms for cell division and cell cycle, along with multiple translation-related processes (translation, translational initiation, cytoplasmic translation, and mRNA splicing regulation). The inclusion of regulatory ncRNA-mediated silencing and spliceosome-related positive regulation reinforces a theme of coordinated gene expression control at both transcriptional and post-transcriptional levels, linking cell proliferation with protein synthesis. Some terms like response to antibiotic or conjugation with cellular fusion are less central but do not obscure the main pattern.","confidence":"High","size":10,"edges":8,"triangles":3,"max_degree":3,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0006412","count":5},{"id":"GO:0007049","count":4},{"id":"GO:0031047","count":3},{"id":"GO:0048026","count":3}]},{"hash":"2130469712937949426","title":"ER Stress and Secretory Pathway","description":"The terms cluster around the endoplasmic reticulum: targeting to ER, COPII vesicle formation, and ER unfolded protein response, plus calcium homeostasis, pointing to ER protein processing and secretory pathway activity.","confidence":"High","size":10,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043066","count":1},{"id":"GO:0044828","count":1},{"id":"GO:0044829","count":1},{"id":"GO:0060304","count":1},{"id":"GO:0070972","count":1}]},{"hash":"259196877246690626","title":"Cell growth, division, and survival signaling","description":"The terms point to regulation of cellular growth and proliferation (mitotic membrane reassembly, TORC1 signaling, endothelial proliferation), transcriptional control (Pol III), nuclear transport, post-translational regulation (kinase activity, serine dephosphorylation), and survival/apoptosis pathways, suggesting a cohesive theme of growth and survival signaling with regulatory control across multiple layers.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007084","count":6},{"id":"GO:0045945","count":6},{"id":"GO:0097711","count":6},{"id":"GO:0001938","count":6},{"id":"GO:0060561","count":6}]},{"hash":"1143085813369973255","title":"Golgi\u2013ER vesicle trafficking during cell division","description":"This cluster is enriched for ER-to-Golgi and Golgi-to-ER transport terms (COPII budding, retrograde transport) and for mitosis-related processes (mitotic spindle assembly, mitotic cell cycle, cell proliferation). The convergence of secretory pathway activity with cell-division markers suggests a coherent module where Golgi\u2013ER trafficking supports mitosis and related growth processes, with ribosome biogenesis reflecting overall protein synthesis needs in proliferating cells.","confidence":"High","size":10,"edges":40,"triangles":87,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007420","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0090114","count":3},{"id":"GO:0090307","count":3}]},{"hash":"1674861035626127604","title":"Unknown","description":"The terms span mitochondrial regulation, cell cycle control, lipid metabolism, DNA processing, and skin development, with almost no cohesive theme and only a single edge linking proteins. This makes it hard to assign a concise, representative function label for the cluster. Unknown","confidence":"","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":1},{"id":"GO:2000134","count":1},{"id":"GO:0070940","count":1},{"id":"GO:1903740","count":1},{"id":"GO:0010867","count":1}]},{"hash":"1129316834737047128","title":"Cell cycle and ER-Golgi transport","description":"The GO terms show a clear focus on mitotic processes (cell division; APC-dependent catabolic process; TORC1 signaling) together with vesicle trafficking between the ER and Golgi (COPII budding; retrograde Golgi-ER transport), plus supporting processes like mRNA transport and GTPase regulation, suggesting a cluster that coordinates cell proliferation with intracellular transport. ","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0038202","count":2},{"id":"GO:0070262","count":2},{"id":"GO:0000060","count":2},{"id":"GO:0043547","count":2}]},{"hash":"1439743155019731901","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090116","count":2},{"id":"GO:0006624","count":1},{"id":"GO:0071374","count":1},{"id":"GO:0090084","count":1},{"id":"GO:1901621","count":1}]},{"hash":"1160835085524554367","title":"DNA replication stress response","description":"The cluster centers on DNA replication and genome integrity maintenance, supported by GO terms for DNA biosynthesis, DNA replication, mitotic DNA replication checkpoint signaling, and error-free translesion synthesis. It also includes stress- and quality-control processes such as proteasomal degradation and cellular response to oxidative stress, as well as ER-Golgi transport, suggesting a coordinated response to stress that preserves replication and protein homeostasis. ","confidence":"Medium","size":10,"edges":19,"triangles":14,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0071897","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0070987","count":3},{"id":"GO:0046034","count":2}]},{"hash":"2047621773651763180","title":"Neuronal Synaptic Regulation and Autophagy","description":"The cluster centers on neuronal and synaptic functions, highlighted by terms like excitatory postsynaptic potential, regulation of synaptic vesicle endocytosis, and substantia nigra development, suggesting involvement in neural signaling and dopaminergic pathways. Additionally, autophagy-related terms (microautophagy and regulation of autophagy) point to cellular clearance processes that interface with neuronal survival and synaptic maintenance. Together, these terms imply a cohesive module of synaptic regulation intertwined with autophagic control in neurons.","confidence":"Medium","size":10,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":3},{"id":"GO:0010507","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0016237","count":2},{"id":"GO:0060079","count":2}]},{"hash":"1043043726326326336","title":"Bacterial biosynthesis and metabolism","description":"These terms cluster around core bacterial metabolic and biosynthetic processes, including amino acid biosynthesis (isoleucine and lysine pathways), biotin and porphyrin/heme biosynthesis, menaquinone production, and central metabolism (TCA cycle), with accompanying antibiotic biosynthesis and antibiotic response. The combination suggests a module of bacterial metabolic enzymes and cofactors, with some regulation related to antibiotic exposure. ","confidence":"Medium","size":10,"edges":41,"triangles":94,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0009234","count":2},{"id":"GO:0009097","count":2},{"id":"GO:0017000","count":2}]},{"hash":"897808004021213060","title":"DNA replication and transcription machinery","description":"Explanation: Top GO terms point to nuclear processes (DNA-templated transcription, DNA replication, mRNA export, cell division), suggesting a core cluster of DNA metabolism and cell-cycle functions. The remaining terms (polarity regulation, endosome transport) imply additional roles in cell organization and growth, but the central theme remains nuclear gene expression and replication.","confidence":"Medium","size":10,"edges":17,"triangles":17,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006260","count":3},{"id":"GO:2000114","count":2},{"id":"GO:0006406","count":2},{"id":"GO:0046677","count":2}]},{"hash":"731331527976313362","title":"Endosomal-Lysosomal Trafficking and Autophagy","description":"The cluster\u2019s GO terms cluster around endosomal transport and lysosomal targeting\u2014endosome to lysosome, early endosome to Golgi/Late endosome routes, microautophagy, and synaptic vesicle endocytosis\u2014plus vacuolar protein targeting. This points to a cohesive role in endosomal-lysosomal trafficking and related autophagic processes, with a few outliers (mitotic cycle, heterochromatin formation) likely representing broader or incidental functions.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0016237","count":2},{"id":"GO:0060079","count":2},{"id":"GO:0006623","count":2}]},{"hash":"1216532254091841949","title":"Satellite cell activation and muscle regeneration","description":"This cluster centers on skeletal muscle regeneration, highlighting satellite cell activation and regulation of muscle differentiation, with supporting signals in calcium signaling, hypoxia response, and kinase activity. The recurring muscle stem cell activation and regeneration themes make this the most coherent label.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0033234","count":3},{"id":"GO:0051281","count":3},{"id":"GO:0014718","count":3},{"id":"GO:0070315","count":3},{"id":"GO:2001015","count":3}]},{"hash":"1263936214199463150","title":"Stress-Induced Transcriptional Response","description":"The dominant signal is DNA-templated transcription (GO:0006351) along with multiple cellular stress responses (gamma radiation, singlet oxygen, nitroglycerin response, arsenite, hypoxia, psychosocial stress). This suggests proteins involved in regulating transcription in response to diverse stresses, i.e., a stress-induced transcriptional regulatory module. A few terms hint at chromatin-level regulation, supporting the transcriptional control theme, though some entries are obsolete. Overall, it fits a stress-responsive transcription cluster.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0033169","count":1},{"id":"GO:1990911","count":1},{"id":"GO:1904843","count":1},{"id":"GO:0071480","count":1}]},{"hash":"2036115049953622705","title":"Developmental differentiation and RNA processing","description":"This cluster seems to group proteins involved in RNA processing (splicing, polyadenylation, translation) and a broad set of developmental differentiation programs (spermatid nucleus differentiation, endodermal fate determination, retinal rod cell differentiation, cornea development), along with stem cell maintenance and anti-apoptotic regulation, suggesting a link between gene expression control and lineage specification across tissues.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007289","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0006412","count":1},{"id":"GO:0007493","count":1}]},{"hash":"1015174870172353864","title":"Mitochondrial gene expression and cell-cycle control","description":"This cluster centers on mitochondrial-related processes (regulation of mitochondrial membrane permeability; protein import into the mitochondrial matrix) together with cell-cycle related terms (cell division; DNA-templated transcription; negative regulation of G1/S transition), suggesting a link between mitochondrial function and cell-cycle regulation. Some terms are less clearly connected (late viral transcription, mammary gland alveolus development), but the mitochondrial/cell-cycle theme appears most representative.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0046902","count":2},{"id":"GO:2000134","count":2},{"id":"GO:0070940","count":2}]},{"hash":"2009960732978996100","title":"Bacterial lipid biosynthesis and related metabolism","description":"The top GO terms cluster around lipid- and small-molecule metabolism in bacteria: fatty acid biosynthesis and transport, menaquinone and bile acid\u2013related processes, and various catabolic pathways (phenylacetate, malonate). There is also a signal for nonribosomal peptide biosynthesis precursor activation, suggesting potential secondary metabolite pathways. An outlier term on transformation competence and a plant-specific seed coat term likely reflect annotation noise rather than core function. Overall, the cluster reads as lipid-centric bacterial metabolism with related small-molecule pathways.","confidence":"Medium","size":10,"edges":8,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006633","count":3},{"id":"GO:0030420","count":2},{"id":"GO:1902987","count":2},{"id":"GO:0010124","count":2},{"id":"GO:0043041","count":2}]},{"hash":"2126189491889167369","title":"Unknown","description":"The GO terms are very diverse (hypoxia response, mRNA transport, kinase and GTPase regulation, mitotic cell cycle, tissue development) and there are no edges linking the proteins, so there is no single cohesive function tying the cluster together. Unknown reflects the lack of a common theme.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071456","count":3},{"id":"GO:0051028","count":3},{"id":"GO:0071902","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0000278","count":3}]},{"hash":"2137169753458251412","title":"Neural Thermosensation and Neuroinflammatory Signaling","description":"This cluster is driven by GO terms for thermosensory behavior and responses linked to TRPV1-related sensing (capsazepine), diet-induced thermogenesis, and related transport, along with inflammatory chemokine production and osmotic-stress\u2013induced apoptosis. Additional terms point to cerebellar molecular layer and vestibular nucleus development and vasoconstriction, suggesting a CNS module that combines sensory thermosensation with inflammatory signaling and neural development processes.","confidence":"Medium","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071642","count":5},{"id":"GO:1901594","count":5},{"id":"GO:0098719","count":5},{"id":"GO:0040040","count":5},{"id":"GO:0071651","count":5}]},{"hash":"2304128079164511143","title":"Neuronal synaptic signaling and axonogenesis","description":"This cluster is dominated by GO terms for glutamatergic and dopaminergic synaptic transmission and CNS projection neuron axonogenesis, pointing to neural communication and neuron development. Endosome transport regulation and signaling modulation terms may reflect vesicle trafficking and pathway control, while some immune and stress-related terms appear as less central signals.","confidence":"High","size":10,"edges":5,"triangles":0,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035249","count":5},{"id":"GO:2000641","count":3},{"id":"GO:0007124","count":3},{"id":"GO:1901621","count":3},{"id":"GO:1904637","count":3}]},{"hash":"2197776731821048597","title":"Cellular trafficking, signaling, and organelle homeostasis","description":"These proteins link intracellular transport and phagosome maturation with signaling complex assembly (Wnt), and maintenance of organelles through autophagy regulation, copper homeostasis, and mitochondrial targeting. While there are also broader processes like cell migration and differentiation, the shared theme is core intracellular logistics and signaling rather than a single pathway, so the label reflects trafficking, signaling, and organelle maintenance.","confidence":"Medium","size":10,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1903215","count":1},{"id":"GO:0001667","count":1},{"id":"GO:0006878","count":1},{"id":"GO:0010507","count":1},{"id":"GO:0043316","count":1}]},{"hash":"2073671922087954157","title":"Unknown","description":"GO terms span DNA replication and telomerase assembly, but also include cytokinin/ethylene signaling, xenobiotic and interleukin-4 responses, hypoxia sensing, nuclear transport, and even bacterial motility. This wide diversity lacks a single cohesive function, so no clear, specific label fits the cluster.","confidence":"","size":10,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006261","count":2},{"id":"GO:0009736","count":2},{"id":"GO:0033160","count":2},{"id":"GO:0035690","count":2},{"id":"GO:1905323","count":2}]},{"hash":"1946517413260713636","title":"Plant hormone signaling and transcriptional regulation","description":"The top GO terms point to transcriptional regulation (GO:0006355) and hormone signaling pathways such as cytokinin (GO:0009736) and ethylene (GO:0010105), suggesting a nucleus-centric cluster where transcriptional control is tied to hormone-responsive signaling. Other terms indicate broader regulatory processes like DNA replication and stress responses (xenobiotic, hypoxia), but the most coherent theme is hormone-driven transcriptional regulation in plants.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":6},{"id":"GO:0009736","count":5},{"id":"GO:0006261","count":4},{"id":"GO:0033160","count":4},{"id":"GO:0035690","count":4}]},{"hash":"472492589556287909","title":"RNA processing and translation regulation","description":"These proteins cluster around post-transcriptional RNA handling: splicing (alternative and spliceosome-mediated), polyadenylation and general mRNA modification, and regulation of mRNA stability under stress. They also involve regulatory ncRNA and miRNA-mediated silencing, plus components linked to translation initiation (eIF4F complex assembly). The common theme is RNA maturation and control of translation, rather than a single enzymatic function, supporting a post-transcriptional regulation role for this cluster.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":2},{"id":"GO:0048025","count":2},{"id":"GO:0035278","count":2},{"id":"GO:0010610","count":2},{"id":"GO:0016556","count":2}]},{"hash":"81495610145291456","title":"Ribosome biogenesis and translation","description":"The cluster shows strong representation of translation- and ribosome-related GO terms, including translation, cytoplasmic translation, translational initiation/termination, and ribosome biogenesis (notably large subunit maturation). This pattern points to core components of protein synthesis and ribosome assembly. A few transcription-related terms and antibiotic response appear but do not define the main function of the cluster.","confidence":"High","size":10,"edges":32,"triangles":46,"max_degree":9,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0042254","count":4},{"id":"GO:0000463","count":3},{"id":"GO:0042273","count":2},{"id":"GO:0006353","count":2}]},{"hash":"551017601620656932","title":"Chromatin regulation and nucleotide metabolism","description":"This cluster shows enrichment for epigenetic/chromatin-related terms (dosage compensation, subtelomeric heterochromatin formation, histone methylation) alongside nucleotide biosynthesis (UTP, CTP, GTP). The co-occurrence suggests a link between chromatin control and nucleotide metabolism, with developmental terms likely reflecting broader roles in gene regulation during development.","confidence":"Medium","size":10,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042464","count":1},{"id":"GO:0051568","count":1},{"id":"GO:1902176","count":1},{"id":"GO:0021591","count":1},{"id":"GO:0006228","count":1}]},{"hash":"1923689361638636159","title":"Unknown","description":"The top GO terms are highly diverse, spanning lipopolysaccharide biosynthesis, membrane repolarization, regulation of ion transport and signaling, muscle contraction regulation, development, and metabolism. There is no clear single function or pathway tying these terms together, and the network shows low connectivity (Edges: 2, Triangles: 0). Therefore, a coherent functional label cannot be assigned.","confidence":"","size":10,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":3},{"id":"GO:0086009","count":2},{"id":"GO:0031947","count":2},{"id":"GO:0051481","count":2},{"id":"GO:0002028","count":2}]},{"hash":"1983216676112033438","title":"Ribosome Biogenesis and Translation","description":"The top GO terms are centered on protein synthesis and ribosome assembly (translation, ribosome biogenesis, large subunit assembly, and translational termination), with an additional emphasis on translational fidelity. While there are a few transcription- and stress-related terms, the prevailing pattern points to a cluster of proteins involved in ribosome formation and the translation process.","confidence":"High","size":10,"edges":37,"triangles":72,"max_degree":9,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0042254","count":4},{"id":"GO:0015968","count":2},{"id":"GO:0006415","count":2},{"id":"GO:0000027","count":2}]},{"hash":"2172069484911127477","title":"RNA Pol II Transcription Regulation","description":"The cluster is dominated by GO terms tied to regulation of transcription by RNA polymerase II, including transcription start site selection and transcription termination, indicating a core theme of transcriptional control. Calcium signaling terms appear, but as secondary context, suggesting regulatory layers that couple transcription to calcium dynamics rather than a primary calcium-handling function.","confidence":"High","size":10,"edges":35,"triangles":58,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0036091","count":5},{"id":"GO:0060303","count":4},{"id":"GO:0071277","count":4},{"id":"GO:0010880","count":3},{"id":"GO:0001178","count":3}]},{"hash":"1654483713762086491","title":"Neuronal development and cell migration","description":"This cluster is dominated by GO terms related to nervous system development and neuronal signaling (e.g., cellular response to dopamine, negative regulation of axonogenesis) and includes ameboid-type migration and chemotaxis terms, suggesting a theme around neuron development and neuronal/immune cell movement. Some terms (e.g., T cell receptor signaling, reticulophagy) appear as distant connections or misannotations, but the core signal points to neuron-related development and motility.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":2},{"id":"GO:0061709","count":1},{"id":"GO:1903215","count":1},{"id":"GO:1902499","count":1},{"id":"GO:0050852","count":1}]},{"hash":"1549740952733819515","title":"Chromatin Organization and Transcription Regulation","description":"The top GO terms cluster around chromatin structure and genome regulation\u2014rDNA heterochromatin formation, nucleosome assembly, and transcription start site selection\u2014along with DNA structural elements such as telomeric D-loop disassembly and G-quadruplex formation. While hormone signaling terms (ABA and cytokinin responses) appear, the shared thread is control of chromatin state and transcription. A cardiac ventricle development term seems out of place and likely represents broader or cross-species annotations rather than a defining feature of this cluster.","confidence":"Medium","size":10,"edges":19,"triangles":10,"max_degree":9,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0000183","count":5},{"id":"GO:0006334","count":4},{"id":"GO:0009737","count":4},{"id":"GO:0061820","count":3},{"id":"GO:0001178","count":3}]},{"hash":"2108337824893616138","title":"Unknown","description":"The terms span both nuclear gene expression (DNA-templated transcription, DNA replication, protein export from nucleus) and various polysaccharide/cell wall biosynthesis processes, with no single, cohesive function linking the proteins, so a specific, representative label isn\u2019t evident.","confidence":"","size":10,"edges":13,"triangles":0,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0032435","count":2},{"id":"GO:0000902","count":2},{"id":"GO:0046827","count":2},{"id":"GO:0006260","count":2}]},{"hash":"574932346807186433","title":"Membrane Trafficking and Lipid Transport","description":"The top terms point to ER-to-endosome/vacuole trafficking and lipid handling, including regulation of ER exit, endosome localization, vacuole organization, phospholipid translocation, and lipid metabolism. This suggests a cohesive role in membrane trafficking combined with lipid movement, with a few peripheral or obsolete terms not changing the core theme.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901407","count":2},{"id":"GO:0044829","count":2},{"id":"GO:0010570","count":1},{"id":"GO:0006855","count":1},{"id":"GO:0070863","count":1}]},{"hash":"155615681117908940","title":"Sphingolipid and phospholipid metabolism","description":"This cluster is dominated by GO terms involved in lipid metabolism, particularly sphingolipids (sphingosine/sphinganine-1-phosphate metabolic processes and regulation of sphingolipid signaling) and phospholipids (phospholipid catabolic/dephosphorylation, phosphatidylglycerol biosynthesis). Although a couple of other terms appear (e.g., glucose-6-phosphate transport, oxidative detoxification) they do not define the group, and the common thread is lipid turnover and signaling related to membrane lipids.","confidence":"Medium","size":10,"edges":11,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009395","count":2},{"id":"GO:1902068","count":1},{"id":"GO:0006668","count":1},{"id":"GO:0098869","count":1},{"id":"GO:0044330","count":1}]},{"hash":"897043057399469307","title":"Ubiquitin-Dependent Proteolysis and Signaling","description":"Dominant terms are ubiquitin-dependent processes (ERAD, protein catabolic process, autoubiquitination) plus signaling and cell-cycle controls (TNF signaling, Wnt receptor catabolic process, spindle orientation checkpoint). This points to a set of proteins linked by ubiquitin-mediated proteostasis that modulates growth and signaling.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0030433","count":5},{"id":"GO:0046621","count":4},{"id":"GO:0033151","count":4},{"id":"GO:0038018","count":4},{"id":"GO:0051865","count":4}]},{"hash":"771263943761654373","title":"Metal and toxin stress response","description":"The top GO terms cluster around cellular responses to metals and toxins (sodium arsenite, cadmium, antibiotics) and transport processes for metal ions and osmolytes (glycine betaine, cobalt, monoatomic anions), suggesting a cohesive theme of adapting to metal/chemical stress through regulatory and transport activities. Some telomere maintenance terms appear as secondary regulatory associations, but the dominant signal is stress response and ion/osmolyte transport.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903936","count":2},{"id":"GO:2001033","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0032212","count":2}]},{"hash":"1727545183106405770","title":"Ubiquitin-Dependent Necroptosis Regulation","description":"The set is strongly enriched for ubiquitination-related processes (polyubiquitination, K48-linked ubiquitination) and regulation of necroptotic signaling (including TNF-mediated pathways), suggesting these proteins function together in ubiquitin-mediated control of necroptosis and related signaling. A few terms about transcription regulation and histone turnover appear, which may reflect broader roles of ubiquitin in transcription/chromatin, but the dominant theme is ubiquitin-mediated regulation of necroptosis.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046621","count":1},{"id":"GO:0051865","count":1},{"id":"GO:0060546","count":1},{"id":"GO:0033209","count":1},{"id":"GO:0036205","count":1}]},{"hash":"554693134793363827","title":"Stress-Response Ubiquitination and Survival Signaling","description":"This cluster centers on protein ubiquitination alongside cellular stress responses (cadmium, hydrogen peroxide, redox changes) and anti-apoptotic regulation, with enrichment in signaling pathways that promote cell survival (PI3K/AKT) and growth control (Hippo). The convergence of ubiquitin-related processes with oxidative and nutrient-stress signals suggests a coherent module that modulates survival under stress through ubiquitin regulation and growth-signaling pathways.","confidence":"Medium","size":10,"edges":19,"triangles":15,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":4},{"id":"GO:0071276","count":3},{"id":"GO:0070301","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0051897","count":2}]},{"hash":"98032494579443210","title":"Amino acid catabolism and NAD biosynthesis","description":"The cluster centers on amino acid degradation (L-alanine, L-cysteine, glutamate, glycine) and the quinolinate/NAD biosynthesis pathway, suggesting a metabolism- and cofactor-focused group. Additional terms point to mitochondrial-related processes (mitochondrial tRNA thio-modification) and Fe-S cluster assembly, supporting a broader mitochondrial/metabolic context. Notch signaling and antibiotic biosynthesis are present but appear less representative, so the overall theme fits amino-acid catabolism with NAD cofactor biosynthesis rather than a single pathway. ","confidence":"Medium","size":10,"edges":41,"triangles":92,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007219","count":4},{"id":"GO:0097053","count":4},{"id":"GO:0042853","count":4},{"id":"GO:0019551","count":3},{"id":"GO:0017000","count":3}]},{"hash":"1471734227611827651","title":"Xenobiotic Detoxification and Aromatic Compound Degradation","description":"The top GO terms point to detoxification and breakdown of xenobiotics and aromatic compounds, including cellular oxidant detoxification, beta-ketoadipate and stilbene pathways, epoxygenase P450 activity, and glucuronoside/triglyceride catabolism, suggesting a cohesive module for chemical degradation and detoxification rather than a single signaling or structural role.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":5},{"id":"GO:0017000","count":5},{"id":"GO:0042952","count":4},{"id":"GO:1905344","count":4},{"id":"GO:0046272","count":4}]},{"hash":"850228762364490513","title":"Ubiquitin-Dependent Degradation & NF-\u03baB Signaling","description":"The cluster is enriched for ubiquitin-mediated proteolysis (K48/K11-linked ubiquitination, autoubiquitination), ubiquitin-dependent protein catabolic processes, ERAD, and histone turnover, with links to inflammatory signaling pathways (NF-\u03baB and TNF). This suggests a cohesive role in ubiquitin-proteasome regulation of protein turnover and inflammatory signaling.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0043123","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0060546","count":3}]},{"hash":"519760185692072095","title":"Neuronal endosomal trafficking and signaling","description":"This cluster shows enrichment for receptor recycling, endosome size regulation, and Rho-mediated signaling, with a neuronal context suggested by glutamatergic synaptic transmission. While transcription regulation terms are present, the strongest cohesive theme centers on membrane trafficking and signaling at neuronal receptors, including endosomal processes and transport. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0034968","count":3},{"id":"GO:0001881","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0051036","count":3},{"id":"GO:0035023","count":3}]},{"hash":"673755587963106505","title":"ER-Linked Synaptic Assembly and Immune Regulation","description":"These proteins collectively show enrichment for endoplasmic reticulum organization/fusion and regulation of synaptic assembly at neuromuscular junction, pointing to ER-associated roles in synaptic organization. The presence of terms about T cell receptor signaling, IL-2 production, and glial differentiation adds an immune and neural-supporting dimension, suggesting a cluster that spans ER-related synaptic processes with some immune modulation. Overall, the theme is plausible but not tightly cohesive across all terms, so a cautious label is appropriate.","confidence":"Low","size":10,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016320","count":1},{"id":"GO:0051124","count":1},{"id":"GO:0050860","count":1},{"id":"GO:0008582","count":1},{"id":"GO:0007019","count":1}]},{"hash":"627405264897620403","title":"Neural and sensory organ development","description":"The top GO terms cluster around sensory perception (visual), brain and neural structures (memory, corpus callosum, cochlea), and broader embryonic patterning (planar polarity, left/right symmetry, nose and forelimb morphogenesis), indicating a cohesive theme of neural and sensory organ development and axis formation. The lack of network edges suggests these are related developmental processes rather than a single interaction pathway.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":2},{"id":"GO:0007613","count":2},{"id":"GO:0090102","count":1},{"id":"GO:0021670","count":1},{"id":"GO:0001736","count":1}]},{"hash":"1920493759228378403","title":"DNA Damage Response and SUMOylation","description":"These GO terms cluster around cellular responses to DNA damage and regulation of SUMO modification (positive regulation of protein sumoylation, autosumoylation, DNA damage\u2013related signaling and translesion synthesis). Several terms point to DNA damage response pathways (intrinsic apoptotic signaling in response to DNA damage, DNA double-strand break attachment to the nuclear envelope, regulation of DNA damage checkpoints), suggesting a cohesive theme of DDR with SUMO regulation. A few terms (vitellogenesis, membrane potential, general cell growth) are more peripheral to this core, but the dominant signal supports a DDR/SUMO-focused cluster.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033235","count":1},{"id":"GO:1902231","count":1},{"id":"GO:1904333","count":1},{"id":"GO:0007296","count":1},{"id":"GO:1990683","count":1}]},{"hash":"1247671413238540444","title":"Sphingolipid and Phospholipid Metabolism","description":"The GO terms are dominated by sphingolipid metabolism and signaling (sphingosine, sphinganine-1-phosphate) and by phospholipid biosynthesis, catabolism, and turnover, pointing to a lipid metabolism-focused cluster. A few other terms (glucose-6-phosphate transport, oxidant detoxification) are present but secondary, and obsolete Wnt terms do not define the core function.","confidence":"Medium","size":10,"edges":14,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1902068","count":2},{"id":"GO:0006668","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0044330","count":2},{"id":"GO:0006670","count":2}]},{"hash":"1138763138434359917","title":"Cell growth and division machinery","description":"This cluster is dominated by core growth-related processes: ribosomal small subunit biogenesis and tRNA modification point to translation readiness, while cell cycle, cell division, and cell septum assembly indicate the machinery driving proliferation. The remaining terms (metal ion response, exosomal secretion regulation, and neuronal synaptic regulation) appear as outliers or broader cellular context annotations, but do not override the central theme of growth/division. Confidence: Medium","confidence":"","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071287","count":2},{"id":"GO:0090394","count":2},{"id":"GO:1903542","count":2},{"id":"GO:0000747","count":2},{"id":"GO:1901001","count":2}]},{"hash":"505693682379826008","title":"Unknown","description":"There are no GO terms or functional hints associated with these proteins (no edges, no terms reported). Without a shared function signal, it\u2019s not possible to assign a meaningful label; thus the cluster remains Unknown.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1656492637814062075","title":"Unknown","description":"The top GO terms include neural myelination in the peripheral nervous system, extrinsic apoptotic signaling, cAMP-related signaling, dephosphorylation, EMT regulation, kinetochore localization, adenosine biosynthesis, connective tissue remodeling, and DNA repair/checkpoint processes. These cover multiple distinct cellular processes across different compartments, with no single cohesive function dominating the cluster. Therefore a specific, representative label cannot be confidently assigned.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0022011","count":2},{"id":"GO:2001241","count":2},{"id":"GO:0045762","count":2},{"id":"GO:0016311","count":1},{"id":"GO:0010719","count":1}]},{"hash":"283865306981065542","title":"Multisubstrate Transmembrane Transport","description":"This cluster is characterized by a collection of GO terms for transmembrane transport of a wide range of substrates (sugars, ions, xenobiotics, vitamins, nitrite/nitrate, phosphate, etc.). The common theme is membrane transport activity across various substrates, rather than a single substrate class, indicating a broad transporter-like function group.","confidence":"High","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015757","count":4},{"id":"GO:0035725","count":4},{"id":"GO:0006855","count":4},{"id":"GO:0015707","count":4},{"id":"GO:0006004","count":4}]},{"hash":"953571720494277445","title":"Transcriptional and ubiquitin-mediated regulation","description":"This cluster includes GO terms for DNA-templated transcription and transcriptional regulation, as well as protein ubiquitination/deubiquitination and various protein trafficking/localization processes (including autophagy-related targeting). The shared theme appears to be regulation of gene expression together with post-translational control of protein fate and localization, rather than a single cohesive pathway. Confidence: Medium","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:2000235","count":1},{"id":"GO:0003197","count":1},{"id":"GO:0010768","count":1},{"id":"GO:0051865","count":1}]},{"hash":"632542051981382903","title":"PM-endosome-Golgi trafficking","description":"The top GO terms cluster around transport between the plasma membrane, endosomes, and the Golgi, including COPII cargo loading and retrograde routes, indicating an intracellular vesicle trafficking function. Rab/Rap signaling terms further support regulation of this trafficking process.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048227","count":1},{"id":"GO:0071955","count":1},{"id":"GO:0006886","count":1},{"id":"GO:0035526","count":1},{"id":"GO:0034499","count":1}]},{"hash":"81695987357062856","title":"RNA processing and translation regulation","description":"This cluster centers on post-transcriptional control of gene expression, with GO terms pointing to mRNA splicing regulation, polyadenylation, mRNA modification, and stability, as well as ncRNA- and miRNA-mediated silencing and initiation of translation, including eIF4F complex assembly. Together these terms indicate a cohesive theme of RNA processing and regulation of translation rather than a single protein function.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":1},{"id":"GO:0048025","count":1},{"id":"GO:0035278","count":1},{"id":"GO:0010610","count":1},{"id":"GO:0016556","count":1}]},{"hash":"605903400354299726","title":"Unknown","description":"The GO terms span disparate biological areas (nervous system and skeletal muscle development; plant signaling and metabolism; tRNA modification; spindle-associated localization; ubiquitin-mediated degradation; germinal center formation; swimming), with little apparent shared function or pathway. The lack of edges and the heterogeneous annotations suggest no cohesive cluster function, hence Unknown.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0007399","count":1},{"id":"GO:0007519","count":1},{"id":"GO:0019762","count":1},{"id":"GO:0031591","count":1}]},{"hash":"698578094184154927","title":"Unknown","description":"The Top Terms are highly diverse and cover metal ion response, innate immune signaling, dopamine signaling, protein ubiquitination, organ size regulation, and developmental polarity. With no cohesive biological process or molecular function tying these terms together and no interactions among proteins (Edges: 0), there isn\u2019t a clear, representative label beyond Unknown.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071287","count":1},{"id":"GO:1903215","count":1},{"id":"GO:0034130","count":1},{"id":"GO:1902499","count":1},{"id":"GO:0035564","count":1}]},{"hash":"19033391165998384","title":"Stress-Responsive RNA Processing and Ubiquitination","description":"GO terms point to stress-related regulation of RNA processing (splicing, mRNA export), chromatin assembly, and ubiquitination, suggesting a theme of gene expression control and protein turnover under stress.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:2000728","count":1},{"id":"GO:1904668","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0061641","count":1}]},{"hash":"1290837520965599809","title":"Stress-responsive developmental signaling and proliferation","description":"These proteins show enrichment in terms tied to regulation of signaling pathways (kinase activity, autophosphorylation, GTPase activity), cell cycle and development (mitotic cycle, multicellular development, proliferation), and stress responses (hypoxia, heat-stress\u2013related mRNA export) including skin development. The common theme is regulation of signaling leading to development and growth under stress, rather than a single isolated pathway, supporting a label of stress-responsive developmental signaling and proliferation.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071456","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0071902","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0043588","count":2}]},{"hash":"1466552866495242701","title":"Stress-Responsive Carbohydrate Metabolism","description":"The cluster clusters around carbohydrate metabolism and stress response: maltose catabolism, trehalose metabolism and related stress-associated processes (desiccation, heat/cold stress), glucosylglycerol biosynthesis, plus glycophagy and regulation of carbon utilization. Although individual GO terms are varied and some are obsolete, the common theme is carbohydrate synthesis/ breakdown tied to environmental stress, especially desiccation, suggesting a coherent functional group.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016311","count":1},{"id":"GO:0000025","count":1},{"id":"GO:0070413","count":1},{"id":"GO:0043609","count":1},{"id":"GO:0046959","count":1}]},{"hash":"2134704854584187732","title":"Unknown","description":"There are no GO terms or network connections provided for this cluster, so there is no identifiable shared function to label. With only a note that one protein was re-added by ReCIPE and no topology information, a meaningful, specific label cannot be inferred.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"142369779263011757","title":"Unknown","description":"The terms include skin development, hair cell differentiation, transcriptional regulation, DNA topology and replication-related processes, DNA restriction-modification, SOS response, and MDA-5 signaling. This combination does not point to a single cohesive biological function or pathway; it appears to mix developmental regulation with DNA maintenance and immune signaling, suggesting a heterogeneous cluster without a unifying function.","confidence":"","size":9,"edges":12,"triangles":5,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043588","count":4},{"id":"GO:0043388","count":4},{"id":"GO:0045944","count":4},{"id":"GO:0009307","count":3},{"id":"GO:0009432","count":3}]},{"hash":"934023205160620179","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0000398","count":7},{"id":"GO:0034475","count":6},{"id":"GO:0016441","count":6},{"id":"GO:0071035","count":6},{"id":"GO:1990416","count":6}]},{"hash":"724722526217624461","title":"Neural development and signaling","description":"The top GO terms strongly point to nervous system development and communication: axonogenesis and neural tube patterning (developmental processes), dopaminergic synaptic transmission (neuronal signaling), and Hedgehog-related pathway regulation. Endosome transport terms suggest neuronal trafficking essential for synaptic function. While a few terms touch on immunity or cartilage, the dominant theme centers on nervous system development and neuronal signaling.","confidence":"Medium","size":9,"edges":2,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":9},{"id":"GO:0007124","count":9},{"id":"GO:1901621","count":9},{"id":"GO:1904637","count":9},{"id":"GO:0001963","count":9}]},{"hash":"792835500254825547","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":32,"triangles":62,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0000463","count":3},{"id":"GO:1902626","count":3},{"id":"GO:0048701","count":3},{"id":"GO:0034475","count":2}]},{"hash":"739913004969246883","title":"Neuronal Microtubule Dynamics and Transport","description":"This cluster centers on microtubule cytoskeleton regulation and neuronal processes, including microtubule depolymerization, spindle\u2013kinetochore attachments, microtubule polarity, dendritic transport of receptor complexes, and neuron projection maintenance, with several terms pointing to neuronal structure such as Purkinje cell layer organization.","confidence":"Medium","size":9,"edges":27,"triangles":38,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0010938","count":2},{"id":"GO:0000743","count":2},{"id":"GO:0001560","count":2},{"id":"GO:0032487","count":2},{"id":"GO:0098971","count":2}]},{"hash":"1849764336042432731","title":"TGF-beta/BMP signaling regulation","description":"The top GO terms cluster around modulation of TGF-\u03b2/BMP pathways, including negative regulation of TGF-\u03b2 receptor signaling, negative regulation of BMP signaling, SMAD-related assembly, and peptidyl-threonine dephosphorylation, which together point to a function in controlling TGF-\u03b2/BMP signaling activity. Some terms (e.g., photosystem stoichiometry adjustment, meristem identity) are less directly connected and may reflect broader annotations, but the core theme is signaling regulation in the TGF-\u03b2/BMP axis.","confidence":"Medium","size":9,"edges":33,"triangles":64,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":8},{"id":"GO:0042347","count":7},{"id":"GO:0071560","count":7},{"id":"GO:0080005","count":7},{"id":"GO:0061191","count":7}]},{"hash":"956881465757620122","title":"Unknown","description":"The GO terms span fungal karyogamy, muscle assembly, insect cuticle development, neuronal growth, kidney development, membrane remodeling, and lipid biosynthesis. There is no coherent function or pathway tying all nine proteins together, so a single informative label cannot be given.","confidence":"","size":9,"edges":9,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000742","count":3},{"id":"GO:0055003","count":2},{"id":"GO:0097274","count":2},{"id":"GO:0008365","count":2},{"id":"GO:0097320","count":2}]},{"hash":"1418536024380131905","title":"Unknown","description":"The top GO terms span diverse themes, including meiotic and mitotic chromosome dynamics, microsporogenesis, rDNA maintenance, and multiple intracellular transport/organellar processes (melanosome organization, synaptic vesicle transport, endosome-to-lysosome transport). No single, cohesive function links these terms, and the cluster has no edges, arguing against a shared biological role. Therefore, the cluster is best labeled Unknown with no confident functional annotation.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051307","count":1},{"id":"GO:0007076","count":1},{"id":"GO:1900126","count":1},{"id":"GO:0048490","count":1},{"id":"GO:0043007","count":1}]},{"hash":"1220992691947943257","title":"Neural development and microtubule dynamics","description":"The top GO terms cluster around nervous system and brain development, indicating neural differentiation/maturation as a core theme. Supporting this, tubulin complex assembly and regulation of synaptic vesicle exocytosis point to cytoskeletal dynamics and synaptic function, which are essential during neural development. A few terms like mitotic cell cycle reflect general cellular proliferation found in developing tissues, but the predominant signal is neural development with cytoskeletal regulation.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007286","count":2},{"id":"GO:0007021","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0007399","count":2}]},{"hash":"1714249999846044552","title":"Neuronal Development and Signaling","description":"The Top Terms prominently include dopaminergic synaptic transmission, CNS projection neuron axonogenesis, and neural tube patterning, which together point to neuronal differentiation and signaling. While other terms touch on general signaling, endosomal transport, calcium responses, and immune or developmental processes, the neural-related terms suggest a core theme around neuronal development and communication. Confidence: Medium","confidence":"","size":9,"edges":35,"triangles":77,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":9},{"id":"GO:0007124","count":9},{"id":"GO:1901621","count":9},{"id":"GO:1904637","count":9},{"id":"GO:0001963","count":9}]},{"hash":"2023637345175008733","title":"TGF-\u03b2/BMP signaling regulation","description":"The cluster centers on regulatory processes for TGF-\u03b2/BMP signaling, including positive/negative regulation of TGF-\u03b2 receptor signaling, BMP signaling, and SMAD complex assembly, as well as peptidyl-threonine dephosphorylation, suggesting phosphatase involvement. A few terms related to photosystem stoichiometry and meristem identity appear unrelated, but the dominant theme is modulation of TGF-\u03b2/BMP signaling pathways.","confidence":"Medium","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046827","count":8},{"id":"GO:0042347","count":5},{"id":"GO:0071560","count":5},{"id":"GO:0080005","count":5},{"id":"GO:0061191","count":5}]},{"hash":"1566716618707896323","title":"Cholesterol homeostasis and innate immune signaling","description":"This cluster is characterized by GO terms centered on cholesterol homeostasis and trafficking (intracellular cholesterol transport, cholesterol homeostasis, cholesterol efflux) together with innate immune signaling (toll-like receptor 4 signaling pathway, lipopolysaccharide-mediated signaling pathway) and the inflammatory response. The co-occurrence of lipid metabolism and TLR/LPS signaling suggests a functional link between membrane cholesterol handling and inflammatory responses, possibly coordinated at the ER given protein targeting to ER. A few outlier terms (signal peptide processing, learning or memory) are less representative but do not override the core theme.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006465","count":1},{"id":"GO:0045047","count":1},{"id":"GO:0006954","count":1},{"id":"GO:0032367","count":1},{"id":"GO:0006689","count":1}]},{"hash":"1096655384288988774","title":"Developmental transcription and cell cycle control","description":"Top GO terms point to transcription (DNA-templated transcription), development (multicellular organism development, neural tube closure, skeletal system development), and cell-cycle control (G1/S, G2/M transitions), with minor stress and sensory terms. This indicates a cluster of proteins coordinating developmental gene expression with cell-cycle progression.","confidence":"High","size":9,"edges":13,"triangles":4,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0007275","count":4},{"id":"GO:0000082","count":3},{"id":"GO:0000320","count":3},{"id":"GO:0001843","count":3}]},{"hash":"1186031711880150121","title":"PKC signaling and ECM remodeling proteins","description":"Top GO terms emphasize protein kinase C signaling, extracellular matrix disassembly, and regulation of cell adhesion molecule production, suggesting a theme of PKC-driven signal transduction linked to ECM remodeling and adhesion processes. Some terms are obsolete or broad, so while the label PKC signaling and ECM remodeling captures the core signal, the assignment is tentative.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045541","count":1},{"id":"GO:0052547","count":1},{"id":"GO:0070528","count":1},{"id":"GO:0022617","count":1},{"id":"GO:0060355","count":1}]},{"hash":"2137759987531562773","title":"Angiogenesis and endothelial cell migration","description":"The top GO terms are dominated by angiogenesis and positive regulation of endothelial cell migration, indicating a vascular development theme for the cluster. While other terms (ion transport, ATP synthesis, flagellum-related processes) appear at lower frequencies and may reflect background noise or multifunctional proteins, the angiogenic signals are the strongest driver of the cluster's function.","confidence":"Medium","size":9,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043536","count":3},{"id":"GO:0001525","count":3},{"id":"GO:0006814","count":2},{"id":"GO:0042777","count":2},{"id":"GO:0044780","count":2}]},{"hash":"2272715348052277615","title":"Unknown","description":"The listed GO terms span very different biological areas: development in endodermal tissues, chlorophyll biosynthesis, innate/adaptive immune processes (complement activation, T cell activation), cell adhesion and integrin signaling, dendrite regeneration, ubiquitin-dependent proteolysis, metallopeptidase regulation, and cellular extravasation. There is no single cohesive function or pathway that ties these terms together for this protein set, suggesting the cluster does not reflect a specific, unified biological theme.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035987","count":2},{"id":"GO:0015995","count":1},{"id":"GO:0006956","count":1},{"id":"GO:0034113","count":1},{"id":"GO:0031104","count":1}]},{"hash":"1417925096521773378","title":"Hypoxia-Responsive Signaling and Proliferation","description":"The terms cluster around positive regulation of kinase and GTPase activity, autophosphorylation, and cell cycle/proliferation, with a notable emphasis on hypoxia response; together they suggest a theme of regulated signaling pathways contributing to cell growth under stress.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071456","count":5},{"id":"GO:0051028","count":5},{"id":"GO:0071902","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0000278","count":5}]},{"hash":"1266060420210547742","title":"Mitotic Chromatin Remodeling and Epigenetic Regulation","description":"The cluster is dominated by GO terms related to chromatin assembly/remodeling and epigenetic control during mitosis (spindle assembly, centrosome cycle, nucleosome assembly, histone modifications, chromatin remodeling, and epigenetic regulation of gene expression), with supporting mitotic DNA replication checkpoint signaling; a non-chromatin term (uterine gland development) is likely incidental. ","confidence":"High","size":9,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051225","count":3},{"id":"GO:0007098","count":3},{"id":"GO:0006334","count":3},{"id":"GO:0034720","count":3},{"id":"GO:0051573","count":3}]},{"hash":"970667963951257944","title":"Ubiquitin-mediated ER quality control and trafficking","description":"The cluster shows enrichment for ubiquitin-dependent degradation pathways (ERAD, protein ubiquitination), ER-to-Golgi and retrograde transport, and autophagosome maturation, all pointing to proteostasis and trafficking in the ER/secretory system. While there are also cell-cycle\u2013related terms (centromeric chromatin assembly, sister chromatid segregation), the dominant pattern centers on ubiquitin-driven quality control and trafficking within the ER and related degradation pathways. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0051260","count":3},{"id":"GO:0061641","count":2},{"id":"GO:0043162","count":2},{"id":"GO:0000070","count":2}]},{"hash":"1421906700821717569","title":"Unknown","description":"The GO terms are diverse, spanning chromatin assembly, kinetochore localization, regulation of cell proliferation and Wnt signaling, cell migration, apoptosis, nuclear export, and innate immune defense. There isn\u2019t a single cohesive theme tying these functions together for this cluster, suggesting these proteins participate in multiple distinct regulatory processes rather than one specific pathway.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006335","count":3},{"id":"GO:0034501","count":3},{"id":"GO:0008285","count":3},{"id":"GO:0090090","count":3},{"id":"GO:0016477","count":3}]},{"hash":"255646935845868069","title":"TGF-\u03b2/BMP Signaling Regulation","description":"Most of the terms point to modulation of transforming growth factor beta and BMP pathways, including negative regulation of receptor signaling, SMAD-related processes, and dephosphorylation, suggesting the cluster centers on signaling pathway control. Some terms hint at plant-specific processes or photosystem adjustments, which may reflect annotation noise or broader roles, but the core theme is regulation of TGF-\u03b2/BMP signaling.","confidence":"High","size":9,"edges":10,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071560","count":4},{"id":"GO:0080005","count":4},{"id":"GO:0061191","count":4},{"id":"GO:0010991","count":4},{"id":"GO:0010074","count":4}]},{"hash":"883890786569208444","title":"Neural development and signaling with endosomal trafficking","description":"This cluster centers on neural development and neurotransmission, as seen in dopaminergic synaptic transmission and central nervous system axonogenesis. Endosomal transport also points to cellular trafficking important for neural signaling. While there are some non-neural terms (NK T differentiation, p53-related signaling), the dominant GO terms describe neural development and signaling, with endosomal trafficking providing a mechanistic link. Confidence: Medium","confidence":"","size":9,"edges":11,"triangles":6,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":5},{"id":"GO:0007124","count":5},{"id":"GO:1901621","count":5},{"id":"GO:1904637","count":5},{"id":"GO:0001963","count":5}]},{"hash":"1335621903555640014","title":"Ribosome biogenesis and translation","description":"The strongest signals are ribosome biogenesis (GO:0042254) and translation (GO:0006412), pointing to proteins involved in making ribosomes and carrying out protein synthesis. Additional annotations suggest RNA processing/import into the nucleus, which is often linked to ribosome assembly and maturation. A developmental term (neural tube closure) is less directly related and may reflect annotation overlap, but the core theme is ribosome-related functions.","confidence":"High","size":9,"edges":28,"triangles":44,"max_degree":8,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0000122","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0001843","count":2}]},{"hash":"667315822214036251","title":"Ciliogenesis and developmental morphogenesis","description":"The cluster is dominated by GO terms for cilium-related processes (intraciliary transport in cilium assembly; cilium assembly; non-motile cilium assembly) and broad developmental morphogenesis (wing imaginal disc morphogenesis, chaeta morphogenesis/development, spermatid elongation, neuron remodeling). A trafficking term (ER to Golgi transport) fits the secretory needs of morphogenesis. One outlier (MHC class II antigen presentation) likely reflects annotation noise, but the core signal points to cilia-associated development.","confidence":"Medium","size":9,"edges":35,"triangles":77,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0000132","count":1},{"id":"GO:0007476","count":1},{"id":"GO:0008407","count":1},{"id":"GO:0035735","count":1},{"id":"GO:0019886","count":1}]},{"hash":"1242286106834021712","title":"Unknown","description":"There are no GO terms or connections to reveal a shared function for these proteins (Top Terms empty; Edges/Triangles/Max Degree = 0), so a coherent functional label cannot be inferred.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2291395368941389121","title":"Bacterial energy metabolism and motility","description":"Top GO terms cluster around microbial energy metabolism pathways (dissimilatory sulfate reduction, methanogenesis, fermentation, electron transport chain, photosystem I electron transport) and motility structures (bacterial-type flagellum assembly and flagellum-dependent movement). A ribosome disassembly term is a general cellular process that does not contradict this theme. Overall, the cluster appears driven by energy-generation and motility functions typical of bacteria/archaea.","confidence":"Medium","size":9,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0019420","count":1},{"id":"GO:0019385","count":1},{"id":"GO:0032790","count":1},{"id":"GO:0009773","count":1},{"id":"GO:0044780","count":1}]},{"hash":"1141863857479445200","title":"Proteostasis and Oxidative Stress Response","description":"The cluster is dominated by terms related to protein quality control (protein homooligomerization, ERAD-related processes, and proteasomal protein catabolic regulation) and cellular defense against stress (oxidative stress response). Additional terms point to energy metabolism and mitochondrial assembly (ATP metabolic process, complex III assembly), suggesting a proteostasis- and energy-management theme. Some outliers (centromeric chromatin assembly, mitotic checkpoint signaling, competence establishment) may reflect broader annotation links or multifunctionality but do not overturn the core proteostasis/mitochondrial stress signal.","confidence":"Medium","size":9,"edges":13,"triangles":13,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051260","count":7},{"id":"GO:0046034","count":6},{"id":"GO:0071712","count":6},{"id":"GO:0033314","count":6},{"id":"GO:1901800","count":6}]},{"hash":"1520670756961112045","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006338","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0034475","count":1},{"id":"GO:0016441","count":1},{"id":"GO:0071035","count":1}]},{"hash":"726354444366520852","title":"Protein folding and trafficking","description":"This cluster centers on protein maturation and localization, highlighted by post-translational targeting to membranes and protein folding in the ER. SnoRNP assembly and regulation of kinase activity also relate to protein biogenesis and functional modulation, while other terms touch on signaling contexts where mature proteins act. Although there are some development and hormone signaling terms present, the core theme is protein processing and trafficking. Confidence: Medium","confidence":"","size":9,"edges":15,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0031204","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0071374","count":1},{"id":"GO:1901621","count":1},{"id":"GO:0000492","count":1}]},{"hash":"520331044910457687","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000466","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0090114","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0000472","count":3}]},{"hash":"1919465008737312311","title":"Neural development and signaling","description":"Top terms include neural differentiation (midbrain dopaminergic neuron differentiation; oligodendrocyte differentiation; sensory perception of touch) and Wnt signalosome assembly, suggesting a core theme around neural development and related signaling. Other terms related to cell migration, adhesion, and phagosome maturation are present but less central, so the label emphasizes neural development and signaling as the primary pattern.","confidence":"Medium","size":9,"edges":8,"triangles":2,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1903215","count":5},{"id":"GO:0001667","count":5},{"id":"GO:0043316","count":5},{"id":"GO:1900026","count":5},{"id":"GO:0090382","count":5}]},{"hash":"1311114673743442706","title":"Neural development and signaling with endosomal trafficking","description":"Although the cluster contains a mix of terms, a core theme centers on neural development and signaling: axonogenesis in CNS neurons, dopaminergic synaptic transmission, and regulation of developmental signaling pathways (e.g., hedgehog/dorsal-ventral patterning) combined with endosomal transport processes. The presence of calcium signaling (ionomycin response) also supports a neural signaling context. Some terms pertain to broader development or immune contexts, which makes the connection imperfect, but the neural development and trafficking thread is the strongest common theme.","confidence":"Low","size":9,"edges":31,"triangles":55,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":9},{"id":"GO:0007124","count":9},{"id":"GO:1901621","count":9},{"id":"GO:1904637","count":9},{"id":"GO:0001963","count":9}]},{"hash":"1934178683941496501","title":"Amino acid catabolism and tryptophan metabolism","description":"The top GO terms are dominated by amino acid catabolic processes (alanine, aspartate, and glutamate) and kynurenine/kynurenic acid production from tryptophan, with oxaloacetate metabolism linking to central carbon metabolism. Lipid biosynthesis and Notch signaling appear as peripheral annotations, but the central pattern points to amino acid breakdown and related metabolic flux.","confidence":"Medium","size":9,"edges":35,"triangles":77,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019878","count":5},{"id":"GO:0006107","count":4},{"id":"GO:0042853","count":4},{"id":"GO:0006686","count":3},{"id":"GO:0006533","count":3}]},{"hash":"1141996621258461287","title":"Unknown","description":"The top GO terms are spread across very different biological processes (cell size regulation, placenta development, glucose metabolism, transcription, endosome transport, chemotaxis, and neural signaling), and there are no edges connecting proteins in this cluster. This lack of a cohesive functional theme suggests the proteins do not share a single representative function, so the label Unknown with no confidence is appropriate.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045793","count":6},{"id":"GO:0001890","count":6},{"id":"GO:0006006","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0033160","count":6}]},{"hash":"2076427674467465022","title":"Mitochondrial import and energy metabolism","description":"The strongest signals are regulation of mitochondrial membrane permeability and protein import into the mitochondrial matrix, suggesting a mitochondria-centered function. Additional terms for triglyceride and glycogen biosynthesis point to broader cellular energy metabolism linked to mitochondria. Some terms (bacillithiol biosynthetic process, response to sucrose) appear peripheral or outdated, but do not override the mitochondrial/metabolic theme. ","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":2},{"id":"GO:2000134","count":2},{"id":"GO:0070940","count":2},{"id":"GO:1903740","count":2},{"id":"GO:0010867","count":2}]},{"hash":"585888803121475771","title":"RNA processing and gene expression","description":"Based on the top GO terms, the cluster is enriched for translation, RNA catabolic processes, and transcription termination, indicating involvement in RNA metabolism and gene expression regulation. While a few terms are unrelated or obsolete, the dominant signal ties to RNA processing, transcription, and translation machinery, suggesting these proteins function together in gene expression pathways.","confidence":"High","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006401","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0006369","count":2},{"id":"GO:0034396","count":1}]},{"hash":"1474222160932762623","title":"DNA replication and ribosome biogenesis","description":"The top terms are dominated by DNA replication and ribosomal large subunit assembly, with supporting signals from cell-cycle checkpoint signaling and protein homeostasis pathways. This points to a cluster centered on core growth-related processes, including DNA replication and ribosome biogenesis, with supplementary connections to proteostasis and metabolism.","confidence":"Medium","size":9,"edges":10,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0000027","count":2},{"id":"GO:0032092","count":2},{"id":"GO:0046034","count":1},{"id":"GO:0071712","count":1}]},{"hash":"1649728861026738940","title":"Central carbon metabolism and redox balance","description":"The cluster centers on GO terms for pyruvate and malate metabolism and NADP-related metabolism, indicating a shared role in central carbon flux and redox homeostasis. Additional terms like protein tetramerization, cytokinin signaling, liver regeneration, and adaptive thermogenesis appear ancillary, possibly reflecting multifunctional proteins or cross-species annotations; overall, the core theme is energy metabolism.","confidence":"Medium","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006090","count":2},{"id":"GO:0051262","count":2},{"id":"GO:1902031","count":2},{"id":"GO:0043464","count":2},{"id":"GO:0006108","count":2}]},{"hash":"1115356777263659807","title":"Mitochondrial translation and respiration","description":"This cluster centers on mitochondrial function: proteins involved in importing to the mitochondrial matrix, assembling mitochondrial ribosomes, and executing translation, along with ATP metabolism and assembly of the respiratory chain. The overlap of these GO terms suggests a cohesive theme of mitochondrially driven protein synthesis and energy production, with oxidative stress response as a related facet. Some terms are less directly connected (cell cycle, competence for transformation) but do not override the mitochondrial core.","confidence":"High","size":9,"edges":35,"triangles":77,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0030150","count":2},{"id":"GO:0000027","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0046034","count":1},{"id":"GO:0071712","count":1}]},{"hash":"1201723422330470984","title":"Multicellular Development and Transcription","description":"The cluster is enriched for organismal development terms (neural tube closure, forebrain and skeletal system development, multicellular organism development) and transcription/cell cycle processes (DNA-templated transcription, mitotic cell cycle), suggesting proteins involved in developmental regulation and gene expression. Some terms like defense response to Gram-positive bacteria are less directly connected, but may reflect shared signaling roles in development. Overall, the theme is developmental regulation and transcriptional control.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001843","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0001501","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0050830","count":3}]},{"hash":"1358120732905870413","title":"Membrane Ion Transport","description":"The cluster's top GO terms cluster around ion movement and membrane dynamics, including regulation of sodium ion transport, potassium ion export across the plasma membrane, monoatomic cation transmembrane transport, and calcium release from the Golgi into the cytosol, all pointing to ion flux across membranes and membrane potential regulation. A few terms (lipopolysaccharide biosynthetic process, stilbene catabolic process, vestibulocochlear nerve formation, cell division, peptidyl-aspartic acid autophosphorylation) appear less related and may reflect noise or broader annotation. Overall, the dominant theme is ion transport and membrane-associated processes, justifying this label.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0086009","count":3},{"id":"GO:0009103","count":3},{"id":"GO:0002028","count":3},{"id":"GO:0046272","count":3}]},{"hash":"2135877660425774124","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":12,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0006626","count":2},{"id":"GO:0071374","count":1},{"id":"GO:0090084","count":1}]},{"hash":"203746516940541456","title":"Unknown","description":"The top GO terms cover a wide range of regulatory processes (transcription, NF-kappaB signaling, apoptosis), membrane trafficking (receptor recycling, endosome size), and even specialized immune/neural processes (V(D)J recombination, glutamatergic transmission). Because these functions are not cohesively tied to a single clear biological role for all proteins in this cluster, there isn\u2019t a specific, representative label beyond Unknown.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034968","count":1},{"id":"GO:0001881","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0051036","count":1},{"id":"GO:0035023","count":1}]},{"hash":"375827815195932772","title":"Unknown","description":"The top terms are broad and divergent, including nuclear events (phosphorylation, chromosome segregation, DNA replication, telomerase assembly) and diverse responses (xenobiotic, IL-4, hypoxia) plus a plant hormone signal and bacterial motility. The lack of a clear shared function among the proteins makes it impossible to assign a coherent label beyond Unknown.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0016310","count":4},{"id":"GO:0007059","count":3},{"id":"GO:0006261","count":2},{"id":"GO:0009736","count":2},{"id":"GO:0033160","count":2}]},{"hash":"597155576151280677","title":"Calcium signaling and transcription regulation","description":"This cluster centers on terms involving calcium release into the cytosol, regulation of kinase activity, and nuclear/cytoplasmic trafficking of transcription factors, pointing to a core theme of calcium signaling coupled with transcriptional control. Some other terms (muscle and cuticle development, obsolete annotations) appear peripheral or species-specific, but the predominant pattern supports signaling-to-transcription regulation.","confidence":"Medium","size":9,"edges":14,"triangles":3,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0055003","count":4},{"id":"GO:0097274","count":4},{"id":"GO:0008365","count":4},{"id":"GO:1905205","count":4},{"id":"GO:0072286","count":4}]},{"hash":"1421493348124431795","title":"NO detox and ESCRT-mediated trafficking","description":"These proteins appear to be involved in nitric oxide detoxification and nitrogen compound metabolism, while also linking to vesicle-mediated protein sorting and trafficking via ubiquitin, ESCRT, and exosomal pathways. The GO terms combine NO catabolism and detox with multivesicular body sorting, endocytosis, and exosomal secretion, suggesting a theme of responding to NO stress while routing and modifying proteins through vesicle trafficking. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046210","count":1},{"id":"GO:0051410","count":1},{"id":"GO:0015671","count":1},{"id":"GO:0052060","count":1},{"id":"GO:0043162","count":1}]},{"hash":"2226437756869513457","title":"Unknown","description":"The top terms cover cardiac muscle membrane potential regulation, muscle adaptation, interferon response, synaptic vesicle recycling, mitochondrial fission, transporter activity, and vascular development, with no single cohesive function tying all proteins together.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0086036","count":1},{"id":"GO:1901998","count":1},{"id":"GO:0014873","count":1},{"id":"GO:0035455","count":1},{"id":"GO:1903423","count":1}]},{"hash":"1363276581653907483","title":"Transcription Regulation and Chromatin Remodeling","description":"This cluster centers on regulation of RNA polymerase II transcription and chromatin state, as shown by GO terms for transcriptional regulation, negative regulation, transcription by II, and chromatin remodeling, with supporting signals like transcription start-site regulation and histone-related processes. Additional terms hint at broader regulatory roles (ABA response, calcium signaling, development), but the core theme tying the proteins together appears to be controlling gene expression through transcriptional regulation and chromatin dynamics. ","confidence":"Medium","size":9,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0036091","count":4},{"id":"GO:0000122","count":4},{"id":"GO:0043044","count":3},{"id":"GO:0009737","count":3},{"id":"GO:0006366","count":3}]},{"hash":"1230066106721780121","title":"Unknown","description":"There are 9 proteins with a reasonably connected network (18 edges, 17 triangles), but no GO terms are listed to reveal a common function, so a meaningful label cannot be inferred.","confidence":"","size":9,"edges":18,"triangles":17,"max_degree":7,"top_function":null,"top_go_terms":[]},{"hash":"255333341104342860","title":"Splicing and mRNA processing regulation","description":"The top GO terms point to RNA maturation and post-transcriptional control (mRNA processing, spliceosomal tri-snRNP assembly, processing body regulation), with some ubiquitin-related regulation of these factors. This suggests the cluster\u2019s proteins mainly participate in splicing and mRNA metabolism rather than other processes.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070537","count":1},{"id":"GO:0006397","count":1},{"id":"GO:0008583","count":1},{"id":"GO:0034394","count":1},{"id":"GO:1900425","count":1}]},{"hash":"936647987968274405","title":"Coenzyme and nucleotide catabolism","description":"The top GO terms are dominated by catabolic processes for small metabolites, including CoA, NAD+, dADP, diadenosine pentaphosphate, and IPP/IP derivatives. This suggests the proteins in the cluster are linked by a shared theme of breaking down cofactors and nucleotides rather than a single specific pathway; the absence of edges supports sparse, context-dependent interactions, but the GO terms collectively point to cofactor and nucleotide catabolism as the common function.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901639","count":1},{"id":"GO:2000233","count":1},{"id":"GO:0015938","count":1},{"id":"GO:0046057","count":1},{"id":"GO:0019677","count":1}]},{"hash":"546246082373648971","title":"PARP-Linked DNA Repair and DDR","description":"The cluster is dominated by terms tied to poly-ADP-ribosylation and multiple DNA repair pathways (base-excision repair, alternative NHEJ, DNA ligation, mitochondrial DNA repair) plus DNA damage response signals and oxidative stress\u2013linked apoptosis regulation, pointing to a PARP-driven DNA damage response module. While some terms are obsolete, the core theme reflects PARP activity coordinating DNA repair and genome stability.","confidence":"High","size":9,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0070212","count":3},{"id":"GO:0097681","count":2},{"id":"GO:0006288","count":2},{"id":"GO:1990966","count":2},{"id":"GO:1903376","count":2}]},{"hash":"1253709657813782850","title":"Multi-tissue development and signaling","description":"The top GO terms point to developmental processes across multiple tissues (skin, spinal cord, metanephric/pronephros development, vulval location) and related signaling (JAK-STAT) with some cell cycle regulation and osmotic stress responses. This suggests a broad theme of organ/tissue development with signaling involvement, rather than a single, tight protein complex. The absence of edges supports a descriptive, multi-function cluster rather than a tight interaction cluster.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034606","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0043588","count":2},{"id":"GO:0034608","count":2},{"id":"GO:0007050","count":2}]},{"hash":"6176111976435683","title":"Epigenetic Regulation of Development","description":"This cluster combines developmental morphogenesis terms (brain, uterus, mammary gland structures) with epigenetic regulation (histone demethylation) and stem cell differentiation, plus RNAi-related regulation (RITS). The common thread appears to be epigenetic control of developmental programs and cell fate decisions across tissues. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021555","count":1},{"id":"GO:0033169","count":1},{"id":"GO:0034630","count":1},{"id":"GO:0060763","count":1},{"id":"GO:0060275","count":1}]},{"hash":"415787359699798361","title":"Membrane potential regulation and ion transport","description":"The cluster is dominated by GO terms for potassium and sodium ion transport across membranes and regulation/stabilization of membrane potential, including cardiac atrial repolarization, which together point to membrane excitability and ion channel control. Also present are cellular responses to cGMP and cAMP and signaling pathway regulation, which can modulate membrane potential. A few terms (aerotaxis, touch perception) are peripheral but do not outweigh the core theme.","confidence":"High","size":9,"edges":32,"triangles":60,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071805","count":9},{"id":"GO:0098719","count":8},{"id":"GO:0071321","count":8},{"id":"GO:0010754","count":8},{"id":"GO:0098914","count":8}]},{"hash":"59793052925720870","title":"Post-transcriptional RNA processing and translation control","description":"This cluster centers on post-transcriptional regulation of gene expression, with GO terms spanning mRNA splicing via the spliceosome, mRNA stability and modification, miRNA- and ncRNA-mediated silencing, and assembly of the EIF4F translation initiation complex. The common theme is RNA processing and control of translation rather than transcriptional regulation, suggesting a coherent post-transcriptional regulatory module among these proteins.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":2},{"id":"GO:0048025","count":2},{"id":"GO:0035278","count":2},{"id":"GO:0010610","count":2},{"id":"GO:0016556","count":2}]},{"hash":"2038451680054888107","title":"Nucleolar RNA Processing and Ribosome Biogenesis","description":"This cluster centers on nucleolar and nuclear RNA processing and ribosome-related steps, as indicated by GO terms for snoRNA processing, RNase MRP-dependent mRNA catabolic process, chromosome condensation, translation, and ribosomal large subunit export from the nucleus. While there are a couple of outliers (maltose transport, pollen sperm cell differentiation, ER organization), the dominant themes point to nucleolar RNA maturation and ribosome assembly/export, suggesting proteins that participate in ribosome biogenesis and early translation-related processes in the nucleus/nucleolus. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030261","count":1},{"id":"GO:0000294","count":1},{"id":"GO:0034965","count":1},{"id":"GO:0048235","count":1},{"id":"GO:1904751","count":1}]},{"hash":"1340739567538554270","title":"Ion Transport and Membrane Potential","description":"The top GO terms emphasize membrane repolarization and transmembrane ion movement (K+, Na+, Ca2+, Cu), including import/export and calcium release, pointing to proteins involved in ion transport and maintaining membrane potential. While there are a few odd terms (nerve development, autophosphorylation, obsolete signaling regulation), the dominant pattern is ion transport across membranes. Therefore, the label Ion Transport and Membrane Potential captures the cluster's main theme.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0086009","count":2},{"id":"GO:0002028","count":2},{"id":"GO:0021650","count":2},{"id":"GO:1990938","count":2},{"id":"GO:0097623","count":2}]},{"hash":"1312006870339134004","title":"Growth and apoptosis signaling","description":"The terms show a mix of apoptotic regulation (extrinsic pathway regulation, apoptotic morphogenesis) and growth/signaling processes (TORC1 signaling, GTPase/Rab regulation, endothelial proliferation), plus related nuclear transport and cell cycle events (nuclear membrane reassembly, NLS import). This suggests a cluster centralized around coordinating cell survival, growth, and intracellular signaling rather than a single narrowly defined function, hence a label like \u201cGrowth and apoptosis signaling.\u201d","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001241","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0032483","count":2},{"id":"GO:0007084","count":1},{"id":"GO:0045945","count":1}]},{"hash":"16434184935290809","title":"Unknown","description":"The top GO terms are diverse, including plant leaf formation regulation, bacterial ectoine biosynthesis, polyamine catabolic and acetylation processes, N-acetylglucosamine metabolism, and mitotic chromatid cohesion, with no single dominant function. Edges are absent, suggesting no cohesive interaction network, so there is no clear unifying theme for this cluster.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000025","count":3},{"id":"GO:0017198","count":3},{"id":"GO:0019491","count":3},{"id":"GO:0046208","count":3},{"id":"GO:0009447","count":3}]},{"hash":"332396050895225763","title":"Ion Transport and Calcium Signaling Regulators","description":"This cluster centers on terms involving ion homeostasis and calcium-dependent signaling (membrane repolarization, regulation of cytosolic Ca2+, regulation of sodium transport, and calcineurin-NFAT pathway), suggesting a shared role in modulating ion flux and related signaling. A few other GO terms (lipopolysaccharide biosynthesis, stilbene catabolism, nerve formation) appear noisy or unrelated, likely reflecting misannotations or cross-species matches, but the core signals point to ion transport regulation. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0086009","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0031947","count":2},{"id":"GO:0051481","count":2},{"id":"GO:0002028","count":2}]},{"hash":"2289303855531144999","title":"Neuromuscular junction assembly and muscle contraction","description":"This cluster\u2019s strongest signals are GO terms for synaptic assembly at the neuromuscular junction and muscle contraction, suggesting a module tied to NMJ formation and muscle function. Other terms (ribosome biogenesis, ER membrane fusion, and others) appear less coherently, indicating some peripheral associations. The sparse network (one edge) supports a small, functionally focused group centered on NMJ-related processes.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0009644","count":1},{"id":"GO:0016320","count":1},{"id":"GO:0032463","count":1},{"id":"GO:0006936","count":1}]},{"hash":"1996573585225500079","title":"RNA Processing and Gene Expression Regulation","description":"The top GO terms cluster around RNA processing (mRNA splicing, export) and translation initiation, along with chromatin assembly and ubiquitination, suggesting regulation of gene expression at multiple levels (transcriptional, post-transcriptional, and protein turnover). Some terms like cytokine production and dendrite development are more downstream, but can reflect expression-driven responses. Overall, a coherent theme is RNA processing and gene expression regulation.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008283","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0002188","count":3},{"id":"GO:2000728","count":2},{"id":"GO:1904668","count":2}]},{"hash":"95649645162590324","title":"Endosome-ER trafficking and neuronal/immune signaling","description":"This cluster's top GO terms center on intracellular trafficking: localization of proteins to endosomes, regulation of ER exit, and reticulophagy, indicating involvement in the secretory pathway and ER quality control. Additional terms touch on nervous system development and immune signaling (T cell receptor signaling, cell migration, axonogenesis). The common thread is coordination of protein trafficking with signaling processes in neurons and immune cells, suggesting this label.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036010","count":2},{"id":"GO:0070863","count":2},{"id":"GO:0061709","count":1},{"id":"GO:1903215","count":1},{"id":"GO:0007399","count":1}]},{"hash":"2095919722382683983","title":"Mitochondrial membrane regulation and matrix import","description":"This cluster is centered on mitochondrial functions, with strong representation for regulation of mitochondrial membrane permeability and protein import into the mitochondrial matrix, plus related mitochondrial dynamics/metabolic processes. Some terms are peripheral or obsolete, and a couple relate to organismal behavior, but the core signal points to mitochondrial maintenance and metabolism. Confidence: High","confidence":"","size":9,"edges":15,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":6},{"id":"GO:2000134","count":6},{"id":"GO:0070940","count":6},{"id":"GO:1903740","count":6},{"id":"GO:0010867","count":6}]},{"hash":"749457945384124521","title":"Steroid Hormone and Retinoid Metabolism","description":"This cluster is dominated by GO terms for androgen and steroid hormone biosynthesis (androgen metabolic process, testosterone biosynthetic process, C21-steroid hormone metabolic process) and retinoid metabolism (retinal and retinol metabolic processes), indicating a core theme of steroid hormone and vitamin A-related metabolism. Other terms mention lipid-related and pigment-related processes, but they are less central to the main signal. Therefore, Steroid Hormone and Retinoid Metabolism best captures the cluster\u2019s function.","confidence":"Medium","size":9,"edges":7,"triangles":1,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0008209","count":5},{"id":"GO:0061370","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0042574","count":5},{"id":"GO:0042572","count":5}]},{"hash":"1751126129597613296","title":"Unknown","description":"The top terms cover a mix of mitochondrial inheritance, nutrient and lipid metabolism (nitrate assimilation, nitric oxide, ergosterol and fatty acid biosynthesis, MIPC metabolism), along with mammalian differentiation and hormone-related processes (sebaceous gland differentiation, CNS myelin maintenance, androgen metabolism) and cell cycle regulation. This lack of a cohesive, single biological theme or pathway makes it unclear what a shared function would be for this cluster.","confidence":"","size":9,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000001","count":5},{"id":"GO:0042128","count":5},{"id":"GO:0006809","count":5},{"id":"GO:0001949","count":5},{"id":"GO:0032286","count":5}]},{"hash":"1660866001849403262","title":"Unknown","description":"The terms are a scattered mix of ubiquitination/ERAD, hormone biosynthesis (androgen, testosterone, brassinosteroid) and development (mammary gland, female gonad), plus a cell-cycle regulation term, with several entries marked obsolete. There is no single coherent function or pathway linking these proteins, and the lack of edges supports the idea of diverse, unrelated roles, so a specific cluster label cannot be confidently assigned.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0008209","count":2},{"id":"GO:1900087","count":2},{"id":"GO:0016132","count":2}]},{"hash":"1763302596127040193","title":"Unknown","description":"There are no GO terms or connectivity signals for this cluster (no edges or triangles, no top terms), so any shared function cannot be inferred. Without a common functional theme, Unknown with no confidence is the appropriate label.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"600703852228542889","title":"Small-molecule catabolism and redox metabolism","description":"The top GO terms center on degradation of small substrates (alkane, leucine, uracil) and related metabolic pathways (lipoate metabolism), with redox-related activities such as protein glutathionylation and cellular response to menadione. Despite some obsolete terms, the overall theme ties together catabolic processes of diverse compounds with redox regulation and oxidative stress responses, justifying a label focused on metabolism and redox.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043448","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0043046","count":1},{"id":"GO:0007369","count":1},{"id":"GO:0006552","count":1}]},{"hash":"2130248799035839409","title":"Mitochondrial metal ion and metabolite transport","description":"This cluster is dominated by GO terms describing transport of metals and metabolites across mitochondrial membranes (manganese ion transport, iron import into the mitochondrion, NAD transmembrane transport, thiosulfate transport) and regulation of mitochondrial permeability, with additional metabolic context terms (adaptive thermogenesis, liver regeneration, response to fatty acid). Together these suggest a coherent theme of mitochondrial metal/ cofactor transport and metabolic regulation, rather than a single, non-mpecific function.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006828","count":2},{"id":"GO:0097421","count":1},{"id":"GO:1990845","count":1},{"id":"GO:0060546","count":1},{"id":"GO:0097274","count":1}]},{"hash":"486582712804391780","title":"Membrane proteolysis and signaling regulation","description":"The top GO terms point to proteolytic processing of membrane proteins (ectodomain and intramembrane proteolysis, autoproteolysis), with additional signals related to signaling pathways (calcineurin-NFAT, cGMP) and physiological regulation (immune response, renin-angiotensin). This suggests a cohesive theme around membrane-protein cleavage modulating downstream signaling and regulatory processes.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051533","count":1},{"id":"GO:0070886","count":1},{"id":"GO:0006509","count":1},{"id":"GO:1904211","count":1},{"id":"GO:0050776","count":1}]},{"hash":"1782031195648863606","title":"RNA processing and translation control","description":"The top GO terms cluster around RNA metabolism, with strong signals for translation-related steps (initiation, termination, translational fidelity, cytoplasmic translation, and ribosome disassembly) as well as spliceosome-related processes (tri-snRNP complex assembly and first transesterification step). This suggests a group of proteins involved in RNA processing and the regulation of protein synthesis. A few terms (response to antibiotic, brain-derived neurotrophic factor stimulus, hematopoietic progenitor differentiation) appear less central, likely reflecting broader regulatory connections rather than core cluster function. ","confidence":"Medium","size":9,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1990145","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0006413","count":1},{"id":"GO:0032790","count":1},{"id":"GO:0002184","count":1}]},{"hash":"293912150377368749","title":"Developmental Serine/Threonine Kinase Regulation","description":"This cluster centers on development-related processes (brain, skin, multicellular organism development) and kinase signaling, with multiple GO terms for regulation of peptidyl-threonine phosphorylation, serine/threonine kinase activity, and autophosphorylation, suggesting proteins involved in developmental signaling that are modulated by phosphorylation.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0010800","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0010801","count":2},{"id":"GO:0071902","count":2}]},{"hash":"2033631165816627696","title":"Ubiquitin-Dependent NF-\u03baB and TNF Signaling","description":"The cluster\u2019s terms are dominated by ubiquitination processes (K48, K63, K6 linkages; ubiquitin-dependent proteolysis; autoubiquitination) and signaling pathways such as canonical NF-\u03baB activation and TNF signaling, with additional notes on negative regulation of necroptosis and histone turnover, pointing to a cohesive group of proteins modulating inflammatory signaling via ubiquitin tagging and degradation.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0043123","count":6},{"id":"GO:0051865","count":6},{"id":"GO:0060546","count":6},{"id":"GO:0042787","count":6},{"id":"GO:0036205","count":6}]},{"hash":"1796306399319028354","title":"Ciliary motility and tubulin PTMs","description":"This cluster is driven by GO terms linked to cilium movement, regulation of axon extension, and post-translational modifications of tubulin (polyglycylation and polyglutamylation), which together point to ciliary/microtubule function and motility. A few terms about membrane targeting and metabolism appear less connected, but the core signals support a ciliary and tubulin modification theme.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031204","count":1},{"id":"GO:0006620","count":1},{"id":"GO:0090180","count":1},{"id":"GO:2001172","count":1},{"id":"GO:0007527","count":1}]},{"hash":"528189850978165246","title":"Unknown","description":"The terms are from very disparate biological areas \u2014 plant hormone biosynthesis, neural tissue organization, mammalian signal transduction and cell cycle regulation, RNA processing, and cell adhesion \u2014 with no dominant common function linking them. There is no clear theme or pathway that ties most proteins together, so a specific functional label cannot be confidently assigned.","confidence":"","size":9,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009688","count":4},{"id":"GO:0032487","count":4},{"id":"GO:0021693","count":4},{"id":"GO:0009190","count":4},{"id":"GO:0070535","count":4}]},{"hash":"74655892040628547","title":"Spliceosome-Driven mRNA Processing","description":"These proteins are strongly enriched for mRNA processing terms, especially splicing via the spliceosome (cis and alternative), plus polyadenylation regulation, mRNA modification, and stress-related mRNA stability, indicating a cluster of spliceosome-associated RNA processing regulators.","confidence":"High","size":9,"edges":34,"triangles":70,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":8},{"id":"GO:0006378","count":8},{"id":"GO:1900363","count":6},{"id":"GO:0048025","count":6},{"id":"GO:0035278","count":6}]},{"hash":"340291470572802800","title":"Sterol and lipid biosynthesis","description":"Most top GO terms center on sterol production and lipid metabolism (cholesterol biosynthetic process via lathosterol, ergosterol biosynthetic process, fatty acid biosynthetic process, ether lipid metabolic process, and related sterol oxidation terms), indicating a cohesive theme around lipid biosynthesis pathways. A few terms (central nervous system myelin maintenance, B cell chemotaxis, sebaceous gland cell differentiation) are less connected to lipid biosynthesis and may reflect broader or incidental annotations. Overall, the cluster is best described by sterol and lipid biosynthesis functions.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033490","count":6},{"id":"GO:0080065","count":6},{"id":"GO:0006696","count":6},{"id":"GO:0001949","count":6},{"id":"GO:0046485","count":6}]},{"hash":"1952970723069431530","title":"Motor Neuron Differentiation and Neuromuscular Movement","description":"GO terms point to spinal cord motor neuron differentiation, neuromuscular processes for balance, and musculoskeletal movement, indicating a shared role in motor neuron development and neuromuscular function. While other terms (IGF signaling, RNA regulation, DNA damage checkpoint) are present, they appear secondary to the neural/motor theme. Confidence: Medium.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050881","count":1},{"id":"GO:0050885","count":1},{"id":"GO:0031571","count":1},{"id":"GO:0048009","count":1},{"id":"GO:0061157","count":1}]},{"hash":"527580131560209638","title":"Unknown","description":"The top GO terms are highly diverse, ranging from mammary gland development and epithelial proliferation to glycoprotein catabolic processes, CD40 signaling, necroptosis regulation, late viral transcription, X-ray response, and various metabolic/regulatory processes. This spread suggests there is no single cohesive function that unites these proteins. Consequently, I cannot confidently assign a specific, representative label beyond Unknown.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006516","count":1},{"id":"GO:0023035","count":1},{"id":"GO:0060546","count":1},{"id":"GO:0019086","count":1},{"id":"GO:0060749","count":1}]},{"hash":"644147215032536939","title":"Mitochondrial Lipid Biosynthesis and Dynamics","description":"The top GO terms center on mitochondrial lipid metabolism (cardiolipin and phosphatidic acid biosynthesis, general lipid catabolism) and mitochondrial dynamics/transport (positive regulation of mitochondrial fusion, microtubule-based movement). While a couple of terms touch broader processes (P granule organization, nervous system development, intracellular viral protein transport), the strongest signal is mitochondria-associated lipid biology and movement, justifying this focused label.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030719","count":1},{"id":"GO:0032049","count":1},{"id":"GO:0016042","count":1},{"id":"GO:0048017","count":1},{"id":"GO:0006654","count":1}]},{"hash":"1057094496135120016","title":"Unknown","description":"There are no GO terms or functional connections present for this cluster (zero edges, no top terms), so no coherent common function can be inferred to assign a specific label. With only 9 proteins and no interactions, the data provide no basis for a representative name; the mention of ReCIPE re-adding 3 proteins does not add functional coherence. ","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2073887301047232251","title":"Glucose-responsive TORC1 and lipophagy signaling","description":"The top GO terms cluster around metabolic sensing and growth control: glucose response and glucose homeostasis, positive regulation of lipophagy, and regulation of TORC1 signaling alongside PI3K/AKT pathway involvement. Leucine responsiveness and ER-stress\u2013related translation regulation further point to amino acid\u2013 and stress-responsive control of mTOR/TORC1 signaling, tying lipid turnover to nutrient signaling. This suggests a coherent module of metabolic regulation, growth, and lipophagy, hence the name. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904504","count":2},{"id":"GO:0009749","count":2},{"id":"GO:1904262","count":2},{"id":"GO:0042593","count":2},{"id":"GO:0036091","count":2}]},{"hash":"754050475939688201","title":"Angiogenesis and Vascular Remodeling Regulators","description":"The GO terms cluster around blood vessel formation and regulation (coronary vasculature development; positive regulation of VEGF receptor signaling; negative regulation of smooth muscle cell migration; sarcomere organization), suggesting roles in angiogenesis and vascular remodeling. Additional terms touch on lipid and inflammatory signaling (lipoprotein stimulus; TLR4 signaling) that commonly accompany vascular processes, while a couple of development terms reflect broader morphogenesis contexts. Overall, the core theme is regulation of vascular growth and remodeling.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071404","count":1},{"id":"GO:0050748","count":1},{"id":"GO:0060976","count":1},{"id":"GO:1901299","count":1},{"id":"GO:0030949","count":1}]},{"hash":"2276963111437098357","title":"Neural development and dopaminergic signaling","description":"The cluster is enriched for neural development and signaling terms, including dopaminergic synaptic transmission and CNS projection neuron axonogenesis, suggesting a module involved in neural growth and neurotransmission; a few items (endosome transport, centrosome separation, and immune-related terms) are peripheral or noisy annotations but do not override the dominant neural theme.","confidence":"Medium","size":8,"edges":5,"triangles":1,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007100","count":7},{"id":"GO:0046827","count":5},{"id":"GO:2000641","count":4},{"id":"GO:0007124","count":4},{"id":"GO:1901621","count":4}]},{"hash":"1518529858830737431","title":"Neural signaling and development with ERK regulation","description":"The cluster shows strong signals for neuronal signaling and development: excitatory postsynaptic potential, calcium-dependent exocytosis, and Schwann cell development, all tied together by ERK1/ERK2 cascade regulation. While there are cell-cycle terms present, they may reflect broader regulatory roles or annotation overlap; the dominant theme centers on synaptic signaling and neural development with active ERK signaling pathways.","confidence":"Medium","size":8,"edges":8,"triangles":3,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0060079","count":8},{"id":"GO:0034501","count":7},{"id":"GO:0042220","count":7},{"id":"GO:0000082","count":7},{"id":"GO:0006260","count":7}]},{"hash":"2044309620163384597","title":"Neural Development and Signaling","description":"The top GO terms point to neural development and function, including CNS projection neuron axonogenesis, dopaminergic synaptic transmission, and dorsal/ventral neural tube patterning, with supporting roles in calcium signaling and endosomal transport. While a few terms touch on immune or cartilage processes, the dominant theme is neuronal development and signaling pathways, justifying this label.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":8},{"id":"GO:0007124","count":8},{"id":"GO:1901621","count":8},{"id":"GO:1904637","count":8},{"id":"GO:0001963","count":8}]},{"hash":"278931020357866462","title":"Redox Homeostasis and Calcium Signaling","description":"This cluster centers on antioxidant and redox-related processes (glutathione metabolism, glutathionylation, cellular oxidant detoxification, and ascorbate metabolism) and includes regulation of calcium release from the sarcoplasmic reticulum via ryanodine receptors. Together these terms point to a coordinated state of redox balance linked to Ca2+ signaling, with a few metabolism terms (homogentisate/aromatic amino acids) that may reflect broader metabolic context but are less central to the core theme.","confidence":"High","size":8,"edges":27,"triangles":50,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":6},{"id":"GO:0045454","count":6},{"id":"GO:0010880","count":4},{"id":"GO:1902000","count":4},{"id":"GO:0042594","count":4}]},{"hash":"1341276667571525175","title":"Unknown","description":"The cluster shows a mix of muscle-related development (skeletal muscle fiber development; cardiac myofibril assembly) and calcium transporter regulation, but also terms for brain development, fungal conjugation, cuticle development, and urea homeostasis, indicating no single coherent function across all proteins. Therefore, there is no clear theme to label it differently; Unknown with None confidence.","confidence":"","size":8,"edges":7,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":3},{"id":"GO:0000742","count":3},{"id":"GO:0048741","count":3},{"id":"GO:0021762","count":3},{"id":"GO:0055003","count":2}]},{"hash":"1479720735773342432","title":"Propionate/TCA Metabolism and Quinone Biosynthesis","description":"The top GO terms cluster around propionate catabolism and the TCA cycle, with concurrent biosynthesis of quinones (phylloquinone and menaquinone) and other central carbon metabolism processes (acetyl-CoA, pyruvate, inositol, and branched-chain amino acid catabolism). This indicates a cohesive metabolic module focused on energy generation and quinone cofactor production in microbes, justifying a label that emphasizes both central carbon metabolism and quinone biosynthesis.","confidence":"High","size":8,"edges":24,"triangles":35,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0019679","count":4},{"id":"GO:0006099","count":4},{"id":"GO:0019629","count":4},{"id":"GO:0006085","count":4},{"id":"GO:0042372","count":2}]},{"hash":"1663739987033645327","title":"Immune Signaling and Redox Regulation","description":"These proteins cluster around immune signaling and oxidative stress responses: Fc-epsilon receptor and T cell receptor pathways indicate immune signaling, while cellular response to hydrogen peroxide and oxidant detoxification reflect redox regulation. Prostaglandin biosynthesis and zinc ion response further connect to inflammatory signaling, with negative regulation of inflammatory response suggesting modulatory control. Some terms about male gonad development and germ cell proliferation may reflect tissue-specific roles rather than core cluster function.","confidence":"Medium","size":8,"edges":13,"triangles":13,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0070301","count":3},{"id":"GO:0002862","count":2},{"id":"GO:2000255","count":2},{"id":"GO:0051897","count":2},{"id":"GO:0098869","count":2}]},{"hash":"1301784275204534289","title":"Cell Cycle and Nuclear Organization","description":"The top GO terms are dominated by cell division and cell cycle, with supporting nuclear-process terms such as pore complex assembly, Cajal body\u2013specific localization, and telomere maintenance via telomerase. Although some terms relate to stress responses, the core theme centers on nuclear organization and genome maintenance during cell-cycle progression, justifying this label.","confidence":"Medium","size":8,"edges":11,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0007049","count":4},{"id":"GO:1901998","count":3},{"id":"GO:1904871","count":3},{"id":"GO:1903427","count":3}]},{"hash":"1951768899609109181","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":9,"triangles":3,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0034475","count":2},{"id":"GO:0016441","count":2},{"id":"GO:0071035","count":2},{"id":"GO:0000398","count":2}]},{"hash":"2075011803483042694","title":"Proteostasis and Stress Response","description":"Top GO terms cluster around protein quality control and stress responses (sumoylation, unfolded protein response, proteasomal degradation, and regulation of inclusion body assembly), along with metal/metal-cofactor stress (cadmium response, iron-sulfur cluster assembly). DNA replication and morphogenesis terms are present but less central, so the label reflects the dominant proteostasis and stress-related functions.","confidence":"Medium","size":8,"edges":8,"triangles":1,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0016925","count":4},{"id":"GO:0006260","count":3},{"id":"GO:0000902","count":3},{"id":"GO:0043433","count":3},{"id":"GO:0071276","count":3}]},{"hash":"1039513941325661035","title":"ECM Organization and Tissue Remodeling","description":"The cluster\u2019s top terms cluster around extracellular matrix organization and tissue remodeling (ECM organization, positive regulation of cell-substrate adhesion, connective tissue replacement), suggesting a cohesive theme of matrix dynamics and tissue morphogenesis, including some related cardiac/muscle structure terms. Some terms like ribosome biogenesis and kinase activation are broader cellular processes that don\u2019t contradict this ECM-centric view. Overall, the label highlights ECM remodeling and tissue adhesion as the primary theme.","confidence":"Medium","size":8,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0032147","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0055003","count":1},{"id":"GO:0033591","count":1},{"id":"GO:0010811","count":1}]},{"hash":"507998306560457305","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":18,"triangles":23,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0048701","count":8},{"id":"GO:0034475","count":4},{"id":"GO:0016441","count":4},{"id":"GO:0071035","count":4}]},{"hash":"321031166995764352","title":"Splicing and mRNA processing machinery","description":"This cluster is dominated by terms related to RNA maturation: spliceosome-mediated splicing, small-subunit processome assembly, alternative splicing, and mRNA export. While a few terms (like virion assembly) are less connected, the strongest signals point to RNA processing and splicing functions as the core theme.","confidence":"Medium","size":8,"edges":22,"triangles":31,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1901407","count":5},{"id":"GO:0031047","count":4},{"id":"GO:0048026","count":4},{"id":"GO:0019068","count":3},{"id":"GO:0000380","count":3}]},{"hash":"805234289119368140","title":"Ubiquitin-Mediated Signaling Regulation","description":"This cluster is dominated by terms tying protein ubiquitination to downstream signaling and turnover. Repeated themes include ubiquitin tagging and autoubiquitination, ubiquitin-dependent degradation (ERAD and general proteolysis), and the modulation of signaling pathways such as TNF and RIG-I, plus Wnt receptor turnover and organ growth regulation. Together, these point to a core role in ubiquitin-controlled regulation of signaling components and protein stability.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046621","count":2},{"id":"GO:0038018","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0033151","count":2}]},{"hash":"8580625907802540","title":"Unknown","description":"The terms cover a wide and unrelated set of processes (neuroblast division, gluconeogenesis, DNA repair checkpoints, protein dephosphorylation, signaling regulation, and vesicular transport to melanosomes, among others) with only single-term associations, offering no clear common function to label the cluster coherently.","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055059","count":1},{"id":"GO:0045722","count":1},{"id":"GO:2001034","count":1},{"id":"GO:0072462","count":1},{"id":"GO:0006470","count":1}]},{"hash":"1309412093199101045","title":"Neural development and dopaminergic signaling","description":"Several top GO terms point to neural development and neurotransmission, notably dopaminergic synaptic transmission and CNS projection neuron axonogenesis, as well as dorsal/ventral neural tube patterning. While other terms touch on broader cellular processes (endosome transport, nuclear export), the neural development and signaling signals dominate, suggesting this cluster centers on neural differentiation and dopamine-related communication.","confidence":"Medium","size":8,"edges":8,"triangles":1,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046827","count":8},{"id":"GO:2000641","count":7},{"id":"GO:0007124","count":7},{"id":"GO:1901621","count":7},{"id":"GO:1904637","count":7}]},{"hash":"729680516849092588","title":"Stress-Responsive Developmental Signaling and RNA Transport","description":"The cluster combines regulatory signaling (positive regulation of kinase activity, autophosphorylation, and GTPase activity) with stress-responsive processes (hypoxia response; heat-stress\u2013related mRNA export) and development-related roles (skin and multicellular development, mitotic cell cycle, proliferation). This pattern suggests proteins that coordinate signaling and gene expression to support development under stress rather than a single, narrow pathway.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071456","count":6},{"id":"GO:0051028","count":6},{"id":"GO:0071902","count":6},{"id":"GO:0043547","count":6},{"id":"GO:0043588","count":6}]},{"hash":"595219711515611290","title":"Unknown","description":"The top GO terms span diverse processes (DNA replication, endosome transport, fungal pseudohyphal growth, neural signaling, p53 regulation, NK T cell differentiation, and CNS axonogenesis), with no clear unifying biological theme across species or systems. This heterogeneity suggests there isn\u2019t a single cohesive function for this cluster, so a generic Unknown label is most appropriate.","confidence":"","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:2000641","count":7},{"id":"GO:0007124","count":7},{"id":"GO:1901621","count":7},{"id":"GO:1904637","count":7}]},{"hash":"791377143123831064","title":"Neuronal development and signaling with endosomal trafficking","description":"This cluster's top terms center on neural development and signaling\u2014axonogenesis, dopaminergic synaptic transmission, and neural tube patterning\u2014suggesting a shared role in neuronal differentiation and communication. The presence of regulation of endosome transport also points to intracellular trafficking that supports neuronal signaling. While some terms touch on immune or cartilage development, the strongest common theme is neural development and signaling with linked endosomal trafficking.","confidence":"Medium","size":8,"edges":21,"triangles":24,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":8},{"id":"GO:0007124","count":8},{"id":"GO:1901621","count":8},{"id":"GO:1904637","count":8},{"id":"GO:0001963","count":8}]},{"hash":"999904599896203527","title":"Ciliogenesis and cell-cycle growth signaling","description":"The top GO terms cluster around ciliary biology\u2014intraciliary transport and basal body docking, cilium assembly\u2014as well as cell-cycle-related processes (mitotic nuclear membrane reassembly) and nuclear import. Additional terms indicate growth regulation (TORC1 signaling, kinase activity) and RNA Pol III transcription. Together these suggest a theme where ciliogenesis is connected with cell-cycle progression and growth signaling, making this label representative of the cluster.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007084","count":2},{"id":"GO:0045945","count":2},{"id":"GO:0097711","count":2},{"id":"GO:0001938","count":2},{"id":"GO:0060561","count":2}]},{"hash":"17467963055047365","title":"Nuclear RNA transport and splicing-factor import","description":"The cluster is dominated by GO terms related to import of RNA-binding and RNA-processing proteins into the nucleus (hnRNPs, snRNPs, splicing factors), as well as nuclear export/import of tRNA. While a couple of terms appear unrelated (kinetochore localization, neuronal signaling), the common theme is nuclear trafficking of RNA-related proteins and RNAs, suggesting a coherent role in nuclear RNA processing and transport.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006609","count":1},{"id":"GO:0006608","count":1},{"id":"GO:0035048","count":1},{"id":"GO:0051031","count":1},{"id":"GO:0071528","count":1}]},{"hash":"1652633495900110738","title":"Neural development and signaling","description":"This cluster is best described by a theme of neural development and signaling: it includes terms tied to CNS neuron axonogenesis and dopaminergic synaptic transmission, as well as regulation of developmental signaling pathways (e.g., Hedgehog-related smoothened signaling) and calcium-responsive processes (ionomycin). While some terms point to broader developmental processes (e.g., cartilage condensation, NK T cell differentiation, p53 signaling), the strongest and most coherent signals center on neural development and neuronal communication.","confidence":"Medium","size":8,"edges":15,"triangles":10,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":8},{"id":"GO:0007124","count":8},{"id":"GO:1901621","count":8},{"id":"GO:1904637","count":8},{"id":"GO:0001963","count":8}]},{"hash":"101543954705984931","title":"Unknown","description":"The GO terms span very different biological contexts\u2014amoeboid cell migration, copper ion homeostasis, cytotoxic T cell degranulation, phagosome maturation, Wnt signalosome assembly, oligodendrocyte differentiation, and mitotic spindle/kinetochore regulation\u2014showing no single cohesive function or pathway tying the proteins together. Therefore, no clear functional theme can be assigned to this cluster.","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1903215","count":3},{"id":"GO:0001667","count":3},{"id":"GO:0006878","count":3},{"id":"GO:0043316","count":3},{"id":"GO:1900026","count":3}]},{"hash":"969088990796284114","title":"RNA processing and ribosome biogenesis under TORC1","description":"This cluster is enriched for mRNA transport, splicing, and export, ribosomal large subunit biogenesis, and TORC1 signaling, pointing to a coordinated RNA-processing and ribosome biogenesis module responsive to TOR signaling; a few terms like chromatin assembly and ubiquitin ligase regulation are present but less central.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051028","count":4},{"id":"GO:0070262","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0042273","count":4},{"id":"GO:0038202","count":4}]},{"hash":"442353354896639348","title":"Neural development and signaling","description":"The top GO terms point to embryonic neural development (forebrain, face, neural tube patterning) and neural signaling (retinoic acid response, dopaminergic transmission). While there are other terms (endosome transport, p53 signaling, NK T differentiation), the dominant theme is neural development and associated signaling pathways, suggesting this cluster reflects neural development programs with related signaling regulation.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071300","count":7},{"id":"GO:0060324","count":7},{"id":"GO:0030900","count":7},{"id":"GO:2000641","count":6},{"id":"GO:0007124","count":6}]},{"hash":"927346658563014260","title":"Ubiquitin-Mediated Degradation and Immune Signaling","description":"These proteins are strongly linked to ubiquitin-dependent proteolysis (including autoubiquitination, ERAD, and specific ubiquitin linkages like K48 and K6) and to immune signaling pathways (TNF-mediated signaling, regulation of JNK cascade, and I\u03baB phosphorylation). The inclusion of V(D)J recombination and histone catabolic processes suggests broader chromatin/DNA processing roles that can intersect with ubiquitin dynamics. Together, the cluster appears to center on the ubiquitin-proteasome system coordinating protein turnover with immune signaling. ","confidence":"High","size":8,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:0051865","count":7},{"id":"GO:0030433","count":7},{"id":"GO:0085020","count":7},{"id":"GO:0033151","count":6}]},{"hash":"302310678452825370","title":"ER-Golgi trafficking and mitosis","description":"This cluster is dominated by GO terms for COPII vesicle budding and ER-Golgi transport, alongside mitotic processes (mitotic spindle assembly, mitotic cell cycle) and cell proliferation. The combination suggests a theme where membrane trafficking supports cell division and growth, with ribosome biogenesis adding to the growth aspect. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090114","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0000278","count":2}]},{"hash":"1788986552273686139","title":"Cytokinin-regulated plant cell division","description":"The dominant terms are cell division and mitotic cell cycle, with a cytokinin-activated signaling pathway term, pointing to cytokinin-mediated control of plant cell proliferation. Some plant-development terms (chlorophyll regulation, sex differentiation) appear as secondary signals, but the core theme is cytokinin-driven cell division in plants, justifying a concise label focused on this process.","confidence":"High","size":8,"edges":4,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0009736","count":5},{"id":"GO:0000278","count":5},{"id":"GO:1902325","count":5},{"id":"GO:1903071","count":5}]},{"hash":"1538673554411104993","title":"Unknown","description":"The top GO terms are a mix of plant hormone signaling (cytokinin pathway), chlorophyll biosynthesis regulation, cell cycle, histone modification, and even interferon response, with several terms labeled obsolete. There isn't a clear, single biological theme uniting these functions, so a coherent cluster label cannot be determined.","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0009736","count":4},{"id":"GO:0000278","count":4},{"id":"GO:1902325","count":4},{"id":"GO:1903071","count":4},{"id":"GO:2001162","count":4}]},{"hash":"1323960079426257347","title":"Unknown","description":"The Top Terms field is empty, so there is no GO-term signal to define a common function. Without GO enrichment or representative terms, I cannot infer a coherent biological theme or give a concise, specific label. If you share GO terms or enriched categories for this cluster, I can propose a descriptive name with a confidence level.","confidence":"","size":8,"edges":14,"triangles":11,"max_degree":6,"top_function":null,"top_go_terms":[]},{"hash":"2176423377243507708","title":"Purine nucleotide biosynthesis and salvage","description":"The dominant GO terms point to purine nucleotide metabolism: AMP salvage, ADP and CDP biosynthesis, nucleoside monophosphate phosphorylation, and interconversion of purine ribonucleotides (ITP, ADP). Although brain and liver development terms appear among the top terms, the cluster's shared annotations mainly reflect biochemical steps in purine nucleotide biosynthesis and salvage, suggesting a cohesive metabolic module.","confidence":"High","size":8,"edges":13,"triangles":6,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":4},{"id":"GO:0044209","count":4},{"id":"GO:0046705","count":4},{"id":"GO:0046940","count":4},{"id":"GO:0015951","count":4}]},{"hash":"863720452236475404","title":"Unknown","description":"The terms cover heat-stimulated mRNA export, ubiquitin-related regulation, dendrite development, splicing, centromere-associated chromatin assembly, cytokine production, polyubiquitination, cell-cycle checkpoint regulation, glial apoptosis, and GPCR signaling. There is no clear shared function or pathway across these terms, suggesting the proteins in this cluster participate in diverse processes rather than a single coherent function.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000728","count":1},{"id":"GO:1904668","count":1},{"id":"GO:0050773","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0061641","count":1}]},{"hash":"697570269932844316","title":"Unknown","description":"The top GO terms come from diverse processes (Wnt signaling, transcription, cell division) plus several unrelated functions (copper homeostasis, phagosome maturation, T cell degranulation). With no clear single theme or network connectivity tying the proteins together, there isn\u2019t a coherent function to label the cluster beyond Unknown.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060070","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0043497","count":2},{"id":"GO:0006351","count":2},{"id":"GO:1903215","count":1}]},{"hash":"1864123011286414216","title":"Stress-Responsive Chromatin Regulation and Proteostasis","description":"These proteins co-occur with GO terms pointing to heterochromatin formation/maintenance (rDNA and silent mating-type cassette) alongside indicators of proteostasis and chaperone activity (Hsp90 deacetylation, chaperone-mediated assembly, and aggrosome formation). The presence of mitophagy and oxidative stress\u2013related death terms suggests stress-adaptive responses that couple nuclear chromatin state with mitochondrial and protein quality control. Taken together, the cluster seems to unite chromatin regulation with protein-folding and degradation pathways under stress conditions.","confidence":"Medium","size":8,"edges":20,"triangles":19,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":3},{"id":"GO:0070846","count":2},{"id":"GO:0045820","count":2},{"id":"GO:0090035","count":2},{"id":"GO:0030466","count":2}]},{"hash":"23694805307300459","title":"Ubiquitin-Dependent Proteostasis and DNA Repair","description":"Most top GO terms center on protein ubiquitination (autoubiquitination, ubiquitin-dependent ERAD, general ubiquitination) and aggresome assembly, indicating a ubiquitin-proteasome\u2013driven protein quality control network. Additional terms point to PML body organization and nucleotide-excision repair, suggesting a link to DNA damage response. The combination of proteostasis and DDR-related terms makes this naming representative of the cluster\u2019s function.","confidence":"High","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":3},{"id":"GO:1903265","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0070911","count":2},{"id":"GO:0030578","count":2}]},{"hash":"887213035595602796","title":"Neuronal spine morphogenesis and actin dynamics","description":"The dominant terms center on neuronal development, especially dendritic spine morphogenesis, lamellipodium and Rac-mediated actin remodeling, and hippocampus-related growth, with supporting links to vesicle transport and ER stress responses. This points to a cohesive theme of neuronal dendritic spine formation and cytoskeletal signaling.","confidence":"High","size":8,"edges":4,"triangles":1,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1903206","count":7},{"id":"GO:0034976","count":7},{"id":"GO:0097178","count":6},{"id":"GO:0045792","count":6},{"id":"GO:0021766","count":6}]},{"hash":"1194659568150396620","title":"Ubiquitin-Dependent Protein Degradation","description":"Most top GO terms describe protein ubiquitination (including autoubiquitination and K48-linked chains) and ubiquitin-dependent proteolysis, including ER-associated degradation (ERAD) and catabolic turnover of proteins and receptors such as Wnt. A few items relate to signaling regulation (TNF) and growth control, likely as outcomes of ubiquitin-mediated signaling. The overall theme is ubiquitin-tagged protein turnover and degradation pathways, which justifies this label.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":6},{"id":"GO:0030433","count":6},{"id":"GO:1903265","count":4},{"id":"GO:0046621","count":3},{"id":"GO:0016567","count":3}]},{"hash":"1211592826496311673","title":"Calcium signaling and ion transport regulation","description":"The top GO terms center on negative regulation of cytosolic calcium concentration, regulation of sodium ion transport, membrane repolarization, and modulation of calcium-dependent signaling pathways (e.g., calcineurin-NFAT), all pointing to control of ion homeostasis and calcium signaling, which often ties to muscle and membrane excitability. Some outliers (lipopolysaccharide biosynthesis, vestibulocochlear nerve formation) may reflect broader regulatory roles or annotation noise, but the dominant theme is ion/Calcium signaling regulation.","confidence":"Medium","size":8,"edges":23,"triangles":33,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":2},{"id":"GO:0086009","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0031947","count":2},{"id":"GO:0051481","count":2}]},{"hash":"164418766248175768","title":"RNA processing and chromatin organization","description":"The top GO terms cluster around RNA metabolism and processing (histone mRNA metabolism, spliceosomal complex assembly, P-body assembly, deadenylation-dependent decapping, termination of transcription, maturation of SSU-rRNA) and chromatin state (pericentric heterochromatin formation). This suggests a cohesive module focused on nuclear RNA processing and chromatin regulation, with a few peripheral terms reflecting broader cell-cycle and stress responses. ","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0008334","count":5},{"id":"GO:0000245","count":5},{"id":"GO:0033962","count":5},{"id":"GO:0000290","count":5},{"id":"GO:0042633","count":5}]},{"hash":"300023037804986415","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0060252","count":1},{"id":"GO:2000208","count":1},{"id":"GO:2000234","count":1}]},{"hash":"187134386667155089","title":"Biosynthesis and Stress Response","description":"The terms show both biosynthetic processes (protoporphyrinogen IX and glycogen) and a range of stress-related responses (hypoxia, oxidative stress, metal ion exposure, amino acid and fatty acid responses, and interleukin-4 signaling). This pattern suggests a cluster linking core metabolism with general stress-adaptation pathways rather than a single, tightly defined function.","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006782","count":2},{"id":"GO:0001666","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0005978","count":2},{"id":"GO:0010044","count":1}]},{"hash":"1190142002451635721","title":"PI Signaling and Synaptic Trafficking","description":"The cluster centers on phosphatidylinositol metabolism (PI dephosphorylation, PI catabolic process), receptor recycling, and synaptic vesicle uncoating, with supporting signals in neuronal signaling and locomotion regulation. This combination points to lipid-mediated signaling that governs membrane trafficking and neural development/synaptic activity, with some terms indicating broader developmental roles.","confidence":"Medium","size":8,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046856","count":2},{"id":"GO:0042518","count":1},{"id":"GO:0001921","count":1},{"id":"GO:0031161","count":1},{"id":"GO:0031642","count":1}]},{"hash":"585641101514165161","title":"RNA Pol II Transcription Regulation","description":"The proteins cluster around regulation of transcription by RNA polymerase II, including negative regulation and preinitiation complex assembly, with additional chromatin-related terms (histone acetylation, nucleosome dynamics) suggesting control of transcription through chromatin state. Some terms like cell division and photomorphogenesis imply broader regulatory roles but remain compatible with transcriptional control networks. Overall, the group appears to consist of factors involved in initiating and modulating RNA Pol II transcription via chromatin and transcription machinery.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0043966","count":1},{"id":"GO:1900446","count":1},{"id":"GO:0000436","count":1}]},{"hash":"391222703973391999","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":11,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0000472","count":2},{"id":"GO:1900363","count":1}]},{"hash":"2169541490311927680","title":"Ubiquitin-Dependent NF-\u03baB Signaling","description":"The cluster is enriched for ubiquitination-related terms (autoubiquitination, K48-linked and histone ubiquitination) and NF-\u03baB\u2013associated signaling (TNF-mediated pathway, activation of NF-\u03baB\u2013inducing kinase) with apoptosis regulation, suggesting a coherent module where ubiquitin tagging controls NF-\u03baB activity and cell fate, with some epigenetic links to histone turnover. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046621","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0033209","count":2},{"id":"GO:0036205","count":2},{"id":"GO:0070936","count":2}]},{"hash":"204147677371023489","title":"Ammonium transport and nitrogen utilization under nutrient stress","description":"This cluster is dominated by GO terms related to ammonium transport and nitrogen utilization (including transepithelial and transmembrane transport, and regulation of nitrogen utilization), along with nutrient-limitation\u2013driven growth responses (pseudohyphal and invasive growth) and related metabolic adjustments; together these suggest a theme of nitrogen uptake and metabolism under nutrient stress across different systems.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006413","count":2},{"id":"GO:0007124","count":2},{"id":"GO:0019740","count":2},{"id":"GO:0070634","count":2},{"id":"GO:0072488","count":2}]},{"hash":"1218154743334313793","title":"Transcription Regulation and Oxidative Stress Response","description":"The top GO terms point to gene expression control (DNA-templated transcription and negative regulation of transcription by RNA Pol II) and redox biology (cellular oxidant detoxification, cellular response to oxidative stress, peptidyl-cysteine oxidation), suggesting a coherent theme around transcriptional regulation linked to oxidative stress. Some other terms (extracellular matrix organization, circulatory system development) may reflect broader roles or context rather than core function, and a few entries are obsolete, but the dominant signal supports transcriptional control with redox response.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0000122","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0098869","count":3},{"id":"GO:0033158","count":2}]},{"hash":"2041428930800079700","title":"Ubiquitin-dependent protein turnover and cell cycle regulation","description":"These GO terms cluster around ubiquitin-mediated protein degradation (autoubiquitination, ERAD-related pathways, general ubiquitin-dependent catabolic processes) and cell-cycle control elements (mitotic spindle orientation checkpoint, spindle pole body localization). Additional terms related to TNF signaling, Wnt receptor catabolism, histone catabolic processes, and V(D)J recombination reflect broader regulatory roles of protein turnover in signaling and chromatin dynamics. Overall, the dominant theme is regulated protein degradation via ubiquitination linked to growth and cell-cycle control.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046621","count":3},{"id":"GO:0033151","count":3},{"id":"GO:0038018","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0030433","count":3}]},{"hash":"796112421136683683","title":"Cytokinesis and Cell Polarity","description":"The top GO terms cluster around mitosis and septin-associated processes (mitotic cell cycle, mitotic cytokinesis, division septum assembly, septin ring disassembly) together with cell polarity-related terms (maintenance of cell polarity, endoplasmic reticulum polarization, regulation of exocytosis). This pattern suggests a cohesive functional module that coordinates cell division with polarity and trafficking, making \"Cytokinesis and Cell Polarity\" a concise and representative label.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034599","count":1},{"id":"GO:0002181","count":1},{"id":"GO:2000384","count":1},{"id":"GO:0000278","count":1},{"id":"GO:0061163","count":1}]},{"hash":"488745355804411809","title":"TLR and TNF innate immune signaling","description":"The GO terms point to Toll-like receptor signaling, TNF-mediated signaling, LPS response, and NF-kappaB pathway regulation, all central to innate immune sensing and inflammatory signaling, with additional but secondary references to apoptosis and stress responses. This suggests a cohesive cluster of proteins involved in triggering and modulating innate immune responses rather than a single effector function.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042771","count":1},{"id":"GO:0071222","count":1},{"id":"GO:0033209","count":1},{"id":"GO:0034051","count":1},{"id":"GO:0042347","count":1}]},{"hash":"1321506228252629396","title":"Spliceosome-driven mRNA processing and regulation","description":"These proteins are enriched for GO terms related to mRNA splicing via spliceosome, alternative splicing, and mRNA modification, plus regulatory processes affecting mRNA stability and translation, indicating a functional cluster centered on pre-mRNA processing and post-transcriptional regulation.","confidence":"High","size":8,"edges":22,"triangles":29,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":6},{"id":"GO:0006378","count":6},{"id":"GO:0010610","count":4},{"id":"GO:1900363","count":3},{"id":"GO:0048025","count":3}]},{"hash":"1895662148002334203","title":"ER-Golgi COPII vesicle trafficking","description":"The top GO terms are regulation of COPII vesicle coating and ER to Golgi vesicle-mediated transport, which strongly point to proteins involved in COPII-mediated ER-Golgi trafficking. While other terms touch on membrane-related processes and cell dynamics (phagosome maturation, Wnt signaling, migration, and differentiation), the core cluster theme is vesicle trafficking between the ER and Golgi. ","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003400","count":3},{"id":"GO:0006888","count":3},{"id":"GO:1903215","count":2},{"id":"GO:0001667","count":2},{"id":"GO:0006878","count":2}]},{"hash":"2210997696598873935","title":"Neuronal Development and Synaptic Signaling","description":"This cluster is dominated by GO terms related to neural processes: synaptic transmission (glutamatergic and dopaminergic), neural development and patterning, and sensory perception, suggesting a cohesive theme of neuronal communication and development. Other terms like transcription and endosome transport appear as supporting cellular processes but do not override the neural focus.","confidence":"Medium","size":8,"edges":13,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":2},{"id":"GO:0019233","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0035249","count":2}]},{"hash":"1396190192438497846","title":"Spliceosome-Dependent mRNA Processing and Regulation","description":"The top GO terms cluster around spliceosome-mediated splicing (including alternative splicing and regulation of splicing) and related post-transcriptional processes such as mRNA modification, stability regulation, and miRNA-mediated translational control, suggesting a cohesive role in RNA processing and post-transcriptional regulation. Some terms are obsolete, but the core theme is mRNA processing via the spliceosome and associated regulatory steps.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":2},{"id":"GO:0006796","count":1},{"id":"GO:1900363","count":1},{"id":"GO:0048025","count":1},{"id":"GO:0035278","count":1}]},{"hash":"677768692622737899","title":"Mitochondrial Transport and Energy Metabolism","description":"This cluster is defined by transport and metabolic regulation tied to mitochondria: NAD and deoxynucleotide transport, iron import into mitochondria, thiosulfate transport, and regulation of mitochondrial membrane permeability, plus energy-related processes such as adaptive thermogenesis and liver regeneration. These terms together suggest a cohesive mitochondrial metabolism module rather than a single transport path.","confidence":"High","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0097421","count":6},{"id":"GO:1990845","count":6},{"id":"GO:0060546","count":6},{"id":"GO:0097274","count":6},{"id":"GO:0070542","count":6}]},{"hash":"616537788383322556","title":"Sodium and potassium transport and ionic homeostasis","description":"The GO terms show consistent emphasis on ion movement across membranes (Na+, K+, proton), vacuolar acidification, and cell volume/homeostasis, with supporting terms for salt stress response. This pattern suggests a coherent cluster of proteins involved in maintaining ion balance and membrane potential, rather than a specific enzyme or signaling pathway.","confidence":"High","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0097623","count":1},{"id":"GO:0009651","count":1},{"id":"GO:0098719","count":1},{"id":"GO:0007035","count":1},{"id":"GO:0036376","count":1}]},{"hash":"2277940673991310327","title":"Mitochondrial tRNA aminoacylation and translation","description":"The cluster is dominated by GO terms for mitochondrial tRNA charging by various aminoacyl-tRNA synthetases (seryl-, threonyl-, glycyl-, prolyl-, histidyl-, etc.) and for translation, with additional related terms on selenocysteine biosynthesis and Sec-tRNA processing. This pattern points to mitochondria-focused translation machinery and tRNA aminoacylation as the unifying function of the cluster.","confidence":"High","size":8,"edges":12,"triangles":3,"max_degree":5,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0070158","count":5},{"id":"GO:0016260","count":5},{"id":"GO:0015966","count":5},{"id":"GO:0097056","count":5}]},{"hash":"1939097224747582488","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":2},{"id":"GO:0070935","count":2},{"id":"GO:0000086","count":2},{"id":"GO:0000082","count":2},{"id":"GO:0033129","count":2}]},{"hash":"1211086242244180111","title":"Transcriptional Regulators and Notch Signaling Components","description":"The top GO terms point to regulatory roles in gene expression and developmental signaling (DNA-templated transcription and Notch signaling), suggesting the cluster mainly comprises transcriptional regulators and signaling components. Other terms related to lipid metabolism and amino acid catabolism are present but less represented, likely reflecting broader annotation. ","confidence":"Medium","size":8,"edges":11,"triangles":5,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0019878","count":3},{"id":"GO:0006686","count":2},{"id":"GO:0006533","count":2},{"id":"GO:0019551","count":2}]},{"hash":"445062173986058682","title":"Unknown","description":"The GO terms in this cluster are highly diverse, spanning nuclear processes (DNA-templated transcription, DNA repair, export from nucleus), nervous system signals (sensory perception of pain, membrane potential regulation, sodium import, drug response), development and cardiac proliferation, and lipid metabolism. There isn\u2019t a single coherent functional theme that ties these proteins together, so a concise, representative label isn\u2019t confidently defined.","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006281","count":2},{"id":"GO:0019233","count":2},{"id":"GO:0007275","count":2}]},{"hash":"1138370753822902677","title":"RNA Processing and Transcription","description":"This cluster centers on RNA-centric processes: maturation of SSU-rRNA, RNA folding, and splicing-related terms, along with DNA-templated transcription. Although some terms (histone methylation) are obsolete or less relevant, the dominant signal points to RNA biogenesis and processing as a unifying theme. Confidence: Medium","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":2},{"id":"GO:0061087","count":2},{"id":"GO:0051568","count":2},{"id":"GO:0034729","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1600900469802763053","title":"Ubiquitin-regulated NF-kappaB and TNF signaling","description":"The proteins in this cluster are linked by multiple ubiquitination activities (K6-, K11-, K48-, K63-linked; autoubiquitination) and ubiquitin-dependent protein turnover, and they're enriched for processes that regulate canonical NF-kappaB signaling and TNF-mediated pathways, including positive regulation of NF-kappaB and TNF signaling and negative regulation of necroptosis. This points to a cohesive role in ubiquitin-mediated signaling control rather than diverse unrelated functions.","confidence":"High","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":5},{"id":"GO:0085020","count":5},{"id":"GO:0043123","count":4},{"id":"GO:0036205","count":4},{"id":"GO:0042787","count":4}]},{"hash":"1419849411324743050","title":"Membrane remodeling during cell division and development","description":"The top GO terms point to membrane-associated processes: mitotic cell cycle, cleavage furrow formation, endocytic recycling, plasma membrane tubulation, and phosphatidic acid biosynthesis, all indicating membrane remodeling and trafficking tied to division. Development-related terms (eye development, osteoblast fate) and sporulation membrane formation add breadth but don\u2019t override the core membrane- and division-centric signal. This label best captures the dominant theme while noting the developmental hints.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0043547","count":2},{"id":"GO:1990126","count":1},{"id":"GO:0097320","count":1},{"id":"GO:0022617","count":1}]},{"hash":"1421911108571401694","title":"Ubiquitin-Mediated Immune Signaling","description":"The cluster is dominated by GO terms linking immune signaling pathways (TRIF-dependent TLR signaling and T cell receptor signaling) and by terms describing ubiquitination processes (autoubiquitination, ubiquitin transferase activity, free ubiquitin chains, and K29-linked ubiquitination). This suggests a coherent theme of ubiquitin-regulated immune signaling and related protein quality control (including ER-associated processes), with some secondary links to DNA repair. ","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035666","count":8},{"id":"GO:0070911","count":8},{"id":"GO:0051443","count":8},{"id":"GO:0051865","count":8},{"id":"GO:0050852","count":8}]},{"hash":"798283793593045827","title":"Membrane trafficking and cytokinesis","description":"This cluster centers on membrane dynamics and trafficking: endocytic recycling, late endosome to Golgi transport, plasma membrane tubulation, and prospore membrane formation all point to membrane remodeling. Phosphatidic acid biosynthesis provides lipid substrates for these processes, and cleavage furrow formation ties directly to cytokinesis requiring membrane delivery and remodeling. Though a couple of terms relate to broader development, the dominant signal is membrane trafficking linked to cell division.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990126","count":1},{"id":"GO:0097320","count":1},{"id":"GO:0000278","count":1},{"id":"GO:0022617","count":1},{"id":"GO:0036089","count":1}]},{"hash":"2019532552934343207","title":"Nuclear envelope dynamics and nucleokinesis","description":"Most terms cluster around the nuclear envelope and movement (nuclear envelope organization, nuclear migration along microfilaments, nucleokinesis in migrating neurons, nuclear matrix anchoring at the nuclear membrane, telomere attachment to the nuclear envelope, centromere clustering at the nuclear envelope). A few terms touch bone biology or spermatogenesis, which may reflect broader roles of nuclear dynamics or annotation noise. Overall, the theme is nuclear envelope\u2013associated movement and organization.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070197","count":1},{"id":"GO:0072766","count":1},{"id":"GO:0006998","count":1},{"id":"GO:0031022","count":1},{"id":"GO:0045669","count":1}]},{"hash":"1217047441777583069","title":"Chromatin modification regulators","description":"The Top Terms include several histone modification/demethylation processes (H3K4, H3K9, H3K27) and RITS complex localization, pointing to epigenetic regulation and chromatin silencing as a unifying theme. While there are some neural/mammary development terms and a few obsolete GO entries, the dominant signal is chromatin-based regulation of transcription. This suggests labeling the cluster as chromatin modification regulators rather than a broad developmental group.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021555","count":1},{"id":"GO:0033169","count":1},{"id":"GO:0034630","count":1},{"id":"GO:0060763","count":1},{"id":"GO:0045663","count":1}]},{"hash":"1712737458031913761","title":"Ubiquitin-dependent protein degradation","description":"Based on the Top Terms, the cluster is enriched for ubiquitination and ubiquitin-dependent proteolysis: autoubiquitination, ubiquitin-dependent ERAD pathway, ubiquitin-dependent protein catabolic process, and K48-linked ubiquitination. These strongly point to proteins involved in tagging substrates for proteasomal degradation. Some terms related to peroxisomal import and X-chromosome regulation appear as noise/older terms, but the dominant theme is ubiquitin-mediated protein turnover.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0046621","count":4},{"id":"GO:0038018","count":4},{"id":"GO:0042787","count":4}]},{"hash":"1880091960490103061","title":"COPII Vesicle Trafficking and Secretion","description":"The top GO terms are dominated by ER-to-Golgi transport and COPII-associated processes (cargo loading into COPII vesicles, COPII vesicle cargo loading, ER to Golgi transport, intracellular transport, and secretion), indicating a cohesive theme of secretory pathway trafficking. Some terms appear more peripheral (e.g., MHC II antigen presentation, pigment regulation), but the strongest signal centers on COPII-mediated vesicle trafficking and secretion.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060088","count":1},{"id":"GO:0090178","count":1},{"id":"GO:1901301","count":1},{"id":"GO:0032876","count":1},{"id":"GO:0006886","count":1}]},{"hash":"344178738623609221","title":"Unknown","description":"The top GO terms are highly diverse, spanning transcription, endosome transport, pseudohyphal growth, dopaminergic synaptic activity, CNS neuron development, NK T cell differentiation, and p53 signaling. This broad mix suggests no single cohesive function tying these proteins together, and the lack of edges reinforces that this cluster cannot be confidently labeled with a specific function. ","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:2000641","count":1},{"id":"GO:0007124","count":1},{"id":"GO:1901621","count":1},{"id":"GO:1904637","count":1}]},{"hash":"1468446837609777564","title":"Membrane lipid biosynthesis and transport","description":"This cluster\u2019s terms cluster around lipid metabolism and membrane-related processes: phosphatidylcholine and phosphatidylglycerol biosynthesis, vitamin transport, and lysosome organization\u2014all pointing to membrane lipid production and membrane compartment dynamics. Some terms appear unrelated or outdated, but the lipid/metabolic theme is the strongest through-line.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007584","count":2},{"id":"GO:2000114","count":1},{"id":"GO:0043942","count":1},{"id":"GO:0001892","count":1},{"id":"GO:0007040","count":1}]},{"hash":"524377640199733700","title":"Cardiac-immune stress response","description":"The top GO terms cluster around cardiac stress adaptation (positive regulation of cardiac muscle hypertrophy in response to stress; regulation of heart rate) and immune modulation (T cell homeostasis; chemokine/chemokine ligand production), suggesting a shared role in stress signaling linking cardiac function and immune regulation. Additional terms related to thermosensory/neural signaling and osmotic-stress\u2013related apoptosis point to a broader stress-response network, but the clearest common theme is stress-induced cardiac and immune coordination.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903244","count":4},{"id":"GO:0043029","count":4},{"id":"GO:0002027","count":3},{"id":"GO:0071642","count":3},{"id":"GO:1901594","count":3}]},{"hash":"2207302360736290417","title":"Plant carbon metabolism and CO2 response","description":"The Top Terms center on carbon utilization and the cellular response to carbon dioxide, with several catabolic processes (beta-ketoadipate, stilbene, triglyceride, uracil, monoacylglycerol) and P450 epoxygenase activity, plus a plant-specific note on stomatal development. This pattern suggests proteins involved in plant carbon metabolism and CO2-responsive regulation, making this a coherent, specific cluster label. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000122","count":3},{"id":"GO:0071244","count":3},{"id":"GO:0015976","count":3},{"id":"GO:0042952","count":2},{"id":"GO:0046272","count":2}]},{"hash":"1227942624842802750","title":"Unknown","description":"No shared GO terms and minimal connectivity (one edge, no triangles) among eight proteins gives no clear common function or process. Without functional signals to tie the members together, a robust label cannot be inferred, so Unknown.","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[]},{"hash":"26395864311734573","title":"Lung branching morphogenesis and basement membrane remodeling","description":"The top GO terms show explicit involvement in epithelial tube branching and lung morphogenesis, plus basement membrane disassembly, indicating a core function in lung development and extracellular matrix remodeling. Other terms (neural proliferation, neuropeptide and bradykinin catabolism, thyroid response) suggest broader regulatory roles, but the strongest signal centers on lung tissue morphogenesis and remodeling.","confidence":"Medium","size":8,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2000179","count":3},{"id":"GO:0010815","count":3},{"id":"GO:0034769","count":2},{"id":"GO:0051603","count":2},{"id":"GO:0050790","count":2}]},{"hash":"2247229782265488562","title":"Immune activation and leukocyte migration","description":"The top GO terms point to immune processes: complement activation, T cell activation, integrin-mediated signaling, and cell adhesion, all of which support leukocyte trafficking and activation. Additional terms like cellular extravasation and substrate-dependent cell migration reinforce a theme of immune cell movement through tissues. Some terms (dendrite regeneration, metallopeptidase activity) relate to tissue remodeling that accompanies migration, but the shared origin appears to be immune response and leukocyte dynamics. Confidence: Medium.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006956","count":2},{"id":"GO:0034113","count":2},{"id":"GO:0031104","count":2},{"id":"GO:0002291","count":2},{"id":"GO:0007229","count":2}]},{"hash":"1192289654851137371","title":"Growth signaling and ribosome biogenesis","description":"The top GO terms cluster around cellular growth and protein synthesis: cell division, positive regulation of TORC1 signaling, and ribosome biogenesis, with supporting hints from GTPase regulation. A few terms point to stress responses (nitric oxide detoxification, heat-stress\u2013related mRNA export), but the dominant theme is growth signaling and ribosome assembly, justifying a label centered on growth and ribosome production. ","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0000747","count":2},{"id":"GO:1904263","count":2},{"id":"GO:0042254","count":2}]},{"hash":"1263993532282568452","title":"Lung branching morphogenesis and ECM remodeling","description":"This cluster is led by GO terms tied to lung development, specifically epithelial tube branching and terminal-unit branching in lung morphogenesis, with basement membrane disassembly highlighting extracellular matrix remodeling during morphogenesis. Some other terms (memory, T cell cytotoxicity, neuropeptide catabolic process) appear unrelated, suggesting annotation noise or multifunctionality, but the dominant theme is lung branching morphogenesis with associated ECM remodeling.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0034769","count":1},{"id":"GO:0051603","count":1},{"id":"GO:0050790","count":1},{"id":"GO:0097067","count":1},{"id":"GO:0060441","count":1}]},{"hash":"606934797555422267","title":"Unknown","description":"The top GO terms cover a wide range of unrelated cellular processes\u2014including energy metabolism, proteasomal degradation/ER-associated pathways, mitochondrial assembly, oxidative stress response, chromatin assembly, cell cycle signaling, and transcription regulation\u2014plus no interactions between proteins (Edges 0). This lack of a cohesive functional theme makes a concise, representative label inappropriate, so I\u2019m deeming the cluster Unknown.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046034","count":1},{"id":"GO:0071712","count":1},{"id":"GO:0033314","count":1},{"id":"GO:1901800","count":1},{"id":"GO:0034551","count":1}]},{"hash":"1720839005657335716","title":"Ribosome Biogenesis and Translation","description":"Most of the top GO terms describe ribosome biogenesis (GO:0042254, GO:0042274), ribosomal subunit export from nucleus (GO:0000055), and cytoplasmic translation (GO:0002181), as well as tRNA modification (GO:0006400). This points to a cluster enriched for ribosome assembly and protein synthesis machinery. A couple of growth-related terms (cell cycle, cell division) likely reflect coordination between ribosome production and cell proliferation rather than a distinct separate function.","confidence":"High","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000747","count":2},{"id":"GO:1901001","count":2},{"id":"GO:0090529","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0042274","count":2}]},{"hash":"1656298216563986514","title":"Unknown","description":"The top GO terms span cytoplasmic translation, autophagy regulation, cell migration, metal ion homeostasis, phagosome maturation, and immune signaling, with no single dominant function tying all proteins together. Because the cluster lacks a cohesive shared theme, a precise label cannot be assigned beyond Unknown.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0002181","count":3},{"id":"GO:1903215","count":2},{"id":"GO:0001667","count":2},{"id":"GO:0006878","count":2},{"id":"GO:0010507","count":2}]},{"hash":"1870824914780308068","title":"Stress-Response Signaling and Development","description":"The terms cluster around stress responses (oxidative/ER stress, MAPK activation, Toll signaling) and signaling pathways that influence development (embryo development, maternal axis specification) as well as basic cellular processes (cytochrome complex assembly). Together these suggest a group of proteins involved in stress-activated signaling with developmental context, despite some obsolete terms. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000187","count":2},{"id":"GO:1902235","count":2},{"id":"GO:0033158","count":2},{"id":"GO:0008063","count":2},{"id":"GO:0034599","count":2}]},{"hash":"1028096579986014207","title":"DNA replication and cell cycle","description":"This cluster centers on processes tied to genome maintenance and proliferation: DNA replication and DNA-templated transcription (with both activation and negative regulation), and the mitotic cell cycle. The presence of nucleotide metabolism terms (CDP and pyrimidine nucleobase interconversions) aligns with the nucleotide supply needed for DNA synthesis, reinforcing a replication/propagation theme. Developmental terms like retina forebrain proliferation suggest tissue-specific proliferation contexts, but the core signal is cell cycle and DNA replication-related functions.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046704","count":1},{"id":"GO:0006206","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0045892","count":1},{"id":"GO:0021846","count":1}]},{"hash":"1169283053262000777","title":"Wnt signaling in embryonic development","description":"The cluster is dominated by GO terms related to Wnt signaling (including both pathway and regulation) and embryonic patterning processes such as neural tube patterning, notochord formation, and pericyte differentiation, suggesting a cohesive role in Wnt-mediated embryogenesis. Some other terms are peripheral or obsolete, but the central theme remains Wnt-driven developmental patterning.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016055","count":2},{"id":"GO:0060316","count":2},{"id":"GO:0006507","count":1},{"id":"GO:0048076","count":1},{"id":"GO:0021532","count":1}]},{"hash":"2200116272400388975","title":"Plant innate immune signaling","description":"The top GO terms show defense response to virus and innate immune response, with a plant-specific cytokinin-activated signaling pathway, suggesting a plant immune signaling theme. A few other terms (mitotic cell cycle, chlorophyll regulation, ubiquitin-related processes) appear only peripherally or as obsolete terms, and there are no network connections, so the core signal is immune-related. This label captures the most representative function of the cluster without overextending into unrelated processes.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009736","count":3},{"id":"GO:0051607","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0000278","count":2},{"id":"GO:1902325","count":2}]},{"hash":"257590504548039225","title":"Mitotic Cell Cycle Regulation","description":"The set is enriched in terms tied to DNA-templated transcription and cell cycle transitions (G1/S, G2/M, re-entry into mitosis), pointing to coordinated control of cell division. While a few terms relate to development or stress responses, the dominant pattern is regulation of mitotic entry and progression.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0000082","count":2},{"id":"GO:0000320","count":2},{"id":"GO:0001843","count":2}]},{"hash":"2267185349355094159","title":"Translation initiation and regulation","description":"The top GO terms show a clear emphasis on translation initiation, including formation of the preinitiation complex and initiation regulation, plus a related term on viral translation reinitiation. A few other terms touch on signaling regulation and ubiquitination, which may reflect broader regulatory roles or annotation noise. Overall, the cluster appears centered on translation initiation machinery with ancillary regulatory links.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0006446","count":1},{"id":"GO:0006413","count":1},{"id":"GO:0075525","count":1},{"id":"GO:1900458","count":1}]},{"hash":"381871344764419815","title":"Unknown","description":"The top terms span RNA processing (mRNA export/splicing), chromatin assembly, ubiquitination, cell cycle regulation, neural development, glial apoptosis, inflammatory cytokine production, and GPCR signaling, with no single dominant theme. This lack of a cohesive functional thread means a concise, representative label cannot be confidently assigned.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000728","count":1},{"id":"GO:1904668","count":1},{"id":"GO:0050773","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0061641","count":1}]},{"hash":"1558977759555569343","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045041","count":1},{"id":"GO:0022417","count":1},{"id":"GO:0033617","count":1},{"id":"GO:0051084","count":1},{"id":"GO:0032543","count":1}]},{"hash":"71779993668904908","title":"Unknown","description":"The terms include immune cytokine/chemokine production (MIP-1\u03b1, CCL5), response to a chemical compound, cardiac cell communication, epithelial polarity, spindle/mitotic assembly, protein localization and post-translational modification, and actin cytoskeleton assembly. This mix spans immune signaling and basic cell biology with no clear shared function.","confidence":"","size":8,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071642","count":2},{"id":"GO:1901594","count":2},{"id":"GO:0086070","count":2},{"id":"GO:0071651","count":2},{"id":"GO:0090162","count":2}]},{"hash":"2154222001533705569","title":"Ubiquitin-Dependent Proteostasis","description":"The top GO terms cluster around ubiquitin-related processes: ubiquitin-dependent protein catabolic processes, various deubiquitination activities (K63- and K11-linked), monoubiquitinated protein deubiquitination, and free ubiquitin chain depolymerization, with ancillary hints toward histone deubiquitination and broader proteostasis (e.g., ERAD-related maintenance). This suggests a functional group focused on ubiquitin signaling, editing, and proteolysis rather than a single structural or signaling pathway. ","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070537","count":1},{"id":"GO:0008583","count":1},{"id":"GO:1900425","count":1},{"id":"GO:0035871","count":1},{"id":"GO:0034729","count":1}]},{"hash":"256221685900000948","title":"Unknown","description":"The terms are diverse, spanning DNA damage response (DSB processing, intra-S checkpoint, kinetochore localization), stress signaling (glucocorticoid pathway, cardiac hypertrophy), EMT/tissue remodeling, metabolism (adenosine biosynthesis), and locomotion. There is no single clear functional theme that ties all proteins together, so a specific, cohesive label cannot be assigned with confidence.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060316","count":2},{"id":"GO:0010719","count":1},{"id":"GO:0034501","count":1},{"id":"GO:0046086","count":1},{"id":"GO:1905205","count":1}]},{"hash":"435986830587716683","title":"Unknown","description":"The eight proteins have no coherent shared function: GO terms span immune chemokine production, uterine gland development, drug response, vitamin D signaling, cardiac cell communication, yeast mating regulation, epithelial polarity, and sugar metabolism/signaling. This diverse, non-overlapping set (with no edges or dominant pathway) provides no clear common theme to name, so Unknown with no confidence.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071642","count":1},{"id":"GO:1903709","count":1},{"id":"GO:1901594","count":1},{"id":"GO:0070562","count":1},{"id":"GO:0086070","count":1}]},{"hash":"877370185886025619","title":"Unknown","description":"The terms are highly diverse and weakly connected (stress response, calcium signaling, cytoskeleton, apoptosis, development, proteolysis, digestion, etc.), with no shared function or strong enrichment, and there are no edges linking proteins, so no coherent cluster function can be assigned.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033234","count":1},{"id":"GO:0071472","count":1},{"id":"GO:0097050","count":1},{"id":"GO:0051281","count":1},{"id":"GO:0042004","count":1}]},{"hash":"109011778485754838","title":"Unknown","description":"The top GO terms are highly diverse (skin development, intracellular pH, ER-Golgi transport, liver regeneration, thermogenesis, necroptosis regulation, fatty acid response, various transport processes) with only single-count appearances and no network connections among the proteins. There isn\u2019t a single cohesive function or pathway tying the cluster together, so a specific, representative label isn\u2019t supported. ","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043588","count":1},{"id":"GO:0051452","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0097421","count":1},{"id":"GO:1990845","count":1}]},{"hash":"1020088324668293501","title":"Rab-regulated vesicle trafficking","description":"The GO terms emphasize regulation and signaling for Rab GTPases, plus endocytic processes (synaptic vesicle endocytosis and endocytic recycling) and GTPase activity, pointing to a shared function in Rab-mediated vesicle trafficking and recycling. The presence of apoptosis execution and TH2 cytokine production annotations are less clearly connected, possibly reflecting broader roles of some cluster members. Overall, the dominant theme is Rab-regulated vesicle trafficking.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032483","count":1},{"id":"GO:0097194","count":1},{"id":"GO:0048488","count":1},{"id":"GO:0032456","count":1},{"id":"GO:0043087","count":1}]},{"hash":"1163311832060263828","title":"DNA Replication and Proteostasis","description":"The top GO terms point strongly to DNA replication and mitotic checkpoint signaling, indicating a core link to genome duplication and cell-cycle control. Additional terms highlight protein quality control and turnover (proteasomal degradation, ERAD) and cellular stress responses, suggesting coordination of replication with proteostasis under stress; ATP metabolism and mitochondrial assembly may reflect energy and redox needs during these processes. Overall, the cluster appears centered on genome replication with linked proteostasis and stress-response functions.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0051260","count":5},{"id":"GO:0046034","count":4},{"id":"GO:0071712","count":4},{"id":"GO:0033314","count":4}]},{"hash":"1743912137660605485","title":"RNA Processing and Transcription with Viral Interactions","description":"The cluster heavily features RNA metabolism terms (RNA processing, nonsense-mediated decay) and transcription-related terms (DNA-templated transcription), suggesting a core theme around RNA processing and gene expression. The presence of viral-related terms (viral RNA replication, viral protein processing) and host autophagy signals alongside a few niche terms (karyogamy) likely reflects diverse annotations within a broader RNA/virus-host interaction context. Overall, the dominant signal is RNA processing and transcription, with some viral/host interaction components.","confidence":"Medium","size":7,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000184","count":3},{"id":"GO:0032508","count":3},{"id":"GO:0000742","count":2},{"id":"GO:0039520","count":2},{"id":"GO:0006396","count":2}]},{"hash":"56721807123879644","title":"Mitotic Kinase Regulation and Cytokinesis Checkpoints","description":"The top GO terms point to negative regulation of kinase activity (CDK, MAPK/ERK) alongside mitotic processes such as kinetochore localization, cytokinesis checkpoint signaling, and actomyosin contractile ring maturation. This suggests a coherent theme of controlling kinase signaling during mitosis and cytokinesis, with some broader kinase-regulation references (e.g., JAK-STAT-related term) that are less central to the core cluster. Overall, the label captures the dominant functional theme of how these proteins modulate mitotic progression and cytokinesis through kinase regulation.","confidence":"High","size":7,"edges":12,"triangles":10,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0034501","count":6},{"id":"GO:0045736","count":6},{"id":"GO:0050860","count":5},{"id":"GO:0000200","count":5},{"id":"GO:0070373","count":5}]},{"hash":"1158186950881771183","title":"Microtubule dynamics and neuronal transport","description":"This cluster centers on microtubule-related processes: cytoplasmic microtubule depolymerization, mitotic spindle-kinetochore interactions, establishment of microtubule cytoskeleton polarity, and anterograde dendritic transport of neurotransmitter receptor complexes, plus neuron projection maintenance and cerebellar Purkinje cell layer organization, all pointing to microtubule-based transport and polarity important for neuron structure and signaling. A couple of terms about chloroplast movement and fungal nuclear migration reflect broader motility roles on cytoskeleton but do not undermine the central theme.","confidence":"High","size":7,"edges":13,"triangles":9,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0010938","count":7},{"id":"GO:0000743","count":7},{"id":"GO:0001560","count":7},{"id":"GO:0032487","count":7},{"id":"GO:0098971","count":7}]},{"hash":"229695556123116418","title":"Diverse Signaling and Trafficking Regulators","description":"The top GO terms span kinetochore localization, CDK activity regulation, endosome transport, fungal pseudohyphal growth, hedgehog-like signaling regulation, calcium response, dopaminergic synaptic transmission, p53 signaling regulation, NK T cell differentiation, and neuron axonogenesis. This combination suggests proteins that broadly influence signaling pathways and intracellular trafficking across different contexts, rather than a single cohesive function. Confidence: Medium","confidence":"","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0034501","count":7},{"id":"GO:0045736","count":7},{"id":"GO:2000641","count":6},{"id":"GO:0007124","count":6},{"id":"GO:1901621","count":6}]},{"hash":"109575955651930240","title":"Neural development and signaling","description":"Most of the top GO terms point to neural development and neuronal signaling, including CNS projection neuron axonogenesis, dopaminergic synaptic transmission, and regulation of neural tube patterning. Endosome transport can underpin synaptic vesicle trafficking, supporting neuronal function. While a few terms are broader or less related (yeast growth, aging, cartilage), the prominent neural-related terms dominate the cluster\u2019s functional theme, justifying this label.","confidence":"Medium","size":7,"edges":19,"triangles":26,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":7},{"id":"GO:0007124","count":7},{"id":"GO:1901621","count":7},{"id":"GO:1904637","count":7},{"id":"GO:0001963","count":7}]},{"hash":"178561774409357952","title":"Heat Shock Response and Protein Refolding","description":"This cluster is dominated by heat-related activity (response to heat) and protein refolding, pointing to a cohort of heat-shock proteins and chaperones that help proteins fold correctly under stress. The DNA replication term and other annotations are weaker and likely incidental, so the core theme remains heat-induced protein folding. ","confidence":"Medium","size":7,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":3},{"id":"GO:0042026","count":2},{"id":"GO:0006260","count":2},{"id":"GO:1901998","count":1},{"id":"GO:1904871","count":1}]},{"hash":"231185821425446222","title":"Neuro-Muscular Development","description":"The top GO terms cluster around neural development and function (axonogenesis, Schwann cell development, visual perception, long-term potentiation) alongside muscle/heart development (myoblast fusion, heart development). This suggests a cohesive theme of neuro-muscular development and neural differentiation, with a few outliers such as ABA signaling that may reflect annotation noise. ","confidence":"Medium","size":7,"edges":6,"triangles":1,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0000086","count":5},{"id":"GO:0060079","count":5},{"id":"GO:0007520","count":5}]},{"hash":"2269041414678651156","title":"Renin-angiotensin system and kidney development","description":"The top GO terms are dominated by renin-angiotensin\u2013related processes (regulation of blood volume, angiotensin maturation, aldosterone production, drinking behavior) and kidney development (mesonephros development), which together point to a coherent theme around renin-angiotensin signaling in renal physiology and development. Some unrelated terms (protein processing, antigen presentation) appear, but they do not override the central kidney/RAS signal.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":1,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0002016","count":3},{"id":"GO:0030163","count":3},{"id":"GO:0016540","count":3},{"id":"GO:0070305","count":3},{"id":"GO:0019886","count":3}]},{"hash":"650562329452300832","title":"Motile cilium assembly and movement","description":"The cluster is characterized by GO terms for axoneme assembly, cilium movement, and motile cilium assembly, indicating a shared role in ciliogenesis and motile cilia function; incidental metabolic and stimulus-response terms do not detract from this central theme.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035082","count":1},{"id":"GO:0060294","count":1},{"id":"GO:0044458","count":1},{"id":"GO:0006541","count":1},{"id":"GO:0008153","count":1}]},{"hash":"1933111826533998899","title":"Calcium-Driven Neurite Outgrowth and Cytoskeleton Signaling","description":"The top GO terms emphasize dendrite/neurite extension, Rho-mediated cytoskeletal regulation, and calcium-dependent signaling and exocytosis, suggesting a theme of calcium-controlled neuronal growth and cytoskeletal dynamics, with some peripheral terms likely noise. ","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:1903861","count":6},{"id":"GO:0035023","count":6},{"id":"GO:1990927","count":5},{"id":"GO:2000235","count":5},{"id":"GO:0034351","count":5}]},{"hash":"113156998057474732","title":"Mitochondrial Electron Transport and Apoptosis","description":"The top GO terms cluster around mitochondrial electron transport (ubiquinol to cytochrome c; cytochrome c to oxygen) and cytochrome c\u2013heme linkage, coupled with apoptotic process and ROS metabolism (hydrogen peroxide). While a plant-specific term like photosynthesis appears, the dominant signal is respiration-linked processes and cytochrome c\u2013mediated apoptosis signaling. Thus, the cluster seems best described as mitochondrial electron transport with apoptosis connections.","confidence":"High","size":7,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006122","count":2},{"id":"GO:0010730","count":2},{"id":"GO:0018063","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0042743","count":2}]},{"hash":"1500326490807821217","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0048701","count":3},{"id":"GO:0006366","count":3},{"id":"GO:0072719","count":2},{"id":"GO:0035563","count":2}]},{"hash":"28332997482584604","title":"Organelle distribution and cell division","description":"The strongest signals are mitochondrial distribution and mitotic cell cycle, pointing to intracellular organization and dynamics during cell division. Additional terms about protein interactions, adhesion, migration, and endosomal processes suggest broader intracellular trafficking and organelle coordination, but the core theme centers on how organelles (notably mitochondria) are positioned and managed during cell division.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0048312","count":6},{"id":"GO:0051301","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0051291","count":6},{"id":"GO:1903215","count":5}]},{"hash":"2048769051729795682","title":"Meiosis: Synapsis and Chromosome Condensation","description":"The cluster is enriched for meiosis-specific terms such as synaptonemal complex assembly, meiotic chromosome condensation and separation, and regulation of meiotic DSB formation, with a few general cell division terms. This pattern points to proteins involved in meiotic chromosome pairing and structural remodeling rather than mitotic processes, making the label Meiosis: Synapsis and Chromosome Condensation appropriate.","confidence":"High","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0030466","count":3},{"id":"GO:0051307","count":3},{"id":"GO:0007076","count":3},{"id":"GO:0043007","count":3}]},{"hash":"967111439436109950","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":4},{"id":"GO:0031047","count":3},{"id":"GO:0019079","count":2},{"id":"GO:0034475","count":2},{"id":"GO:0016441","count":2}]},{"hash":"1961177149842195056","title":"Growth and Development Regulation","description":"This cluster spans IGF-stimulated growth, adipocyte differentiation and triglyceride/metabolic regulation, circadian timing, miRNA transcription, and diverse developmental processes (eye morphogenesis, olfactory interneuron development) plus nerve sprouting. The unifying theme is regulation of growth, metabolism, and development across tissues, rather than a single specific pathway, so a label centered on Growth and Development Regulation fits best.","confidence":"Medium","size":7,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1990418","count":3},{"id":"GO:0035470","count":3},{"id":"GO:0061614","count":3},{"id":"GO:0035356","count":3},{"id":"GO:0021891","count":3}]},{"hash":"2192517293107048325","title":"Neuronal development and signaling","description":"The terms repeatedly point to nervous system processes, including dopaminergic synaptic transmission, CNS projection neuron axonogenesis, and neural tube patterning. Additional terms suggest related signaling and trafficking (endosome transport, ionomycin response, p53-mediated signaling), while a few items touch on non-neuronal processes, but neural themes are the strongest signal.","confidence":"Medium","size":7,"edges":7,"triangles":1,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":7},{"id":"GO:0007124","count":7},{"id":"GO:1901621","count":7},{"id":"GO:1904637","count":7},{"id":"GO:0001963","count":7}]},{"hash":"48351470243303550","title":"Neuronal development and synaptic signaling","description":"This cluster's frequent GO terms center on neural development and neurotransmission: dopaminergic synaptic transmission, CNS projection neuron axonogenesis, and regulation of neural patterning. Endosomal transport and calcium signaling (ionomycin response) also fit neuronal signaling contexts. A few terms are unrelated (immune differentiation, cartilage condensation, pseudohyphal growth), but the dominant pattern points to neuronal development and synaptic communication.","confidence":"Medium","size":7,"edges":18,"triangles":22,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":6},{"id":"GO:0007124","count":6},{"id":"GO:1901621","count":6},{"id":"GO:1904637","count":6},{"id":"GO:0001963","count":6}]},{"hash":"1797533253641115192","title":"Exocytosis and Secretory Vesicle Trafficking","description":"The top GO terms point toward vesicle trafficking and secretion: exocytosis (GO:0006887), exocyst localization (GO:0051601), SNARE complex assembly regulation (GO:0035544), and peptide hormone secretion (GO:0030072). The presence of rhabdomere membrane biogenesis suggests a membrane delivery aspect in specialized cells, consistent with vesicle exocytosis to membranes. Together, these indicate a cluster centered on the exocytic secretory pathway, with regulatory aspects.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035544","count":1},{"id":"GO:0030072","count":1},{"id":"GO:0045313","count":1},{"id":"GO:0051601","count":1},{"id":"GO:0006887","count":1}]},{"hash":"1694735898235440477","title":"ER-Golgi vesicle trafficking","description":"The top GO terms are dominated by COPII-coated vesicle budding and ER-Golgi transport in both directions, indicating a primary role in the secretory pathway. Other terms like ribosome biogenesis and mitotic processes may reflect broader growth-related functions or annotation overlap, but the strongest signal centers on ER-Golgi trafficking.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090114","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0090307","count":4},{"id":"GO:0007420","count":4},{"id":"GO:0000278","count":4}]},{"hash":"2217113514141678320","title":"Endosomal trafficking and autophagy regulation","description":"The top terms cluster around endosome transport, nuclear export, and xenophagy, pointing to a shared role in intracellular trafficking and autophagic/quality-control pathways. Although there are outliers related to development and signaling, the recurring themes of endosomal dynamics and cellular cleanup support labeling this cluster as trafficking and autophagy\u2013related regulation.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046827","count":7},{"id":"GO:2000641","count":6},{"id":"GO:0007124","count":6},{"id":"GO:1901621","count":6},{"id":"GO:1904637","count":6}]},{"hash":"2087503659133022826","title":"Ciliogenesis and Basal Body Docking","description":"The top GO terms are dominated by cilia-related processes, including ciliary basal body-plasma membrane docking, intraflagellar transport for ciliogenesis, and cilium assembly, suggesting this cluster centers on ciliogenesis and related centrosomal functions. Other terms touch on nuclear transport and cell cycle signaling, which can be linked to centrosome/cilium biology, providing some supporting context but not redefining the main theme. Overall, the cilia-centric terms give a coherent core function for the cluster, with moderate confidence due to the presence of a few non-specific terms.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007084","count":2},{"id":"GO:0045945","count":2},{"id":"GO:0097711","count":2},{"id":"GO:0001938","count":2},{"id":"GO:0060561","count":2}]},{"hash":"1159764963408557030","title":"Immune signaling and stress-response pathways","description":"The cluster is dominated by immune-related signaling terms (T cell receptor signaling, TNF-mediated signaling, Fc-epsilon receptor signaling, non-canonical NF-kappaB) and a broader inflammatory/developmental signal (Wnt/PCP). The presence of proteasome core complex assembly hints at a proteostasis link to these pathways, while salt and cadmium stress responses suggest coupling to cellular stress adaptation. Together, these terms point to a cohesive module of immune signaling interconnected with proteostasis and stress responses.","confidence":"High","size":7,"edges":17,"triangles":21,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0080129","count":6},{"id":"GO:0009651","count":6},{"id":"GO:0060071","count":6},{"id":"GO:0038095","count":6},{"id":"GO:0050852","count":6}]},{"hash":"329408616650030093","title":"Neural development and dopaminergic signaling","description":"This cluster is dominated by terms relating to neural development and synaptic function, including CNS projection neuron axonogenesis, dopaminergic synaptic transmission, and dorsal/ventral neural tube patterning. Endosome transport and signaling regulation terms appear as supporting cellular processes that can intersect with neuronal signaling. Taken together, the neural development and dopaminergic signaling theme best explains the GO term enrichment in this cluster.","confidence":"Medium","size":7,"edges":15,"triangles":13,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":7},{"id":"GO:0007124","count":7},{"id":"GO:1901621","count":7},{"id":"GO:1904637","count":7},{"id":"GO:0001963","count":7}]},{"hash":"770293520075645665","title":"Steroid Hormone and Lipid Biosynthesis","description":"This cluster is enriched for GO terms tied to steroid hormone metabolism (androgen, estrogen, testosterone biosynthesis and C21-steroid hormone metabolic process) and various lipid biosynthetic pathways (sphingolipid, phylloquinone catabolic, melanin biosynthesis). The predominance of these biosynthetic processes suggests the proteins function in steroid and lipid metabolism. A couple of terms like response to antibiotic appear, but they are peripheral and do not define the cluster.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0046677","count":4},{"id":"GO:0008207","count":3},{"id":"GO:0042376","count":3},{"id":"GO:0008209","count":3},{"id":"GO:0061370","count":3}]},{"hash":"2189232165711295081","title":"Glycosylated ECM and adhesion proteins","description":"The cluster\u2019s top GO terms cluster around extracellular matrix organization, N-linked glycosylation, and cell-substrate adhesion, pointing to secreted or membrane-associated proteins involved in ECM assembly and adhesion. Some terms like phototransduction and cuticle development are more divergent, perhaps reflecting species-specific annotations or multifunctionality, but the core theme appears to be glycoprotein processing and ECM/adhesion roles.","confidence":"Medium","size":7,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":2},{"id":"GO:0009585","count":2},{"id":"GO:0006487","count":2},{"id":"GO:0055003","count":1},{"id":"GO:0033591","count":1}]},{"hash":"497059905078529181","title":"ER protein quality control and membrane targeting","description":"This cluster\u2019s enriched GO terms point to protein quality control (ubiquitination and ERAD), stress of unfolded proteins, and targeting of nascent polypeptides to membranes via SRP-dependent or post-translational pathways. Together they describe processes involved in handling and directing proteins for proper folding and membrane localization, suggesting a cohesive theme of ER-associated protein quality control and membrane biogenesis. Some terms (iron-sulfur cluster assembly, DNA replication) appear as outliers and complicate the picture, so confidence is moderate.","confidence":"Medium","size":7,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0090084","count":1},{"id":"GO:0016226","count":1},{"id":"GO:0034620","count":1}]},{"hash":"1658387249884959455","title":"Unknown","description":"The GO terms span diverse processes: mitotic cell cycle and CENP-A chromatin assembly (cell division and chromatin maintenance), mRNA splicing and heat stress\u2013related mRNA export (RNA processing), ubiquitin ligase activity and polyubiquitination (protein modification), regulation of GTPase activity, protein homooligomerization, dendrite development, and cytokine production in inflammation. With no edges linking proteins, there isn\u2019t a single cohesive function or pathway tying these terms together, so there is no clear common theme beyond broad cellular regulation. ","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0043547","count":3},{"id":"GO:2000728","count":2},{"id":"GO:1904668","count":2}]},{"hash":"2131808136982989099","title":"Wnt signaling and cell migration","description":"Top GO terms reveal a core emphasis on canonical Wnt signaling components (GO:0060070) and Wnt signalosome assembly (GO:1904887), with supporting terms for cell movement and adhesion (ameboidal-type cell migration; positive regulation of substrate adhesion-dependent cell spreading). This pattern points to proteins involved in Wnt-mediated development that coordinate cytoskeletal remodeling and cell motility. Other highlighted terms (phagosome maturation, intracellular copper ion homeostasis, cytotoxic T cell degranulation, and oligodendrocyte differentiation) suggest additional roles in vesicle trafficking and broader differentiation contexts, but these are less central to the main theme. Therefore, a concise label focusing on Wnt signaling and cell migration best captures the cluster\u2019s dominant function.","confidence":"Medium","size":7,"edges":12,"triangles":5,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060070","count":4},{"id":"GO:0051301","count":4},{"id":"GO:1903215","count":3},{"id":"GO:0001667","count":3},{"id":"GO:0006878","count":3}]},{"hash":"60721270282443009","title":"NF-kB-driven antiviral immunity and ubiquitination","description":"Top terms show strong emphasis on immune signaling (positive regulation of canonical NF-kappaB signaling; defense response to virus; regulation of viral transcription) and protein turnover/quality control (protein autoubiquitination; ubiquitin-dependent ERAD). Additional terms touch on host defense against symbionts and regulation of LPS signaling, supporting a theme of innate immune regulation. Some microtubule-related terms may reflect intracellular transport associated with signaling, but the dominant signal is NF-kB\u2013mediated antiviral defense coordinated by ubiquitination. Confidence: High","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0043123","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0046597","count":2}]},{"hash":"1992928172811918990","title":"Cell signaling and motility","description":"The top GO terms cluster around signaling and movement/trafficking processes, including Wnt signalosome assembly, amoeboid migration, adhesion-dependent spreading, phagosome maturation, and T cell degranulation, suggesting a shared theme of cellular communication and movement. Some terms (copper homeostasis, cytokinesis, oligodendrocyte differentiation) appear peripheral, indicating a mixed functional set; thus a label focused on signaling and motility with moderate confidence.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000186","count":4},{"id":"GO:1903215","count":3},{"id":"GO:0001667","count":3},{"id":"GO:0006878","count":3},{"id":"GO:0043316","count":3}]},{"hash":"1324067035970296771","title":"Unknown","description":"The top GO terms are highly diverse (nuclear protein export regulation, DNA-templated transcription, multicellular development, endosome transport, pseudohyphal growth, dopaminergic synaptic transmission, calcium signaling, ubiquitin ligase regulation), spanning yeast to animals with no single dominant function. Because there\u2019s no cohesive theme tying the terms together, there isn\u2019t a meaningful, specific label beyond Unknown.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":2},{"id":"GO:0019233","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0006351","count":2},{"id":"GO:2000641","count":1}]},{"hash":"103708500167282300","title":"Maternal egg-laying and embryonic Wnt signaling","description":"These terms center on maternal control of oogenesis and early embryonic axis formation (egg-laying behavior, dorsal/ventral axis specification) and on protein secretion through the ER-Golgi pathway (Wnt secretion, COPI vesicles, ER exit). This combination points to a cohesive theme of maternal provisioning for embryogenesis and associated secretory processes, rather than unrelated functions.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048042","count":3},{"id":"GO:0061357","count":3},{"id":"GO:0002121","count":3},{"id":"GO:0007311","count":3},{"id":"GO:0070863","count":3}]},{"hash":"258342417014073620","title":"RNA Processing and Chromatin Regulation","description":"This cluster is enriched for RNA metabolism and processing terms, including histone mRNA metabolism, spliceosome assembly, P-body assembly, and deadenylation-dependent decapping, as well as transcription termination and rRNA maturation. The presence of pericentric heterochromatin formation and a cell-cycle related term suggests a broader link between RNA processing and chromatin dynamics, with some stress-related terms as potential secondary associations.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0008334","count":4},{"id":"GO:0000245","count":4},{"id":"GO:0033962","count":4},{"id":"GO:0000290","count":4},{"id":"GO:0042633","count":4}]},{"hash":"138668065702525345","title":"RNA polymerase preinitiation complex components","description":"This cluster is enriched for terms related to assembly and initiation of transcription by RNA polymerases I, II, and III, including preinitiation complex assembly and DNA-templated transcription, with minor Pol I\u2013related activity; together these suggest a set of factors that function in transcription initiation across multiple polymerases.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051123","count":2},{"id":"GO:0070893","count":2},{"id":"GO:0070898","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0045893","count":1}]},{"hash":"937307029636451104","title":"Calcium-Dependent Synaptic Transmission","description":"This cluster is dominated by terms tied to calcium ion responses, neurotransmitter secretion, regulation of synaptic vesicle exocytosis, and long-term potentiation, pointing to a core function in calcium-driven neuronal signaling and vesicle trafficking. Some VEGF signaling and abscisic acid pathway terms appear, but the strongest, recurrent annotations describe synaptic transmission and calcium-PI signaling, supporting a neuronal exocytosis theme.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0071277","count":7},{"id":"GO:0030948","count":7},{"id":"GO:0007520","count":7},{"id":"GO:0007269","count":7},{"id":"GO:0036324","count":7}]},{"hash":"2295830888042369074","title":"Neuronal development and signaling","description":"This cluster shows several neural-development related terms (central nervous system projection neuron axonogenesis, dopaminergic synaptic transmission, neural tube patterning regulation), suggesting a theme around neuronal development and signaling. Other terms touch on general signaling or non-neuronal processes (endosome transport, immune differentiation, aging), indicating some diversity but a core neural-related function. Confidence: Medium","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":7},{"id":"GO:0007124","count":7},{"id":"GO:1901621","count":7},{"id":"GO:1904637","count":7},{"id":"GO:0001963","count":7}]},{"hash":"127916958107895043","title":"Cortical development and glutamatergic signaling","description":"This cluster centers on neuronal development and synaptic function, including cortical layer formation, visual learning, and glutamatergic synaptic transmission, alongside signaling pathways like ERK1/ERK2 that modulate synaptic plasticity. The combination of cortical development terms and synaptic signaling terms suggests proteins involved in shaping neural circuits and regulating synaptic strength, rather than general cellular processes.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":2},{"id":"GO:0035924","count":2},{"id":"GO:0036120","count":2},{"id":"GO:0008542","count":2},{"id":"GO:0007257","count":2}]},{"hash":"194539193109433347","title":"Neural development and axon guidance signaling","description":"The top GO terms are dominated by neural-related processes: hippocampus development, positive regulation of axon extension, ephrin receptor signaling, and ERK cascade regulation, all pointing to neuronal differentiation and axon growth/guidance. Some cell cycle terms appear but are less representative of the cluster\u2019s main theme. Overall, the functions converge on neural development and axon pathfinding.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0006260","count":4},{"id":"GO:0070374","count":4},{"id":"GO:0051893","count":4},{"id":"GO:0043366","count":4}]},{"hash":"851857004623961691","title":"Spliceosome-Mediated mRNA Splicing Regulation","description":"The top GO terms cluster around spliceosome-driven mRNA processing, including cis-splicing, alternative splicing, and both positive and negative regulation of splicing, with additional ncRNA/miRNA\u2013mediated post-transcriptional gene silencing, pointing to a cohesive function in mRNA maturation and regulation.","confidence":"High","size":7,"edges":6,"triangles":1,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":4},{"id":"GO:0048026","count":4},{"id":"GO:0045292","count":4},{"id":"GO:0006378","count":4},{"id":"GO:1900363","count":3}]},{"hash":"790500695118626054","title":"Endosomal trafficking and Golgi-to-vacuole transport","description":"The top GO terms cluster around intracellular trafficking: Golgi-to-endosome transport, multivesicular body sorting, endocytosis, and endosome-to-Golgi/vacuole transport, with actin patches linked to vesicle movement. This suggests the proteins participate in endosomal sorting and vesicle trafficking between Golgi, endosomes, and vacuole; a couple of unrelated terms appear as annotation noise.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006895","count":1},{"id":"GO:0071985","count":1},{"id":"GO:0006897","count":1},{"id":"GO:0007565","count":1},{"id":"GO:0032511","count":1}]},{"hash":"1855422382670336641","title":"Ubiquitin-regulated TNF-NF-\u03baB/JNK signaling","description":"These proteins are dominated by ubiquitin-related regulation and pro-inflammatory signaling; autoubiquitination, ubiquitin-dependent protein catabolic processes, and TNF-mediated signaling with I-kappaB phosphorylation and JNK cascade regulation. The combination points to a module of ubiquitin ligases or regulators coordinating protein turnover with NF-\u03baB/JNK immune signaling.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0033151","count":6},{"id":"GO:0051865","count":6},{"id":"GO:0090073","count":6},{"id":"GO:0033209","count":6},{"id":"GO:0042787","count":6}]},{"hash":"147605004622868221","title":"Autophagy-Linked Carbohydrate Catabolism","description":"The top terms include glycophagy and positive regulation of macroautophagy, indicating an autophagy-focused cluster. In addition, several carbohydrate catabolic processes (maltose, starch) and a lipid catabolic process (glycerophospholipid) point to a broader metabolism theme centered on autophagy-related degradation pathways.","confidence":"High","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000025","count":1},{"id":"GO:0043609","count":1},{"id":"GO:0046959","count":1},{"id":"GO:0061723","count":1},{"id":"GO:0046475","count":1}]},{"hash":"1618319860642308264","title":"Ribosome Biogenesis and rRNA Processing","description":"The top GO terms are centered on ribosome assembly and rRNA maturation (ribosome biogenesis, small subunit biogenesis, SSU-rRNA maturation, rRNA processing), indicating a core function in ribosome production. A few unrelated terms appear but with low representation, so the dominant theme remains ribosome-related. ","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043248","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0042274","count":1},{"id":"GO:0000469","count":1},{"id":"GO:0009553","count":1}]},{"hash":"983294983659059518","title":"Redox Stress Response and Inflammation Regulation","description":"This cluster centers on oxidative/redox biology (glutathione metabolism, response to toxic substances, nitric oxide storage, response to ascorbic acid) and anti-inflammatory regulation (negative regulation of IL-1\u03b2 production, neutrophil aggregation). While there are additional hints of tissue remodeling and aging (organ regeneration, cellular senescence), the strongest common theme ties to managing oxidative stress and limiting inflammatory signals, suggesting a coordinated redox-immune response module.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":3},{"id":"GO:0031100","count":3},{"id":"GO:0033591","count":2},{"id":"GO:0035732","count":2},{"id":"GO:0032691","count":2}]},{"hash":"870962014229898862","title":"Unknown","description":"Top GO terms span oxidative stress responses and a broad mix of unrelated metabolic and processing functions, with no single cohesive theme to tie them together; thus a precise, representative label cannot be assigned.","confidence":"","size":7,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071276","count":3},{"id":"GO:0070301","count":3},{"id":"GO:0008209","count":2},{"id":"GO:0061370","count":2},{"id":"GO:0055114","count":2}]},{"hash":"1906887208079324534","title":"Ribosome Biogenesis and Translation","description":"Most terms point to ribosome biogenesis and translation (ribosome biogenesis, cytoplasmic translation, ribosomal subunit export, and tRNA modification). Other terms like cell cycle/division and septum assembly may reflect growth/division coupling rather than core function. Overall, the dominant signal is ribosome production and protein synthesis machinery.","confidence":"High","size":7,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006400","count":3},{"id":"GO:0000747","count":2},{"id":"GO:1901001","count":2},{"id":"GO:0090529","count":2},{"id":"GO:0051301","count":2}]},{"hash":"1592139198789242424","title":"Transcription Regulation & Chromatin Modification","description":"Most terms point to control of gene expression at the transcriptional level (regulation of start site selection and termination by RNA polymerase II) and epigenetic regulation (histone H3-K9 trimethylation, DNA methylation). Some outliers touch on developmental signaling and hormone secretion, but the core signal is transcriptional regulation and chromatin state management, suggesting these proteins function as transcription regulators/epigenetic modifiers.","confidence":"Medium","size":7,"edges":15,"triangles":14,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010880","count":4},{"id":"GO:0001178","count":4},{"id":"GO:0021553","count":4},{"id":"GO:2001229","count":4},{"id":"GO:0036124","count":4}]},{"hash":"2086989477640018134","title":"NAD+ Biosynthesis and Neural Development Cues","description":"The terms are dominated by NAD+ biosynthesis and quinolinate pathways, with neural/dopaminergic terms (neuron projection extension, dopamine biosynthesis/metabolism) also present, suggesting a modest link between NAD+ metabolism and neural signaling. Several outlier terms (chromatin binding regulation, erythrocyte differentiation, stem cell proliferation) prevent a tight, exclusive theme, hence a cautious Low confidence.","confidence":"Low","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009435","count":1},{"id":"GO:1990138","count":1},{"id":"GO:0045964","count":1},{"id":"GO:0035563","count":1},{"id":"GO:0010044","count":1}]},{"hash":"845085255505873401","title":"Translation Initiation and Regulation","description":"The top GO terms are dominated by translation-related processes: initiation (preinitiation complex formation, translation initiation, IRES-dependent initiation), ribosome dynamics (ribosome disassembly, maintenance of translational fidelity, translation regulation). A few non-translation terms appear but are sparse and likely incidental; overall the cluster centers on factors involved in starting and controlling protein synthesis.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990145","count":1},{"id":"GO:0006417","count":1},{"id":"GO:0032790","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0009048","count":1}]},{"hash":"1330873964379393093","title":"Golgi-ER vesicle trafficking","description":"The top terms are dominated by Golgi/ER transport and intra-Golgi processes (ER-to-Golgi transport, Golgi ribbon formation, intra-Golgi transport, vesicle fusion with Golgi, and retrograde transport to Golgi), indicating a coherent function in the Golgi secretory pathway. Some development-related terms (Wnt secretion, maternal axis specification) may reflect broader involvement in secretion, but the core pattern points to Golgi-ER vesicle trafficking.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0090161","count":3},{"id":"GO:0048280","count":2},{"id":"GO:0042147","count":2},{"id":"GO:0006891","count":2}]},{"hash":"1679708453528084350","title":"Translation and immune signaling regulators","description":"The cluster shows enrichment for translation-related GO terms (translation, rRNA maturation, mitochondrial translation) alongside several immune-regulatory terms (dendritic cell/neutrophil chemotaxis, negative regulation of IL-12, RIG-I/MDA-5 signaling). This points to proteins involved in both protein synthesis machinery and modulation of innate immune pathways.","confidence":"Medium","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0000462","count":1},{"id":"GO:2000510","count":1},{"id":"GO:0035042","count":1},{"id":"GO:0090023","count":1}]},{"hash":"1497610366148249169","title":"ER-Golgi Trafficking and Membrane Localization","description":"Top GO terms center on vesicle transport between the endoplasmic reticulum and Golgi, including both anterograde and retrograde routes, together with signals for protein retention in the ER lumen and for localization of proteins to the plasma membrane. This points to a shared function in secretory pathway maturation and membrane targeting. While other terms (methylation processes, phylloquinone biosynthesis, and aerobic respiration) are present, they appear less connected to this cluster's core theme.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071340","count":1},{"id":"GO:0006890","count":1},{"id":"GO:0090004","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0006621","count":1}]},{"hash":"1431915372244553588","title":"Plant stress response and cytokinin signaling","description":"The cluster shows strong plant-specific signals: responses to cadmium and hydrogen peroxide indicate oxidative/heavy-metal stress; cytokinin-activated signaling is a clear plant hormone pathway; additional terms like cellular response to peptide and chlorophyll biosynthesis regulation point to plant growth and development connections, suggesting a plant-focused module combining stress response with cytokinin signaling.","confidence":"Medium","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071276","count":3},{"id":"GO:0070301","count":3},{"id":"GO:0009736","count":3},{"id":"GO:0055114","count":2},{"id":"GO:1901653","count":2}]},{"hash":"944491538463469231","title":"Unknown","description":"The top GO terms are highly diverse (dephosphorylation, membrane repolarization, various biosynthetic and regulatory processes across metabolic and signaling pathways), with only a single count per term and no shared edges or triangles. This makes it hard to identify a common function or theme tying all seven proteins together, so a specific label isn\u2019t justifiable. Unknown is the most appropriate designation.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016311","count":1},{"id":"GO:0086009","count":1},{"id":"GO:0051479","count":1},{"id":"GO:0009103","count":1},{"id":"GO:0031947","count":1}]},{"hash":"837466273328071368","title":"RNA processing and translation regulation","description":"The top terms cluster around mRNA processing (splicing, export regulation) and translation initiation/reinitiation, with additional association to ER targeting, suggesting a core role in RNA metabolism and early protein synthesis/processing. Other terms (chromatin assembly, dendrite development, cytokine production) seem ancillary rather than defining the cluster\u2019s primary function.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0006465","count":2},{"id":"GO:0045047","count":2},{"id":"GO:2000728","count":1}]},{"hash":"1684128535444692152","title":"Ubiquitination Machinery and NF-\u03baB Signaling","description":"The cluster\u2019s top GO terms are dominated by ubiquitination-related processes (autoubiquitination, ubiquitin-dependent protein catabolic process, and various ubiquitin linkages like K48, K6, K11), along with positive regulation of canonical NF-kappaB signaling and TNF-mediated signaling. This points to a set of proteins involved in ubiquitin-mediated proteolysis and inflammatory signaling pathways, with NF-\u03baB as a central functional output. Minor terms such as histone catabolic process and manganese response likely reflect broader stress-response roles but do not override the central theme. High","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051865","count":6},{"id":"GO:0042787","count":6},{"id":"GO:0036205","count":6},{"id":"GO:0070936","count":6},{"id":"GO:1903265","count":6}]},{"hash":"119645769756523368","title":"Ion transport and membrane potential with sensory cues","description":"The GO terms center on ions moving across the plasma membrane (potassium and sodium import/export) and maintaining membrane potential, including intracellular potassium homeostasis and repolarization. A subset of terms also relates to sensory perception (touch and thermosensation), suggesting a link between ion transport and sensory signaling. This justifies a label that combines ion homeostasis with sensory cues.","confidence":"Medium","size":7,"edges":5,"triangles":0,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0097623","count":6},{"id":"GO:0030322","count":6},{"id":"GO:1990573","count":6},{"id":"GO:0030007","count":6},{"id":"GO:0098914","count":6}]},{"hash":"5912554056965360","title":"Ubiquitin-Dependent Gene Expression","description":"This cluster centers on ubiquitination as a regulatory hub (K11- and K63-linked ubiquitination, autoubiquitination, and positive regulation of ubiquitin ligase activity) and links to transcription and RNA processing (DNA-templated transcription, mRNA splicing, and mRNA export regulation in response to heat stress) as well as chromatin assembly (CENP-A). The co-enrichment of these terms suggests proteins that coordinate gene expression and RNA processing through ubiquitin-mediated regulation and chromatin dynamics, with some involvement in stress or inflammatory signaling.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0070979","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0051865","count":3},{"id":"GO:0070534","count":3},{"id":"GO:2000728","count":3}]},{"hash":"994345336351168293","title":"Neuronal development and signaling","description":"Several top GO terms point to nervous system development and function, including neuron axonogenesis, dopaminergic synaptic transmission, and neural tube patterning. While there are some unrelated terms in the set, the neural-centric terms suggest the cluster's proteins are related to neuronal development and signaling, giving a Moderate confidence.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2000641","count":1},{"id":"GO:0007124","count":1},{"id":"GO:1901621","count":1},{"id":"GO:1904637","count":1},{"id":"GO:0001963","count":1}]},{"hash":"957449712506236796","title":"Oxidative Stress and ECM in Circulatory Development","description":"The GO terms point to extracellular matrix organization and oxidative stress response, with links to MAPK signaling regulation and circulatory system development, suggesting a cluster tied to redox-modulated ECM remodeling in cardiovascular formation.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033158","count":1},{"id":"GO:0030198","count":1},{"id":"GO:0034599","count":1},{"id":"GO:0019471","count":1},{"id":"GO:0018171","count":1}]},{"hash":"1587981872813880102","title":"Unknown","description":"The GO terms span several unrelated processes, including carbon fixation, various catabolic pathways, chlorophyll biosynthesis, cell growth, and host-cell interaction, with no clear single function tying the proteins together. This makes a cohesive, specific label unlikely.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043427","count":2},{"id":"GO:0033611","count":2},{"id":"GO:0042413","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0031623","count":2}]},{"hash":"173851682774546528","title":"Unknown","description":"No shared GO terms or functional signals are listed for this cluster (Top Terms is empty). With only one edge among seven proteins and a max degree of 1, there is no clear common function to name the cluster. Therefore I label it Unknown.","confidence":"","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[]},{"hash":"935292274712481579","title":"Ubiquitin-Dependent Protein Degradation","description":"Top GO terms center on ubiquitin-mediated protein catabolic processes, including K48-linked ubiquitination and autoubiquitination, and ERAD-related degradation. The presence of peroxisomal matrix import and Wnt receptor breakdown suggests broader roles for ubiquitin signaling in receptor turnover and protein recycling. Overall, the cluster is best described as ubiquitin-dependent proteolysis and related quality-control processes.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0046621","count":3},{"id":"GO:0038018","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0042787","count":3}]},{"hash":"2182417497376611903","title":"Neuronal Signaling and Transcription Regulation","description":"The cluster includes terms related to receptor recycling, endosome size regulation, Rho signaling, and glutamatergic synaptic transmission, which point to intracellular trafficking and neuronal signaling. It also contains transcription-related terms (regulation of DNA-templated transcription) and histone methylation, suggesting involvement in gene expression regulation. While the terms are diverse, the combination implies proteins that participate in both synaptic signaling/trafficking and transcriptional control, though the links are not uniformly strong across all members.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034968","count":1},{"id":"GO:0001881","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0051036","count":1},{"id":"GO:0035023","count":1}]},{"hash":"522452626517955417","title":"Endomembrane trafficking and secretion","description":"The GO terms center on vesicle trafficking within the secretory pathway\u2014ER to Golgi transport, exit from the ER, endosome localization, and lysosomal enzyme secretion\u2014along with phospholipid translocation and vacuole organization. This suggests the proteins participate in the endomembrane system and secretory processes, with a note that some terms also reflect growth regulation under nutrient stress. ","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070863","count":2},{"id":"GO:0001403","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0010570","count":1}]},{"hash":"2078187209665153610","title":"Neurodevelopment and Neuronal Signaling","description":"The top GO terms cluster around brain development, neuronal processes (neurotransmitter secretion, axis specification), and signaling-related activities (GTPase regulation, transcription), suggesting a group of proteins involved in neural development and neuronal communication rather than a single metabolic function.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0006907","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1081077027168231884","title":"Stress-Response Signaling and Translation Control","description":"GO terms point to stress-induced signaling and regulation of protein synthesis (ER stress\u2013related eIF2alpha phosphorylation, cytoplasmic translation regulation in response to stress, UV-C response, and HIF-1alpha signaling). Additional terms reflect signaling modulation (GTPase activation, sumoylation, and autophosphorylation) and a trafficking component (endosome\u2013Golgi transport). Taken together, the cluster seems to center on stress-responsive signaling with translational control, with some peripheral connectivity to trafficking and broader signaling regulation.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034499","count":2},{"id":"GO:0090630","count":2},{"id":"GO:1990138","count":1},{"id":"GO:0031333","count":1},{"id":"GO:1990497","count":1}]},{"hash":"1935691038437767099","title":"Cytoskeleton Dynamics and Microtubule Transport","description":"The cluster is dominated by microtubule-based movement and microtubule-dependent transport terms, along with regulation of cytoskeleton organization. Neural development and neuron projection morphogenesis also appear, suggesting developmental roles tied to cytoskeletal remodeling. Together, these point to a core function in cytoskeleton dynamics and intracellular transport.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007018","count":1},{"id":"GO:0019060","count":1},{"id":"GO:0008340","count":1},{"id":"GO:0007399","count":1},{"id":"GO:0048812","count":1}]},{"hash":"547005094478195750","title":"Neural tube and embryonic development","description":"This cluster shows a strong representation of neural development and embryogenesis terms (neural tube closure, forebrain development, multicellular organism development, and cell migration), suggesting the proteins collectively participate in developmental processes of the nervous system and organism formation. A few terms related to stress or immune responses are present but appear less central to the core theme.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":2},{"id":"GO:0001843","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0001501","count":2},{"id":"GO:0007275","count":2}]},{"hash":"1118206743222761281","title":"ER\u2013Golgi\u2013Endosome Vesicle Trafficking","description":"Proteins here cluster around intracellular transport within the endomembrane system: plasma membrane to endosome, endosome to Golgi, and COPII-mediated ER-to-Golgi cargo loading. The presence of Rab/Rap signaling terms and regulation of kinases supports a coordinated trafficking regulatory module. A few cell-cycle related terms appear but do not define the primary function of the cluster, which remains membrane trafficking.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048227","count":2},{"id":"GO:0071955","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0035526","count":2},{"id":"GO:0034499","count":2}]},{"hash":"1860734279229537259","title":"Unknown","description":"The GO terms are highly heterogeneous: cuticle development, kidney tubule development, nuclear import, cytokinesis regulation, calcium response, kinase activity regulation, and oxidative processes. No single theme or shared pathway stands out across all proteins, so a cohesive functional label cannot be assigned.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097274","count":1},{"id":"GO:0008365","count":1},{"id":"GO:1905205","count":1},{"id":"GO:0072286","count":1},{"id":"GO:0006607","count":1}]},{"hash":"121066676017144880","title":"Auxin transport and signaling","description":"This cluster is dominated by GO terms related to auxin transport and signaling, including polar transport, export across the plasma membrane, transmembrane transport, and auxin-activated signaling, as well as adventitious root development, which together point to a cohesive role in auxin distribution and response. The single base-excision repair term appears incidental and does not align with the main theme, reinforcing the auxin-centric interpretation.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006284","count":1},{"id":"GO:0080162","count":1},{"id":"GO:0010252","count":1},{"id":"GO:0009734","count":1},{"id":"GO:0048830","count":1}]},{"hash":"193352606345366727","title":"DNA damage response and cell cycle control","description":"This cluster is dominated by terms related to genome maintenance and cell-cycle regulation, including DNA double-strand break repair via synthesis-dependent strand annealing and mitotic intra-S DNA damage checkpoint signaling. Additional terms point to stress-related remodeling and signaling (e.g., glucocorticoid signaling, cardiac hypertrophy), suggesting a broader cellular stress response context. The core connection appears to be DNA damage response and cell-cycle control, with ancillary stress signaling support.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010719","count":6},{"id":"GO:0034501","count":6},{"id":"GO:0046086","count":6},{"id":"GO:1905205","count":6},{"id":"GO:0010791","count":6}]},{"hash":"461664625667479861","title":"Neuronal microtubule dynamics and polarity","description":"The top GO terms cluster around microtubule regulation (depolymerization, spindle/kinetochore interactions, polarity) along with neuron-specific processes (neuron projection maintenance, dendritic transport, Purkinje cell layer organization). This suggests a cohesive theme of microtubule/cytoskeleton dynamics governing neuronal structure and transport, with some broader cytoskeletal functions in other cell types. ","confidence":"High","size":6,"edges":13,"triangles":13,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0010938","count":6},{"id":"GO:0000743","count":6},{"id":"GO:0001560","count":6},{"id":"GO:0032487","count":6},{"id":"GO:0098971","count":6}]},{"hash":"1635696586207732910","title":"Neuronal microtubule dynamics and projection maintenance","description":"The top GO terms cluster around microtubule cytoskeleton regulation and transport, including depolymerization, spindle/kinetochore dynamics, polarity establishment, and dendritic receptor transport, all of which point to roles in neurite stability and neuron projection maintenance. A few terms reference non-neuronal contexts (e.g., chloroplast movement), but the dominant theme is microtubule dynamics linked to neuronal structure and transport.","confidence":"High","size":6,"edges":11,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0010938","count":6},{"id":"GO:0000743","count":6},{"id":"GO:0001560","count":6},{"id":"GO:0032487","count":6},{"id":"GO:0098971","count":6}]},{"hash":"1848773104393563745","title":"DNA damage response and stress signaling","description":"The proteins show enrichment for DNA repair and cell-cycle checkpoints (DSB repair via SDSA and intra-S checkpoint, kinetochore localization) alongside diverse stress-response terms (cardiac hypertrophy, glucocorticoid signaling, response to cocaine) and metabolism (adenosine biosynthesis), suggesting a theme centered on stress-related signaling and DNA damage control.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010719","count":6},{"id":"GO:0034501","count":6},{"id":"GO:0046086","count":6},{"id":"GO:1905205","count":6},{"id":"GO:0010791","count":6}]},{"hash":"656098576221895401","title":"Neuronal microtubule organization and dendritic transport","description":"Most terms point to microtubule cytoskeleton dynamics (polarity establishment, spindle-kinetochore attachments) and neuronal maintenance (neuron projection maintenance, anterograde transport of neurotransmitter receptors), with some cross-species terms (chloroplast movement) likely noise. Together, this cluster reflects neuronal microtubule organization and dendritic transport processes.","confidence":"Medium","size":6,"edges":6,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000147","count":3},{"id":"GO:0010938","count":2},{"id":"GO:0001560","count":2},{"id":"GO:0032487","count":2},{"id":"GO:0098971","count":2}]},{"hash":"1830734833917715653","title":"Neuronal microtubule transport and projection maintenance","description":"The terms are dominated by neuronal and cytoskeletal functions: anterograde dendritic transport of neurotransmitter receptor complex, neuron projection maintenance, and cerebellar Purkinje cell layer organization, all pointing to microtubule-based transport and structural maintenance in neurons. Some terms relate to microtubule dynamics and spindle attachment, which fit within a broader microtubule/cytoskeleton theme. Overall, the cluster reflects microtubule-mediated neuronal transport and projection maintenance rather than unrelated processes.","confidence":"High","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0048364","count":4},{"id":"GO:0010938","count":3},{"id":"GO:0000743","count":3},{"id":"GO:0001560","count":3},{"id":"GO:0032487","count":3}]},{"hash":"1292464556970020253","title":"DNA Damage Response and Stress Signaling","description":"The cluster centers on DNA double-strand break processing and mitotic intra-S DNA damage checkpoint signaling, indicating a core DNA damage response role. Additional terms reflect broader cellular stress signaling and adaptation (glucocorticoid signaling, cardiac hypertrophy under stress, response to cocaine) along with cell-cycle components (kinetochore localization, EMT regulation). Together, these proteins likely participate in maintaining genome integrity while engaging diverse stress-response pathways.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010719","count":6},{"id":"GO:0034501","count":6},{"id":"GO:0046086","count":6},{"id":"GO:1905205","count":6},{"id":"GO:0010791","count":6}]},{"hash":"975779363544076185","title":"DNA replication and cell cycle control","description":"Dominant terms center on DNA replication and cell cycle regulation (DNA replication, mitotic cell cycle, centrosome cycle, and regulation of nuclear DNA replication), indicating these proteins are involved in replication and division. Some terms refer to development or signaling and may reflect multifunctionality or annotation noise, but the core pattern supports replication/mitosis involvement.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010571","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0007098","count":5},{"id":"GO:0048701","count":5},{"id":"GO:0007601","count":4}]},{"hash":"2180147646486351627","title":"Nuclear chromatin regulation and nucleolar transcription","description":"The top GO terms converge on chromatin state control and nucleolar transcription: histone deacetylation, Hsp90 deacetylation, negative regulation of transcription by RNA polymerase I, and localization to nucleolar rDNA repeats, plus cohesin-related regulation. While a few terms touch on development, the central theme is chromatin remodeling and nucleolar transcription regulation.","confidence":"High","size":6,"edges":13,"triangles":13,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0031939","count":4},{"id":"GO:0070846","count":4},{"id":"GO:0048742","count":4},{"id":"GO:0045668","count":4},{"id":"GO:0016479","count":4}]},{"hash":"726040459920298227","title":"Unknown","description":"The annotated GO terms are a mix of cilium-related processes (regulation of non-motile cilium assembly; protein localization to photoreceptor outer segment; centrosome microtubule anchoring), nuclear receptor signaling (steroid hormone receptor complex assembly; positive regulation of glucocorticoid signaling), RNA processing (box C/D snoRNP assembly), innate immune response, and cell-cycle\u2013related catabolic processes. This diversity provides no single cohesive function or theme for all proteins, so a concise, representative label isn\u2019t supported.","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000492","count":3},{"id":"GO:0006463","count":3},{"id":"GO:2000324","count":3},{"id":"GO:0045087","count":3},{"id":"GO:1903546","count":3}]},{"hash":"425116510559195022","title":"Pollen exine formation and glycosylation","description":"This cluster centers on pollen development features, especially exine formation and anther dehiscence, and is linked with protein N-linked glycosylation and nucleotide-sugar (UDP, GDP, CDP) catabolic pathways, suggesting coordinated glycosylation and carbohydrate metabolism during pollen wall biosynthesis.","confidence":"High","size":6,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006487","count":2},{"id":"GO:0046032","count":2},{"id":"GO:0009901","count":2},{"id":"GO:0010584","count":2},{"id":"GO:0046706","count":2}]},{"hash":"252205431347992709","title":"Neuronal development and synaptic proteostasis","description":"This cluster centers on neuron development, dendritic spine morphogenesis, and visual perception, with involvement in proteasomal degradation and protein stability, suggesting roles in neuronal growth and synapse remodeling; endosome transport relates to neuronal receptor trafficking, while some cell cycle/pseudohyphal terms appear incidental.","confidence":"Medium","size":6,"edges":4,"triangles":1,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0032435","count":4},{"id":"GO:0048666","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0007601","count":4},{"id":"GO:0060044","count":4}]},{"hash":"1493893506454996379","title":"Telomere maintenance and DNA replication","description":"These terms cluster around nuclear genome maintenance: telomere maintenance via telomerase, DNA replication, DNA repair, and DNA-templated transcription, plus mitotic cell cycle. This suggests the proteins work in genome stability and replication. A few terms (response to cocaine, pseudohyphal growth) appear as outliers or broader annotations, but the dominant signal ties to telomere and replication functions.","confidence":"Medium","size":6,"edges":10,"triangles":7,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0032212","count":4},{"id":"GO:0042220","count":4},{"id":"GO:0051973","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0006281","count":4}]},{"hash":"1657160375665860135","title":"Neural development and signaling","description":"The top GO terms show several nervous system\u2013related processes (visual perception, CNS projection neuron axonogenesis, dopaminergic synaptic transmission, neural tube patterning, and neural signaling regulation), suggesting the cluster centers on neural development and neuronal communication. While other terms pertain to general cell biology (endosome transport, mitotic cycle), the neural-theme terms predominate enough to label accordingly, though some ambiguity remains from non-neural terms. ","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":6},{"id":"GO:0000278","count":6},{"id":"GO:2000641","count":5},{"id":"GO:0007124","count":5},{"id":"GO:1901621","count":5}]},{"hash":"533047394319717887","title":"Vacuolar amino acid transporters","description":"This cluster is characterized by multiple GO terms for import of several amino acids (histidine, serine, tyrosine, arginine, proline, alanine) into the vacuole, plus at least one export term, suggesting a shared function as vacuolar amino acid transporters and roles in amino acid homeostasis under nutrient stress. The presence of nitrogen starvation-related terms supports a context where vacuolar transport is important for nutrient redistribution. ","confidence":"High","size":6,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051365","count":2},{"id":"GO:0090513","count":2},{"id":"GO:1901481","count":2},{"id":"GO:0089708","count":2},{"id":"GO:0090516","count":2}]},{"hash":"1946360535662682045","title":"Cytoskeleton remodeling and membrane trafficking","description":"The GO terms cluster around actin cortex assembly, endocytic recycling, and membrane remodeling (tubulation, Golgi regulation), with additional links to calcium signaling and membrane potential, implying a cohesive role in cytoskeleton-driven trafficking and membrane organization that influences processes like neurite extension and muscle cell fusion.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0086036","count":1},{"id":"GO:0097320","count":1},{"id":"GO:0032456","count":1},{"id":"GO:1903861","count":1},{"id":"GO:0007120","count":1}]},{"hash":"1142412521444787105","title":"Neural development and signaling","description":"This cluster includes terms tied to neural development and neuronal signaling, such as CNS projection neuron axonogenesis, dopaminergic synaptic transmission, and dorsal/ventral neural tube patterning. Endosome transport regulation aligns with vesicle trafficking important for neurons, while other terms reflect broader cellular signaling. Overall, the shared theme appears to be neural development and neuronal signaling.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":6},{"id":"GO:0007124","count":6},{"id":"GO:1901621","count":6},{"id":"GO:1904637","count":6},{"id":"GO:0001963","count":6}]},{"hash":"1496560135891495628","title":"Plant light and ethylene signaling regulators","description":"The terms cluster around ethylene signaling regulation, light detection and phototransduction (including red/far-red), hypoxia sensing, and transcriptional regulation, with phosphorylation activity. This points to plant signaling proteins that link light and environmental cues to transcriptional responses and hormone signaling, forming a cohesive light/ethylene-responsive regulatory module.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0010105","count":3},{"id":"GO:0000160","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0070483","count":2}]},{"hash":"2130284988365241814","title":"Neural development and dopaminergic signaling","description":"This cluster centers on neural development and signaling: axonogenesis of CNS neurons and dopaminergic synaptic transmission, with supporting terms on neural tube patterning and endosomal regulation; a few terms (immune, cartilage, and yeast growth) appear less connected, but the core theme is neuronal development and signaling.","confidence":"Medium","size":6,"edges":3,"triangles":1,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":6},{"id":"GO:0007124","count":6},{"id":"GO:1901621","count":6},{"id":"GO:1904637","count":6},{"id":"GO:0001963","count":6}]},{"hash":"195271151387549020","title":"DNA damage response and nuclear transport","description":"The cluster is enriched for nuclear-centric processes: global genome nucleotide-excision repair, PML body organization, and protein localization to the nuclear pore, all tied to genome maintenance and nuclear signaling. The presence of autoubiquitination points to ubiquitin-regulated protein turnover linked to these nuclear processes. Additional stress-response terms (ER stress, immune signaling) suggest broader cellular stress integration with nuclear functions, though some items are peripheral. Overall, the common theme is nuclear maintenance and stress response.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0070911","count":6},{"id":"GO:0051865","count":6},{"id":"GO:0030578","count":6},{"id":"GO:1901896","count":6},{"id":"GO:0017085","count":6}]},{"hash":"2110225548265429833","title":"Unknown","description":"The top terms span muscle assembly, cuticle development, oxidative stress generation, signaling, morphogenesis, and gene expression, with no obvious shared function or pathway. The cluster has no edges or triangles, suggesting no cohesive interaction or common mechanism linking these proteins in this dataset.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055003","count":2},{"id":"GO:0008365","count":2},{"id":"GO:0042554","count":2},{"id":"GO:0031284","count":2},{"id":"GO:0048855","count":2}]},{"hash":"688754687753890487","title":"Ubiquitin-Dependent ERAD and ER Stress Signaling","description":"The top GO terms point to ubiquitination processes, ER-associated degradation (ERAD), and regulation of ER stress-related signaling (including TNF and TLR3 pathways). While nucleotide-excision repair appears, the strongest signal is ubiquitin-mediated proteostasis at the ER and its link to stress and immune signaling, suggesting a cohesive function around ER quality control and ubiquitin-dependent regulation.","confidence":"Medium","size":6,"edges":11,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":4},{"id":"GO:1903265","count":4},{"id":"GO:0006289","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0017085","count":3}]},{"hash":"970270076994895392","title":"Cellular Stress Responses","description":"The top terms point to responses to a variety of stressors (radiation, oxidative conditions, hypoxia, chemical exposures) and a few chromatin/regulatory adjustments linked to stress, suggesting the proteins participate in general stress-response signaling rather than a single specific pathway. Some terms are obsolete, but the overarching theme remains stress adaptation and damage response.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033169","count":1},{"id":"GO:1990911","count":1},{"id":"GO:1904843","count":1},{"id":"GO:0071480","count":1},{"id":"GO:0000304","count":1}]},{"hash":"957868786037188875","title":"Unknown","description":"This cluster includes terms spanning motility (amoeboid migration, cell spreading), vesicle trafficking (phagosome maturation, degranulation), mitosis-related processes (spindle microtubule attachment, cleavage furrow ingression), signaling (Wnt signalosome assembly), copper ion homeostasis, and neural differentiation (oligodendrocyte differentiation). There is no single cohesive theme uniting these diverse functions, so a specific, representative label cannot be assigned with confidence.","confidence":"","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1903215","count":6},{"id":"GO:0001667","count":6},{"id":"GO:0006878","count":6},{"id":"GO:0043316","count":6},{"id":"GO:1900026","count":6}]},{"hash":"767926204291866628","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071374","count":2},{"id":"GO:0090084","count":2},{"id":"GO:1901621","count":2},{"id":"GO:0006458","count":2},{"id":"GO:0070843","count":2}]},{"hash":"267983029206082276","title":"Membrane trafficking and cytokinesis","description":"GO terms in this cluster emphasize membrane dynamics (endocytic recycling, endosome-Golgi transport, membrane tubulation) and lipid signaling (phosphatidic acid biosynthesis), alongside division-related processes (cleavage furrow formation, mitotic cell cycle). While a few terms relate to broader development, the core signals converge on membrane trafficking/dynamics coupled with cell division, supporting this label. Medium","confidence":"","size":6,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1990126","count":1},{"id":"GO:0097320","count":1},{"id":"GO:0000278","count":1},{"id":"GO:0022617","count":1},{"id":"GO:0036089","count":1}]},{"hash":"256321236038454758","title":"Unknown","description":"The GO terms are highly diverse, spanning vacuolar pH/ion transport, RNA export and processing, transcription regulation, plant hormone signaling, DNA replication/repair processes, and immune regulation. With no clear shared function or pathway and no edges connecting the proteins, there isn\u2019t a cohesive theme to label a more specific cluster name. Therefore, this cluster is Unknown.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007035","count":1},{"id":"GO:1902600","count":1},{"id":"GO:0031990","count":1},{"id":"GO:0046784","count":1},{"id":"GO:0010267","count":1}]},{"hash":"211167752639875262","title":"Unknown","description":"The GO terms for this cluster are highly heterogeneous, covering endosome transport, fungal growth, hedgehog-related signaling, ionomycin response, dopaminergic synaptic transmission, p53-mediated signaling, NK T cell differentiation, CNS neuron axonogenesis, age-related oxidative stress, and cartilage condensation. There is no single cohesive biological process that ties these functions together, making a confident, specific cluster label unattainable.","confidence":"","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":6},{"id":"GO:0007124","count":6},{"id":"GO:1901621","count":6},{"id":"GO:1904637","count":6},{"id":"GO:0001963","count":6}]},{"hash":"967667001519889754","title":"Unknown","description":"The top terms span immune processes, cytoskeletal dynamics, signaling, and cell cycle events with no single cohesive function linking the proteins; representation is scattered (mostly two occurrences each), so there is no clear representative function for the cluster.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903215","count":2},{"id":"GO:0001667","count":2},{"id":"GO:0006878","count":2},{"id":"GO:0043316","count":2},{"id":"GO:1900026","count":2}]},{"hash":"2034107421743753864","title":"Membrane Ion Transport","description":"The top GO terms are dominated by ion transport and membrane-related processes (sodium, potassium, copper transport; monoatomic cation transmembrane transport; membrane repolarization), pointing to a common function in moving ions across membranes. Some terms appear as outliers (lipopolysaccharide biosynthesis, nerve formation, stilbene catabolism, epoxygenase P450), but the clearest shared theme is membrane ion transport.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":3},{"id":"GO:0007049","count":2},{"id":"GO:0086009","count":2},{"id":"GO:0002028","count":2},{"id":"GO:0046272","count":2}]},{"hash":"1083756424079012460","title":"DNA replication and chromosome maintenance","description":"The top GO terms cluster around DNA replication initiation, mitotic DNA replication checkpoint signaling, and telomere maintenance, suggesting a core function in replication and chromosome integrity. While there are also terms related to ER-associated degradation and mRNA export, the strongest signals point to replication-related processes. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0006406","count":2},{"id":"GO:1904515","count":1},{"id":"GO:1904263","count":1},{"id":"GO:0072443","count":1}]},{"hash":"670073766613056992","title":"Unknown","description":"The GO terms show a broad mix of processes (glucose metabolism, DNA-templated transcription, chemotaxis, development, signal responses, and endosome transport) with no clear shared function. Because of this heterogeneity, there isn't a well-supported, concise label that captures a common theme for the cluster.","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0033160","count":5},{"id":"GO:0006006","count":5},{"id":"GO:0042220","count":5},{"id":"GO:0045793","count":5},{"id":"GO:0006351","count":5}]},{"hash":"2068934160667863934","title":"Meiosis and embryogenesis via ubiquitin-proteasome regulation","description":"This cluster centers on ubiquitin-dependent proteolysis with SCF- and K11-linked ubiquitination, and includes processes governing meiosis I, sister chromatid segregation, and metaphase/anaphase transitions, along with in utero embryonic development and stem cell differentiation. The shared theme is regulation of cell cycle and development through targeted proteolysis, especially in meiotic and embryonic contexts.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0001701","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0000715","count":2},{"id":"GO:1902104","count":2},{"id":"GO:0042787","count":2}]},{"hash":"1963121013893354124","title":"Cell Division and SnoRNP Assembly","description":"The strongest signals are mitotic cell cycle and box C/D snoRNP assembly, pointing to roles in cell proliferation and ribosomal RNA processing. Some other GO terms (immune response, viral genome regulation) appear less coherent with this core theme and may reflect annotation noise. Overall, the cluster seems best described by cell division-related function with snoRNP assembly as a supporting process.","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000492","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0055114","count":2}]},{"hash":"84642462811689689","title":"Unknown","description":"The top GO terms span mitosis (cell division, spindle assembly) and broader cellular processes, but also include cytokine/immune signaling, oxidative/stress responses, epithelial polarity, and cardiac cell communication. This broad mix lacks a single cohesive function tying the proteins together, making a specific, intuitive label difficult.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0071353","count":2},{"id":"GO:0033197","count":2},{"id":"GO:0071642","count":2},{"id":"GO:1901594","count":2}]},{"hash":"522291316562195626","title":"Diverse Solute and Ion Transmembrane Transport","description":"Based on the top GO terms, the cluster centers on transport across membranes for a variety of substrates and ions (xenobiotic, vitamin, glycine betaine, taurine, cobalt ion, monoatomic anion), with ceramide translocation and related stress signals, suggesting a cohesive theme of diverse transmembrane solute/ion transport rather than a single substrate or process. The SOS response and cytochrome complex assembly appear as ancillary stress/respiratory links but do not override the central transport focus.","confidence":"High","size":6,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":6},{"id":"GO:0035461","count":6},{"id":"GO:0046677","count":4},{"id":"GO:0031460","count":4},{"id":"GO:0099133","count":4}]},{"hash":"1997236928979767475","title":"Endodermal and ocular development with stem cell regulation","description":"This cluster\u2019s GO terms converge on development of endoderm-derived organs (endodermal fate, intrahepatic bile duct and gallbladder development) and ocular structures (retinal rod differentiation, cornea development), along with themes of stem cell maintenance/proliferation and transcriptional regulation. Together they suggest a broad developmental program linking endodermal organogenesis and eye development with stem cell control, rather than a single specific pathway.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007493","count":2},{"id":"GO:0060221","count":2},{"id":"GO:0035019","count":2},{"id":"GO:0071866","count":2},{"id":"GO:0061303","count":2}]},{"hash":"1059108254756693564","title":"Viral budding and host RNA processing factors","description":"This cluster shows terms related to viral release/budding and translation reinitiation, suggesting involvement in viral processes, alongside multiple mRNA splicing and processing terms, implying a role in RNA processing. The combination points to host factors that interface with viral replication while regulating RNA processing steps.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019076","count":1},{"id":"GO:1900363","count":1},{"id":"GO:0048025","count":1},{"id":"GO:0035278","count":1},{"id":"GO:0039702","count":1}]},{"hash":"2142184802966184307","title":"Eye-Antennal Disc Development","description":"The top GO terms point to imaginal disc development in Drosophila (eye-antennal disc development and regulation of imaginal disc growth), suggesting a developmental role related to imaginal discs. The other terms (nucleolus organization and an obsolete methylation term) are not strongly coherent with this theme, making the connection tentative but the imaginal-disc development signal the strongest among the terms provided.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035214","count":1},{"id":"GO:0007000","count":1},{"id":"GO:0045572","count":1},{"id":"GO:0090116","count":1}]},{"hash":"766551974113968132","title":"Mitochondrial Translation and Respiration","description":"The presence of translation and ribosome biogenesis terms (GO:0006412, GO:0000462) alongside mitochondrial electron transport (GO:0006120) points to a cluster centered on protein synthesis and mitochondrial energy metabolism, with other development/aging terms likely representing noise. ","confidence":"Medium","size":6,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0000462","count":1},{"id":"GO:0070584","count":1},{"id":"GO:0072358","count":1},{"id":"GO:0061458","count":1}]},{"hash":"76482541891353345","title":"Ubiquitin-Dependent Protein Degradation and Antiviral Defense","description":"Top GO terms are dominated by ubiquitin-related processes (protein autoubiquitination; ubiquitin-dependent proteolysis) and antiviral/immune signaling (defense response to virus; negative regulation of viral transcription; NF-kappaB signaling). This suggests a cluster centered on ubiquitin-mediated proteostasis that modulates antiviral responses. Some microtubule-related terms appear, possibly reflecting trafficking or cytoskeletal regulation, but the core theme is ubiquitin-dependent regulation of antiviral defense.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":4},{"id":"GO:0042787","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0043123","count":3},{"id":"GO:0046597","count":3}]},{"hash":"110357849403411955","title":"Ubiquitin-Dependent Immune Signaling","description":"The top GO terms cluster around immune signaling pathways (tumor necrosis factor-mediated signaling, JNK cascade, I-kappaB phosphorylation) and ubiquitin-related regulation (autoubiquitination, ubiquitin-dependent protein catabolic processes, ERAD). This points to a group of proteins involved in immune signal transduction modulated by ubiquitin turnover, with some related terms touching on broader immune regulation and chromatin dynamics. Overall, the shared theme is immune signaling governed by ubiquitin-dependent regulation.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033209","count":4},{"id":"GO:0033151","count":3},{"id":"GO:0090073","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0030433","count":3}]},{"hash":"555761540251085104","title":"Developmental signaling and transcriptional regulation","description":"The cluster includes terms tied to transcription (DNA-templated transcription), development (multicellular development, pseudohyphal growth), and signaling pathways (p53 mediator signaling, hedgehog-related smoothened signaling), plus related cellular processes like endosome transport and calcium responses. This combination suggests a shared theme of coordinated transcriptional control and signaling that governs development and cellular responses, though there are outliers (e.g., dopaminergic synaptic transmission) reflecting broader cross-species signaling roles.","confidence":"Medium","size":6,"edges":12,"triangles":10,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":5},{"id":"GO:0019233","count":5},{"id":"GO:0007275","count":5},{"id":"GO:0006351","count":5},{"id":"GO:2000641","count":4}]},{"hash":"488467627438879786","title":"Chromatin remodeling and histone modification","description":"The top GO terms are dominated by chromatin-related processes: nucleosome assembly/disassembly and regulation of histone acetylation, along with sperm DNA decondensation. A few terms touch on microtubule dynamics and budding, but the core signal points to chromatin remodeling and histone modification as the cluster\u2019s theme.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015031","count":2},{"id":"GO:0006337","count":1},{"id":"GO:0006334","count":1},{"id":"GO:0043085","count":1},{"id":"GO:0031116","count":1}]},{"hash":"1478394759946931161","title":"Unknown","description":"The six proteins show highly diverse GO terms spanning chromosome condensation, RNA/snoRNA processing, pollen sperm differentiation, membrane repolarization, lipopolysaccharide biosynthesis, and various regulatory processes, with no evident shared pathway or function (no edges/triangles, all terms occur once). This lack of a coherent theme makes a specific functional label inappropriate.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030261","count":1},{"id":"GO:0000294","count":1},{"id":"GO:0034965","count":1},{"id":"GO:0048235","count":1},{"id":"GO:0086009","count":1}]},{"hash":"2256512275753205005","title":"Ion transport and calcium homeostasis","description":"Most terms point to ion transport and calcium signaling across membranes (potassium and sodium transport, membrane repolarization, potassium ion movement, intracellular calcium homeostasis, and calcium release). A developmental term for vestibulocochlear nerve formation is less representative. Overall, the cluster appears to encompass proteins involved in maintaining membrane potential and Ca2+ balance. ","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0086009","count":4},{"id":"GO:0002028","count":4},{"id":"GO:0021650","count":4},{"id":"GO:1990938","count":4},{"id":"GO:0097623","count":4}]},{"hash":"1768526541594884915","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning myelination, muscle growth, sterol transport, chromatin remodeling, egg activation, pronucleus assembly, and fungal membrane formation. There is no single coherent function or pathway linking these terms, so a meaningful, specific cluster label cannot be assigned.","confidence":"","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031642","count":1},{"id":"GO:0048633","count":1},{"id":"GO:0046856","count":1},{"id":"GO:0032366","count":1},{"id":"GO:0032120","count":1}]},{"hash":"654502450187534708","title":"Neural development and signaling","description":"These proteins cluster around nervous system development and function: myelin assembly and its negative regulation suggest glial/neural maturation; synaptic vesicle uncoating points to synaptic transmission; receptor recycling and phosphatidylinositol metabolism indicate membrane trafficking and signaling essential for neurons; regulation of locomotion aligns with neural control of movement. The dorsal closure term is an outlier from a broader morphogenesis context but does not overturn the dominant neural theme. Overall, the cluster is best described as neural development and signaling.","confidence":"Medium","size":6,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042518","count":1},{"id":"GO:0001921","count":1},{"id":"GO:0031161","count":1},{"id":"GO:0031642","count":1},{"id":"GO:0032288","count":1}]},{"hash":"607568618169426279","title":"Sodium-Potassium Transport and Homeostasis","description":"These terms cluster around ion transport across the plasma membrane, especially sodium import and potassium export, plus maintenance of intracellular potassium levels. While a few terms touch on neural or stress-related processes, the dominant pattern is Na+/K+ transport and homeostasis, suggesting proteins involved in ionic balance and membrane potential regulation.","confidence":"High","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0098719","count":2},{"id":"GO:0097623","count":2},{"id":"GO:0030007","count":2},{"id":"GO:0071642","count":1},{"id":"GO:1901594","count":1}]},{"hash":"926044537384902566","title":"Unknown","description":"The top GO terms are very diverse, spanning plant hormone signaling (cytokinin, ethylene), immune signaling (interleukin-4), xenobiotic and hypoxia responses, bacterial motility, and fundamental DNA processes (DNA replication, topological changes, telomerase assembly). With no edges or clear functional linkage, there is no cohesive theme connecting the proteins, so a generic Unknown label with None confidence is appropriate.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009736","count":3},{"id":"GO:0006261","count":2},{"id":"GO:0033160","count":2},{"id":"GO:0035690","count":2},{"id":"GO:1905323","count":2}]},{"hash":"473150956822808631","title":"Chromatin remodeling and ubiquitin signaling","description":"The top GO terms point to chromatin regulation (histone exchange, heterochromatin formation, histone catabolic process) and ubiquitin-dependent protein turnover (autoubiquitination, ubiquitin-mediated catabolism). Immune signaling terms (NF-kappaB, TNF pathways) plus V(D)J recombination suggest a role in lymphocyte chromatin dynamics during immune processes. Overall, the cluster seems to connect chromatin state control with ubiquitin-regulated signaling in immune contexts.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043486","count":2},{"id":"GO:0006348","count":2},{"id":"GO:0043123","count":2},{"id":"GO:0033151","count":2},{"id":"GO:0051865","count":2}]},{"hash":"688169770386688459","title":"Renin-angiotensin kidney function and development","description":"The top GO terms cluster around renin-angiotensin signaling and regulation (blood volume, aldosterone production, angiotensin maturation), along with kidney development (mesonephros). There are also related processes like drinking behavior, which ties to fluid regulation. Some terms (protein catabolic/autoprocessing and antigen presentation) are less central but do not override the renal-centric pattern. Overall, the cluster seems best described as renal physiology centered on the renin-angiotensin system.","confidence":"Medium","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0002016","count":1},{"id":"GO:0030163","count":1},{"id":"GO:0016540","count":1},{"id":"GO:0070305","count":1},{"id":"GO:0019886","count":1}]},{"hash":"2044811028370264924","title":"Ion transport and membrane potential regulation","description":"The top GO terms cluster around membrane repolarization and various ion transport processes (sodium, potassium, calcium, copper) and transmembrane transport, suggesting proteins that maintain ionic gradients and calcium signaling. A developmental term (vestibulocochlear nerve formation) is present but less central; overall, the shared theme is ion transport. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0086009","count":2},{"id":"GO:0002028","count":2},{"id":"GO:0021650","count":2},{"id":"GO:1990938","count":2},{"id":"GO:0097623","count":2}]},{"hash":"2046841114904642142","title":"mRNA Splicing and RNA Silencing Regulation","description":"The cluster's top GO terms converge on post-transcriptional control of gene expression: regulation of mRNA stability, spliceosome-mediated splicing (positive/negative and alternative splicing), mRNA modification, and ncRNA/miRNA\u2013mediated gene silencing. This pattern suggests a cohesive module centered on RNA processing and silencing rather than transcriptional regulation.","confidence":"High","size":6,"edges":8,"triangles":5,"max_degree":4,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":4},{"id":"GO:0031047","count":4},{"id":"GO:0048026","count":4},{"id":"GO:1900363","count":3},{"id":"GO:0048025","count":3}]},{"hash":"210056490592894108","title":"Chromatin Organization and Histone Modification","description":"Several GO terms point to chromatin biology: nucleosome assembly and histone modifications (H3-K4 methylation/demethylation, H3-K27 acetylation, H3-K23 acetylation). These collectively reflect chromatin packaging and transcriptional regulation. Although a few terms are marked obsolete and a couple relate to morphogenesis or spindle assembly, the dominant theme across the set is chromatin state control.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070562","count":1},{"id":"GO:0051569","count":1},{"id":"GO:0097536","count":1},{"id":"GO:1901674","count":1},{"id":"GO:0006334","count":1}]},{"hash":"2042577046728400580","title":"Nuclear RNA Processing and Ribosome Biogenesis under Stress","description":"This cluster is dominated by nuclear processes: ribosomal large subunit biogenesis, transcription, mRNA splicing, and chromatin/assembly functions, plus a stress-responsive link to mRNA export. The presence of ubiquitin-related regulation and cell cycle checkpoint hints suggests coordinated protein turnover and cell-cycle control during stress, supporting a cohesive theme of nuclear gene expression and ribosome biogenesis in a stress context.","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042273","count":3},{"id":"GO:0006351","count":3},{"id":"GO:2000728","count":2},{"id":"GO:1904668","count":2},{"id":"GO:0000398","count":2}]},{"hash":"989045920584913320","title":"Ribosome biogenesis and translation with cell division","description":"This cluster centers on GO terms related to ribosome assembly and function (cytoplasmic translation, ribosome biogenesis, ribosomal subunit export, tRNA modification) and also includes cell cycle/division processes (cell division, cell cycle, cell septum assembly). The combination suggests proteins involved in the protein synthesis machinery and its coordination with cell division. A peripheral term about conjugation with cellular fusion is likely incidental noise.  ","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002181","count":1},{"id":"GO:1901001","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0042274","count":1},{"id":"GO:0006400","count":1}]},{"hash":"983770530288817041","title":"Neuronal Synaptic Exocytosis and Plasticity","description":"GO terms are dominated by neuronal synaptic functions: calcium-dependent exocytosis, long-term potentiation, and regulation of synaptic plasticity, with supporting roles from membrane lipid biosynthesis and activity-driven ribosomal transcription. A couple of terms (myoblast fusion, ABA signaling) are off-target, but the prevailing pattern points to proteins involved in neurotransmitter release and synaptic strength. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001324","count":2},{"id":"GO:0007520","count":2},{"id":"GO:0045956","count":2},{"id":"GO:0060291","count":2},{"id":"GO:0043065","count":2}]},{"hash":"1364211339313805866","title":"Sugar transporters and osmotic stress response","description":"These proteins show strong enrichment for transmembrane transport of sugars (glucose, galactose, fructose) and related compounds, along with responses to glucose availability and osmotic stress. The cluster likely represents a membrane transporter module involved in sugar uptake and osmotic stress adaptation, making the label representative of its function.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0052106","count":2},{"id":"GO:0006970","count":2},{"id":"GO:1904659","count":2},{"id":"GO:0015757","count":2},{"id":"GO:1990539","count":2}]},{"hash":"1050353869868678260","title":"Telomere-Chromatin Regulation","description":"The top GO terms point to telomere biology (telomeric D-loop disassembly, negative regulation of telomere localization), nucleosome assembly and G-quadruplex DNA formation, and transcription-related processes (snRNA transcription). This combination suggests a theme of chromatin dynamics and DNA structure influencing transcription and telomere maintenance, with some plant-specific signaling terms echoing broader regulatory context. Therefore, a concise label like Telomere-Chromatin Regulation captures the core function represented, with moderate confidence.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0061820","count":2},{"id":"GO:0009736","count":2},{"id":"GO:1901347","count":2},{"id":"GO:0072362","count":2},{"id":"GO:0006334","count":2}]},{"hash":"558185714271634423","title":"Neuronal signaling and endosomal trafficking","description":"The top GO terms point to processes related to neuronal communication (glutamatergic synaptic transmission, sodium ion import, calcium-release channel regulation) and membrane trafficking (receptor recycling, regulation of endosome size), suggesting a functional grouping around neuronal signaling coupled with endocytic/trafficking control. Some nuclear processes (histone methylation, transcription regulation) appear less cohesive with the rest, but do not outweigh the clearer signaling/trafficking theme. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034968","count":2},{"id":"GO:0001881","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0051036","count":2},{"id":"GO:0035023","count":2}]},{"hash":"1463592342393230993","title":"Unknown","description":"The GO terms are highly diverse (metabolic regulation, development, transcription, neuron/eye morphogenesis, plant hormone response) with no clear shared function, and several terms are obsolete; the proteins appear isolated with no common biological theme, so no coherent label fits.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090180","count":1},{"id":"GO:2001172","count":1},{"id":"GO:0007527","count":1},{"id":"GO:1903212","count":1},{"id":"GO:0061614","count":1}]},{"hash":"1731303532975315535","title":"RNA Pol II Regulation and Epigenetic Control","description":"This cluster is dominated by terms about transcription regulation by RNA polymerase II (start-site selection, termination, and regulation under stress) and by epigenetic processes (H3K9 methylation, DNA methylation regulation). A few outliers (olfactory development, growth hormone secretion) exist, but the core theme is transcriptional control and chromatin state. ","confidence":"Medium","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0036091","count":4},{"id":"GO:0010880","count":2},{"id":"GO:0001178","count":2},{"id":"GO:0021553","count":2},{"id":"GO:2001229","count":2}]},{"hash":"2154928620078323544","title":"Unknown","description":"No shared GO terms are available for this cluster, and the network is very disconnected (one edge, max degree 1) among six proteins, so there is no clear common function to name.","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[]},{"hash":"1670099925021600178","title":"Unknown","description":"The top GO terms are scattered among nuclear DNA processes (DNA replication, DNA topology, telomerase assembly) and diverse signaling/stress responses (cytokinin, ethylene, interleukin-4, xenobiotic response, hypoxia) plus a bacterial motility term, with no single cohesive function linking the proteins. This lack of a clear theme leads to labeling as Unknown.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006261","count":5},{"id":"GO:0009736","count":5},{"id":"GO:0033160","count":5},{"id":"GO:0035690","count":5},{"id":"GO:1905323","count":5}]},{"hash":"2095630032047548444","title":"Hormone Biosynthesis and Development","description":"This cluster centers on hormone production, including androgen/testosterone biosynthesis and brassinosteroid biosynthesis, with accompanying developmental processes like mammary gland and female gonad development. However, the mix includes terms less clearly related (methylation, macrophage chemotaxis) and spans plant and animal contexts, lowering specificity.","confidence":"Low","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0008209","count":1},{"id":"GO:1900087","count":1},{"id":"GO:0016132","count":1},{"id":"GO:0071615","count":1},{"id":"GO:0033076","count":1}]},{"hash":"1645911002521800712","title":"Unknown","description":"The GO terms are highly diverse (immune signaling, neural development, vascular functions, osmotic stress responses, and metabolism) with no single dominant process. Because there isn\u2019t a coherent, common function tying the six proteins together, a specific, intuitive label cannot be justified.","confidence":"","size":6,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071642","count":1},{"id":"GO:1901594","count":1},{"id":"GO:0098719","count":1},{"id":"GO:0071651","count":1},{"id":"GO:0002024","count":1}]},{"hash":"220194034402742887","title":"Mitochondrial protein import and inner membrane insertion","description":"Label reflects the strongest shared annotations: protein import into the mitochondrial matrix (GO:0030150) and insertion of proteins into the mitochondrial inner membrane (GO:0045039). These two terms point to mitochondrial protein biogenesis and membrane assembly, which anchor the cluster. Other terms (proton transmembrane transport, vacuolar acidification, oxygen transport) fit membrane/energy-related processes but are less central, and a few terms (cell wall mannoprotein biosynthetic process, nitric oxide detox) may be ancillary or organism-specific. Overall, the dominant theme is mitochondrial protein targeting and inner membrane assembly.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015991","count":1},{"id":"GO:0007035","count":1},{"id":"GO:0000032","count":1},{"id":"GO:0016049","count":1},{"id":"GO:0046210","count":1}]},{"hash":"935093646849358826","title":"Canonical NF-kappaB Signaling","description":"The dominant GO term is canonical NF-kappaB signal transduction, implying the proteins are linked to NF-kappaB pathway signaling. Despite a lack of network edges, the shared annotation suggests a coherent NF-kappaB signaling theme for this cluster.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007249","count":1}]},{"hash":"1850843340092496972","title":"Unknown","description":"These proteins show two unrelated GO terms: carbohydrate metabolic process and protein deglycosylation, each represented by a single protein, with no edges connecting proteins. The lack of overlap or a unifying function makes it unclear how they cluster functionally, so a cohesive label cannot be reliably assigned.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0005975","count":1},{"id":"GO:0006517","count":1}]},{"hash":"132266658833504418","title":"Nuclear DNA replication and maintenance","description":"The dominant GO terms point to nuclear DNA processing: telomerase holoenzyme assembly, DNA-templated replication, and DNA topology changes, all core to genome maintenance in the nucleus. While other terms reflect signaling pathways (cytokinin, ethylene, IL-4) or stress responses, they appear as peripheral annotations rather than the cluster\u2019s central function. Hence, a label focused on nuclear DNA replication/maintenance best captures the core theme.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1905323","count":2},{"id":"GO:0006261","count":1},{"id":"GO:0009736","count":1},{"id":"GO:0033160","count":1},{"id":"GO:0035690","count":1}]},{"hash":"1378696381881908210","title":"Developmental signaling and tissue formation","description":"This cluster centers on development-related processes (multicellular development, skin development, cardiac muscle assembly) and on regulation of signaling pathways (kinase and GTPase activity, autophosphorylation) with associated cellular stress responses (hypoxia) and gene expression control (mRNA transport), suggesting proteins that coordinate signaling during tissue formation and development.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071456","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0071902","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0043588","count":2}]},{"hash":"565509425287913264","title":"Meiosis-Associated DNA Replication and Telomere Maintenance","description":"The top GO terms center on telomere maintenance (via telomerase and lengthening, plus capping) and various DNA replication stages (premeiotic, mitotic) with meiotic processes (male meiosis I, reciprocal meiotic recombination). This points to a module of proteins involved in chromosome maintenance and DNA replication during meiosis, with one outlier term (plasma membrane repair) likely representing annotation noise. ","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001778","count":2},{"id":"GO:0007131","count":1},{"id":"GO:0006279","count":1},{"id":"GO:0032212","count":1},{"id":"GO:0007004","count":1}]},{"hash":"1967583502493545050","title":"Neural development and synaptic signaling","description":"This cluster centers on neuronal growth and connectivity, with terms like hippocampus development, axon extension, and actin remodeling, alongside synaptic function indicators such as excitatory postsynaptic potential and calcium-dependent exocytosis, plus signaling pathways (ERK cascade, ephrin signaling) and dopamine responsiveness that tie together neural development and neurotransmission.","confidence":"High","size":5,"edges":6,"triangles":2,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070374","count":5},{"id":"GO:0045956","count":5},{"id":"GO:0051893","count":5},{"id":"GO:0060079","count":5},{"id":"GO:0043366","count":5}]},{"hash":"148755882068303267","title":"Unknown","description":"The GO terms span mitosis, development, hormone and toxin responses, tissue remodeling, and other diverse processes, with no single dominant theme linking the proteins. Because the terms are scattered and only a few proteins share obvious connections, there isn\u2019t a cohesive function that defines this cluster.","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0007100","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0034769","count":2}]},{"hash":"9676506468141036","title":"Unknown","description":"The terms span diverse processes including kinetochore localization, CDK activity regulation, endosome transport, yeast pseudohyphal growth, hedgehog pathway regulation, calcium signaling, dopaminergic synaptic transmission, p53 signaling, NK T cell differentiation, and neuronal axonogenesis. There is no single cohesive function linking these proteins, suggesting heterogeneous roles or annotation noise; thus no concise, representative label can be assigned.","confidence":"","size":5,"edges":6,"triangles":2,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0034501","count":5},{"id":"GO:0045736","count":5},{"id":"GO:2000641","count":4},{"id":"GO:0007124","count":4},{"id":"GO:1901621","count":4}]},{"hash":"1453524216889203976","title":"Neuronal microtubule dynamics and transport","description":"These terms converge on microtubule cytoskeleton dynamics and organization, especially in neurons. They include microtubule depolymerization, polarity establishment, spindle-kinetochore attachment, and neuronal transport/maintenance of projections. A few items (chloroplast movement) reflect generic microtubule dynamics across cell types but do not override the central theme. Therefore, 'Neuronal microtubule dynamics and transport' is an appropriate, representative label.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0010938","count":4},{"id":"GO:0000743","count":4},{"id":"GO:0001560","count":4},{"id":"GO:0032487","count":4},{"id":"GO:0098971","count":4}]},{"hash":"797539986108431353","title":"Microtubule dynamics and transport","description":"The top GO terms cluster around microtubule-based functions: spindle assembly and kinetochore interactions, microtubule remodeling, MT-dependent neuronal transport and projection maintenance, plus structural organization in neural tissues; chloroplast movement is also MT-associated. While there are a few broader signaling terms, the overall pattern supports cytoskeletal microtubule roles, giving a moderate level of confidence.","confidence":"Medium","size":5,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":3},{"id":"GO:0010938","count":2},{"id":"GO:0000743","count":2},{"id":"GO:0001560","count":2},{"id":"GO:0032487","count":2}]},{"hash":"1376448422387898983","title":"Microtubule Cytoskeleton and Neuronal Transport","description":"The terms cluster around microtubule dynamics and organization (depolymerization, spindle/kinetochore attachments, cytoskeleton polarity) with clear ties to neuronal transport and projection maintenance (dendritic transport, neuron projection maintenance), implying a cohesive role in microtubule-based structure and signaling in neurons; a few terms reflect shared microtubule functions across species (e.g., plant chloroplast movement).","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0010938","count":5},{"id":"GO:0000743","count":5},{"id":"GO:0001560","count":5},{"id":"GO:0032487","count":5},{"id":"GO:0098971","count":5}]},{"hash":"195771350396416173","title":"Neuronal microtubule organization and transport","description":"The top GO terms point to microtubule cytoskeleton dynamics, polarity, and movement, including cytoplasmic microtubule depolymerization, maintenance of microtubule polarity, and especially anterograde dendritic transport of receptor complexes and neuron projection maintenance. Several terms mention neuronal structure and cerebellar Purkinje cell layer organization, reinforcing a neuronal, microtubule-based functional theme. A plant-specific term about chloroplast movement appears but the dominant signal is microtubule organization and neuronal transport. ","confidence":"Medium","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0010938","count":2},{"id":"GO:0000743","count":2},{"id":"GO:0001560","count":2},{"id":"GO:0032487","count":2},{"id":"GO:0098971","count":2}]},{"hash":"2099361530653073913","title":"Amino acid metabolism and nitrogen stress response","description":"The top GO terms cluster around amino acid handling (L-glutamine metabolism, response to amino acids, response to amine) and nitrogen-related stress (ammonium ion, starvation), suggesting a shared function in amino acid/nitrogen metabolism and nutrient stress responses. Some terms also touch glucagon signaling and hepatocyte differentiation, indicating a metabolic regulation context typical of liver- or nutrient-responsive pathways.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":3},{"id":"GO:0008153","count":3},{"id":"GO:1903718","count":3},{"id":"GO:0043200","count":3},{"id":"GO:0071377","count":3}]},{"hash":"236362165714340544","title":"Neural development and signaling cluster","description":"The top GO terms point to neural processes: visual perception, dopaminergic synaptic transmission, CNS projection neuron axonogenesis, and neural tube patterning (regulated by hedgehog signaling). While there are outliers related to cell cycle and endosome transport, the dominant theme across the terms is neural development and neuronal signaling, suggesting the cluster centers on proteins involved in neural guidance and communication. ","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":5},{"id":"GO:0000278","count":5},{"id":"GO:2000641","count":4},{"id":"GO:0007124","count":4},{"id":"GO:1901621","count":4}]},{"hash":"77765294599961288","title":"Neural Development and Signaling with Trafficking","description":"The terms concentrate on neuronal development and function\u2014axonogenesis, dopaminergic synaptic transmission, and neural tube patterning\u2014paired with endosomal transport regulation, suggesting a cluster centered on neural differentiation and signaling with intracellular trafficking. A few terms touch on broader cellular processes (DNA replication, pseudohyphal growth, NK T cell differentiation), which may reflect annotation breadth, but do not override the main neural theme.","confidence":"Medium","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0048701","count":5},{"id":"GO:2000641","count":4},{"id":"GO:0007124","count":4},{"id":"GO:1901621","count":4}]},{"hash":"1544680663016892423","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006096","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0006094","count":2},{"id":"GO:0006099","count":2},{"id":"GO:0006006","count":1}]},{"hash":"1474194117197526328","title":"Mitotic cell cycle control and transcription","description":"This cluster is dominated by GO terms for DNA-templated transcription and multiple mitotic cell cycle transitions (G1/S, G2/M, and re-entry into mitosis), plus related processes like spindle pole separation and cell size regulation. While a few terms (e.g., placenta development, insulin signaling) are peripheral, the core theme centers on cell cycle progression and transcriptional control during division, making this label a concise representation of the cluster\u2019s function.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0000082","count":3},{"id":"GO:0000320","count":3},{"id":"GO:0000086","count":3},{"id":"GO:0045793","count":3}]},{"hash":"2203316198861815328","title":"Cell growth and gene expression regulation","description":"This cluster features GO terms tied to DNA replication and transcription, cell size regulation, and metabolic processes, plus endosome transport and morphological growth (pseudohyphal growth). While some terms (placenta development, response to cocaine) appear unrelated or cross-species, the majority point to core cellular growth, gene expression control, and trafficking. The set suggests a broad but coherent theme around growth and intracellular regulation rather than a single pathway.","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0045793","count":4},{"id":"GO:0001890","count":4},{"id":"GO:0006006","count":4},{"id":"GO:0006351","count":4}]},{"hash":"878885034488062710","title":"Cytoskeletal Dynamics in Migration and Mitosis","description":"This cluster highlights amoeboid-type cell migration, positive regulation of cell spreading, and spindle-kinetochore interactions, all tied to cytoskeletal remodeling and adhesion. The presence of mitotic cleavage furrow ingression and kinetochore-attached spindle regulation points to mitotic cytoskeleton functions, while migration and spreading terms reflect actin dynamics and cell movement. Some terms like phagosome maturation and Wnt signalosome assembly hint at broader signaling and endocytic roles, but the dominant theme remains cytoskeletal-driven cellular movement and division.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1903215","count":3},{"id":"GO:0001667","count":3},{"id":"GO:0006878","count":3},{"id":"GO:0043316","count":3},{"id":"GO:1900026","count":3}]},{"hash":"1034141585104797108","title":"Unknown","description":"Top terms are diverse (proteasome assembly, proton transport, vacuolar acidification, eye pigmentation, retina development, gamete formation, meiotic replication), showing no single cohesive biological theme to label the cluster confidently.","confidence":"","size":5,"edges":8,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0070682","count":1},{"id":"GO:0015991","count":1},{"id":"GO:0007035","count":1},{"id":"GO:0048069","count":1},{"id":"GO:0061075","count":1}]},{"hash":"1452461904922415555","title":"Unknown","description":"The GO terms are highly diverse, spanning neural development and synaptic activity (nervous system development, Schwann cell development, excitatory postsynaptic potential) as well as broad processes like cell cycle transitions, DNA replication, and various tissue developments (kinetochore localization, skeletal muscle development, meiotic cell cycle, B cell signaling). This heterogeneity provides no single cohesive functional theme to label the cluster, so an Unknown label with None confidence is appropriate.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007399","count":4},{"id":"GO:0034501","count":4},{"id":"GO:0042220","count":4},{"id":"GO:0060079","count":4},{"id":"GO:0000082","count":4}]},{"hash":"798199727192447627","title":"Unknown","description":"Top terms are heterogeneous, including dephosphorylation, EMT regulation, kinetochore localization, DNA repair/checkpoint signaling, and various stress-related/metabolic pathways, indicating no single unifying function for this cluster.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070940","count":2},{"id":"GO:0016311","count":1},{"id":"GO:0010719","count":1},{"id":"GO:0034501","count":1},{"id":"GO:0046086","count":1}]},{"hash":"2073616955802704366","title":"Endomembrane and synaptic vesicle trafficking","description":"The top GO terms cluster around vesicle-mediated transport within the endomembrane system, including retrograde and anterograde ER\u2013Golgi transport, endosome-to-melanosome transport, melanosome organization, and synaptic vesicle and receptor trafficking. This suggests a cohesive role in vesicle movement and membrane organization across neuronal and pigment-related organelles.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006890","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0035646","count":2},{"id":"GO:1900126","count":1},{"id":"GO:0048490","count":1}]},{"hash":"1387739066944454624","title":"Unknown","description":"The top GO terms span endosomal transport, neural development and signaling, immune differentiation, and cartilage formation, with additional disparate terms like pseudohyphal growth and ionomycin response. This broad and incongruent mix provides no single coherent functional theme to define the cluster, so an Unknown label with None confidence is appropriate.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":4},{"id":"GO:0007124","count":4},{"id":"GO:1901621","count":4},{"id":"GO:1904637","count":4},{"id":"GO:0001963","count":4}]},{"hash":"1501667193222689595","title":"Unknown","description":"The top GO terms span endosomal transport, fungal growth, neural development and signaling, calcium response, dopaminergic synaptic activity, p53-mediated signaling, NK T cell differentiation, CNS neuron axonogenesis, and cartilage condensation, with no clear shared function across the cluster. This lack of a cohesive theme makes it inappropriate to assign a precise, representative label.","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":5},{"id":"GO:0007124","count":5},{"id":"GO:1901621","count":5},{"id":"GO:1904637","count":5},{"id":"GO:0001963","count":5}]},{"hash":"1236393814155189365","title":"Actin Cytoskeleton Remodeling in Meiosis","description":"The top GO terms are dominated by actin-related processes (actin filament network formation, actin nucleation, actomyosin contractile ring assembly, regulation of cell shape), suggesting a core theme of actin cytoskeleton remodeling. Additionally, terms related to meiosis and female gamete generation (centrosome localization, chromosome movement toward spindle poles) point to a role for actin dynamics during meiotic progression in oocytes. Some terms (histamine response, synaptic depression) appear more peripheral, but do not overwhelm the central actin/meiosis signal. Overall, the cluster seems to reflect actin-driven cytoskeleton remodeling linked to meiosis/oocyte development.","confidence":"Medium","size":5,"edges":7,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051639","count":2},{"id":"GO:0045010","count":2},{"id":"GO:0055003","count":1},{"id":"GO:0060292","count":1},{"id":"GO:0007292","count":1}]},{"hash":"371903698085054899","title":"DNA replication and chromosome segregation","description":"The top GO terms are dominated by DNA replication and chromosome dynamics, including DNA-templated replication, strand elongation, DNA topological changes, chromosome separation, mitotic DNA integrity checkpoints, and meiosis-related segregation. A developmental term appears but the core cluster signal centers on replication and chromosome segregation processes, supporting this label.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051304","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0006261","count":1},{"id":"GO:0000019","count":1},{"id":"GO:0043007","count":1}]},{"hash":"642138534273971344","title":"Mitotic chromosome segregation and vesicle trafficking","description":"This cluster's strongest signals are mitosis-related: mitotic cell cycle and chromosome passenger complex localization to kinetochore. Additional terms point to intracellular trafficking and signaling (receptor recycling, endosome size regulation, cilium assembly), which align with cell division and membrane dynamics, supporting a theme around chromosome dynamics and vesicle trafficking.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0010224","count":4},{"id":"GO:0006547","count":4},{"id":"GO:0001881","count":4},{"id":"GO:0019236","count":4}]},{"hash":"1749077363093035916","title":"Unknown","description":"The top GO terms span distinct biological themes (DNA-templated transcription, DNA replication, and mitotic cell cycle) alongside diverse contexts such as GM-CSF signaling, ABA signaling, heart and Schwann cell development, and visual perception. This mixture suggests no single cohesive function or pathway tying the five proteins together, and the lack of edges further supports a non-specific or heterogeneous set. Therefore, Unknown with no clear representative theme.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097011","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0000086","count":2},{"id":"GO:0009738","count":2}]},{"hash":"709588564170896940","title":"Unknown","description":"The top GO terms include visual perception, neural development and signaling, endosome transport, cell cycle, and immune differentiation, suggesting a heterogeneous set of functions without a single cohesive theme. There isn't a clear common process that ties all five proteins together based on these terms, so a specific, representative label cannot be confidently assigned.","confidence":"","size":5,"edges":7,"triangles":4,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":5},{"id":"GO:0000278","count":5},{"id":"GO:2000641","count":4},{"id":"GO:0007124","count":4},{"id":"GO:1901621","count":4}]},{"hash":"1892081905287568143","title":"Cellular stress response and DNA damage repair","description":"The term set centers on cellular responses to diverse stresses (psychosocial stress, nitroglycerin, gamma radiation, singlet oxygen, arsenite, hypoxia) and on regulation of DNA damage repair (e.g., NHEJ). A chromatin-related note (H3-K9 demethylation) supports stress-induced chromatin remodeling. Overall, the cluster reflects cellular stress signaling intertwined with DNA repair.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033169","count":2},{"id":"GO:1990911","count":2},{"id":"GO:1904843","count":2},{"id":"GO:0071480","count":2},{"id":"GO:0000304","count":2}]},{"hash":"1231662844438851802","title":"Apoptosis and TNF/NF-\u03baB signaling","description":"The top GO terms cluster around immune and stress-response signaling, including p53-mediated apoptosis, TNF signaling, NF-kappaB regulation, and LPS response. These indicate a core theme of inflammatory signaling and programmed cell death, with one plant-specific term likely representing cross-kingdom noise. Overall, the proteins appear to be involved in apoptosis and inflammatory signaling pathways.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042771","count":1},{"id":"GO:0071222","count":1},{"id":"GO:0033209","count":1},{"id":"GO:0034051","count":1},{"id":"GO:0042347","count":1}]},{"hash":"873624304386536790","title":"Unknown","description":"The GO terms across this cluster do not point to a single shared function: they span vascular wound healing, adiponectin signaling, zinc ion homeostasis, regulation of non-canonical NF-kappaB signaling, cytolysis, and tail spike morphogenesis. This mix of tissue repair, metabolism/signaling, metal handling, immune signaling, and viral structure suggests no cohesive biological theme linking all members, so a clear representative label cannot be assigned. ","confidence":"","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0061042","count":2},{"id":"GO:0033211","count":2},{"id":"GO:0006882","count":2},{"id":"GO:1901223","count":2},{"id":"GO:0019835","count":2}]},{"hash":"81868791728122999","title":"Developmental vesicle trafficking and mitosis","description":"The terms point to ER-Golgi COPII vesicle budding and related transport, plus mitotic processes like spindle assembly and the mitotic cell cycle, all within a developmental/growth context (brain development, multicellular growth). This suggests a theme of secretory/trafficking functions tied to cell division during development.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0008283","count":2}]},{"hash":"1438454663121876265","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":3},{"id":"GO:0071374","count":2},{"id":"GO:0090084","count":2},{"id":"GO:1901621","count":2},{"id":"GO:0006458","count":2}]},{"hash":"2040810076774815359","title":"Unknown","description":"The terms span fungi-specific growth regulation, tRNA modification, redox homeostasis, development in animals, metabolism, and cell cycle processes, with no clear, shared function uniting the proteins. The absence of interactions (edges 0) and the heterogeneous GO terms make a cohesive, confident label inappropriate.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000220","count":2},{"id":"GO:0032447","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0002143","count":2},{"id":"GO:0045454","count":2}]},{"hash":"117719809642522710","title":"RNA processing and RNAi machinery","description":"The top GO terms cluster around RNA maturation and regulation of gene expression, including tRNA splicing (GO:0006388), RNA Pol I transcription termination (GO:0006363), rRNA processing at ITS2 (GO:0000448), mRNA cleavage and gene silencing (GO:0030423), and RISC complex assembly (GO:0035087). These point to components involved in RNA processing and RNA interference pathways. An outlier term for cerebellar cortex development and a few obsolete terms likely reflect annotation noise, but the core signal is cohesive around RNA processing and silencing. Overall, the proteins are best viewed as RNA-processing/RNAi-related factors rather than a single distinct non-RNA function cluster.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000448","count":1},{"id":"GO:0016310","count":1},{"id":"GO:0090202","count":1},{"id":"GO:0006388","count":1},{"id":"GO:0098789","count":1}]},{"hash":"1648598497977306928","title":"Unknown","description":"These proteins are linked to a highly diverse set of GO terms spanning DNA replication, endosome transport, yeast pseudohyphal growth, hedgehog/p53 signaling regulation, ionomycin response, dopaminergic synaptic transmission, neural development, and immune differentiation. The lack of a single, cohesive biological function or pathway, and no observed network connections, indicates no clear common theme. ","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:2000641","count":4},{"id":"GO:0007124","count":4},{"id":"GO:1901621","count":4},{"id":"GO:1904637","count":4}]},{"hash":"80463336895150561","title":"Neuronal signaling and synaptic plasticity","description":"The terms are dominated by neuronal functions: excitatory postsynaptic potential, cellular response to dopamine, positive regulation of axon extension, calcium-dependent exocytosis, and ERK signaling\u2014together pointing to synaptic transmission and plasticity. A few outliers (bone resorption, beta selection) may reflect shared signaling pathways rather than a neuron-specific cluster. Overall, the cluster appears to capture neuronal signaling and synaptic regulation rather than unrelated processes.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045453","count":4},{"id":"GO:0070374","count":3},{"id":"GO:0045956","count":3},{"id":"GO:0051893","count":3},{"id":"GO:0060079","count":3}]},{"hash":"28493170128348050","title":"Cell Morphogenesis and Signaling","description":"Based on the prominence of cell morphogenesis (GO:0000902) and the presence of terms related to development, signaling pathways (MAPK-related term), and intracellular trafficking (endosome transport), the cluster seems to be centered on shaping cell form and coordinating signaling rather than a single specific pathway. The mix of morphogenesis, development, and trafficking terms suggests a broad morphogenetic/signaling theme rather than a narrow function. ","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000902","count":2},{"id":"GO:0071374","count":1},{"id":"GO:0007124","count":1},{"id":"GO:2000641","count":1},{"id":"GO:0000187","count":1}]},{"hash":"260434911553816493","title":"TLR-driven innate immune signaling","description":"The top GO terms cluster around Toll-like receptor signaling (TLR1), Toll signaling, inflammatory response, and cytokine regulation (dendritic cell cytokine production and IL-8), indicating a cohesive theme of innate immune sensing and inflammatory signaling with possible links to adaptive responses. A few terms appear unrelated (e.g., manganese ion response or plant-specific growth regulation) but do not override the dominant TLR- and inflammation-focused theme.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071287","count":2},{"id":"GO:0002730","count":2},{"id":"GO:1903215","count":2},{"id":"GO:0034130","count":2},{"id":"GO:0008063","count":2}]},{"hash":"398744295268087766","title":"Neuronal development and signaling","description":"The terms converge on neural development and signaling: axonogenesis in the CNS, dopaminergic synaptic transmission, and regulation of dorsal/ventral neural tube patterning. Endosome transport regulation fits with neuronal vesicle trafficking, while ionomycin response and p53-mediated signaling reflect broader cellular signaling relevant to neurons. A couple of items appear less related (fungal pseudohyphal growth, cartilage condensation) and may be peripheral annotations.","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":5},{"id":"GO:0007124","count":5},{"id":"GO:1901621","count":5},{"id":"GO:1904637","count":5},{"id":"GO:0001963","count":5}]},{"hash":"562718043086168699","title":"Thermoregulation and Vasomotor Signaling","description":"The cluster is dominated by GO terms related to temperature sensing and thermogenic responses (thermosensory behavior, diet-induced thermogenesis, response to capsazepine) and vascular control (vasoconstriction). These point to a shared function in temperature regulation and regulation of blood flow, with additional, more minor associations to inflammatory signaling and neural development that may reflect broader stress and neural context. Confidence: Medium","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071642","count":5},{"id":"GO:1901594","count":5},{"id":"GO:0098719","count":5},{"id":"GO:0040040","count":5},{"id":"GO:0071651","count":5}]},{"hash":"234970379543245421","title":"Chromatin remodeling, nucleosome dynamics, and snoRNP assembly","description":"This cluster centers on chromatin organization and nucleosome dynamics, with GO terms for chromatin remodeling and nucleosome assembly/disassembly. It also includes box C/D snoRNP assembly and snoRNA localization, suggesting linked nuclear RNA processing alongside chromatin-related functions.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006338","count":1},{"id":"GO:0000492","count":1},{"id":"GO:0031063","count":1},{"id":"GO:0048254","count":1},{"id":"GO:0015031","count":1}]},{"hash":"792687601753706178","title":"Mitochondrial respiratory chain assembly","description":"Based on GO terms highlighting the assembly of mitochondrial respiratory chain complexes II and IV and regulation of cytochrome-c oxidase activity, the cluster is best described as related to mitochondrial energy production through electron transport chain assembly. The presence of translation-related terms is incidental and does not define the main theme.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0034553","count":1},{"id":"GO:1904960","count":1},{"id":"GO:0033132","count":1},{"id":"GO:0008535","count":1},{"id":"GO:0006412","count":1}]},{"hash":"1985132941952072340","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning immune cell activity, migration, signaling, and neuronal differentiation, with only a single connection among five proteins. There isn\u2019t a clear, single cohesive function tying the cluster together, so a safe label is Unknown with no confidence.","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1903215","count":3},{"id":"GO:0001667","count":3},{"id":"GO:0043316","count":3},{"id":"GO:1900026","count":3},{"id":"GO:0090382","count":3}]},{"hash":"510337423293329897","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0071374","count":1},{"id":"GO:0090084","count":1},{"id":"GO:1901621","count":1},{"id":"GO:0006458","count":1}]},{"hash":"1173918217543082212","title":"Organogenesis and Stem Cell Regulation","description":"The top GO terms point to developmental and organ formation processes across multiple tissues (endodermal fate, bile duct and gallbladder development, cornea and retinal differentiation) along with notes on somatic stem cell maintenance and regulation of stem cell proliferation. In contrast, inflammatory terms are present but less central, suggesting the core theme is developmental differentiation and organogenesis with an emphasis on stem cell control. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007493","count":1},{"id":"GO:0060221","count":1},{"id":"GO:0002437","count":1},{"id":"GO:0035019","count":1},{"id":"GO:0071866","count":1}]},{"hash":"1698206287444440722","title":"Ubiquitin-Dependent Protein Regulation","description":"The top terms cluster around ubiquitination processes (protein autoubiquitination, K63-linked ubiquitination, ubiquitin-dependent ERAD pathway), pointing to a shared theme of ubiquitin-mediated regulation and protein turnover. Additional terms touch on immune regulation, cell division, and DNA repair, suggesting broader but related roles for ubiquitin signaling across these proteins. ","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043029","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0070534","count":2},{"id":"GO:0010446","count":1}]},{"hash":"1608987087865327142","title":"Glutathione-driven redox homeostasis and detoxification","description":"These proteins show strong enrichment for redox balance and detoxification, driven by glutathione metabolism, glutathionylation, and oxidant detoxification. The inclusion of starvation response and toxin catabolism terms supports a stress-adaptation/metabolic angle associated with antioxidant defenses. Overall, the cluster appears to coordinately manage redox state and detoxification via glutathione-related pathways.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":5},{"id":"GO:0098869","count":4},{"id":"GO:0042594","count":3},{"id":"GO:0010731","count":3},{"id":"GO:0019852","count":3}]},{"hash":"1288340665882881941","title":"Ribosome Biogenesis and Translation","description":"The top GO terms are dominated by ribosome-related processes: maturation of SSU-rRNA, translation, ribosome biogenesis, and small subunit assembly. These recurring terms strongly tie the cluster to ribosome production and protein synthesis. The additional terms appear incidental and do not shift the main theme.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0000028","count":2},{"id":"GO:0071374","count":1}]},{"hash":"1560051934982317615","title":"Oxidative stress and aging response","description":"Based on GO terms dominated by removal of superoxide radicals, ROS-related aging terms, and redox-related processes, this cluster appears enriched for oxidative stress signaling and redox homeostasis. A few terms like Rho signaling and vasodilation are peripheral and may be incidental.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001302","count":1},{"id":"GO:0019430","count":1},{"id":"GO:0010447","count":1},{"id":"GO:0001320","count":1},{"id":"GO:0003069","count":1}]},{"hash":"2254571766624852201","title":"Unknown","description":"The top terms span highly diverse processes (amoeboid migration, phagosome maturation, copper homeostasis, T cell degranulation, Wnt signaling, oligodendrocyte differentiation, mitotic cleavage, kinetochore-microtubule regulation) with no single cohesive function tying all proteins together, so a reliable, concise label isn\u2019t evident.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903215","count":1},{"id":"GO:0001667","count":1},{"id":"GO:0006878","count":1},{"id":"GO:0043316","count":1},{"id":"GO:1900026","count":1}]},{"hash":"467532049502494054","title":"Mitochondrial respiration components","description":"This cluster is dominated by GO terms for aerobic respiration and mitochondrial electron transport (ubiquinol to cytochrome c) and proton transmembrane transport, indicating a core association with mitochondrial respiratory chain function. Some RNA-processing terms appear among annotations, which may reflect annotation noise or multi-functional proteins in a small cluster; however, the strongest signal points to mitochondrial respiration. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009060","count":1},{"id":"GO:0006122","count":1},{"id":"GO:1902600","count":1},{"id":"GO:0031086","count":1},{"id":"GO:0090503","count":1}]},{"hash":"849019979323934606","title":"Ion Transport and Neuromuscular Signaling","description":"This cluster is dominated by GO terms tied to membrane transport and neuromuscular activity, including membrane repolarization, monoatomic cation transmembrane transport, regulation of sodium ion transport, involuntary skeletal muscle contraction, neuromuscular processes controlling posture, and vestibulocochlear nerve formation, suggesting a coherent theme around ion movement and muscle/nerve signaling. A few terms (lipopolysaccharide biosynthetic process, stilbene catabolic process, positive regulation of B cell differentiation) appear unrelated and may reflect annotation noise or distant functional associations.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0086009","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0002028","count":2},{"id":"GO:0050884","count":2},{"id":"GO:0046272","count":2}]},{"hash":"1739499237186609731","title":"Golgi\u2013Endosome Trafficking","description":"The proteins appear enriched for intracellular transport functions centered on the Golgi and endosomal compartments: transport into the Golgi, endocytic recycling, retrograde transport from endosomes to Golgi, and protein retention in the Golgi. Proteasome assembly and endopeptidase regulation may reflect processing aspects within the secretory pathway. While glutathione and spermidine metabolism and tRNA processing regulation are present, they seem less tightly connected to the main trafficking theme. Therefore, the label captures the cluster's core function.","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006886","count":2},{"id":"GO:0006749","count":1},{"id":"GO:0008216","count":1},{"id":"GO:0043248","count":1},{"id":"GO:0010950","count":1}]},{"hash":"1081170141932896541","title":"Mitotic chromatin assembly and cell cycle control","description":"The strongest signals are CENP-A containing chromatin assembly and mitotic cell cycle, plus regulation of cell cycle checkpoints and ubiquitin ligase activity, pointing to roles in chromosome segregation and cell-cycle control. Less dominant terms like mRNA processing or inflammatory processes may reflect multifunctionality or annotation noise but do not override the core mitotic/chromatin theme. Therefore this label captures the cluster\u2019s primary function.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0000278","count":2},{"id":"GO:2000728","count":1},{"id":"GO:1904668","count":1},{"id":"GO:0000398","count":1}]},{"hash":"925152916483068327","title":"Unknown","description":"The top GO terms include insulin receptor signaling, angiogenesis, endosome transport regulation, pseudohyphal growth, neural patterning differentiation, ionomycin response, dopaminergic synaptic transmission, p53-mediated signaling, and NK T cell differentiation. They span very different biological contexts with no clear common function, so there is no cohesive theme to label the cluster. Unknown is the most appropriate name with no confidence.","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0060358","count":2},{"id":"GO:2000641","count":1},{"id":"GO:0007124","count":1}]},{"hash":"2297658890159858101","title":"Membrane Ion Transport and Calcium Release","description":"Most of the top GO terms point to ion transport across membranes (sodium, potassium, monoatomic cations) and the release of calcium ions into the cytosol, suggesting a theme of membrane ion homeostasis and calcium signaling. The presence of a few unrelated terms (lipopolysaccharide biosynthesis, stilbene catabolic process, vestibulocochlear nerve formation, epoxygenase P450 pathway) likely reflects annotation noise or broad membership in small clusters. Confidence: Medium","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0086009","count":4},{"id":"GO:0009103","count":4},{"id":"GO:0002028","count":4},{"id":"GO:0046272","count":4},{"id":"GO:0021650","count":4}]},{"hash":"2285581761778517738","title":"Transmembrane ion and metabolite transport","description":"Top GO terms indicate a broad set of transmembrane transport activities, including bicarbonate, chloride, sulfate, oxalate, and fructose transport, along with intracellular pH regulation and membrane potential modulation. Additional terms related to gastric acid secretion and sperm capacitation point to tissue-specific transporter roles, but collectively the cluster centers on membrane transport of ions and small metabolites. This supports a general label of transmembrane transporters rather than a single specific pathway, hence the High-level name chosen. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001696","count":1},{"id":"GO:0015701","count":1},{"id":"GO:1902358","count":1},{"id":"GO:0051454","count":1},{"id":"GO:1902476","count":1}]},{"hash":"2267748262587473395","title":"Ubiquitin-Mediated Immune Signaling","description":"The cluster centers on ubiquitination processes (positive regulation of ubiquitin-protein transferase activity, autoubiquitination, free ubiquitin chain polymerization, K29-linked ubiquitination) and includes key immune signaling pathways (TRIF-dependent Toll-like receptor signaling and T cell receptor signaling). This suggests proteins act to regulate immune signaling via ubiquitin-based modification systems. Some GO terms also touch DNA repair and protein trafficking, but the strongest shared theme is ubiquitin-mediated modulation of immune signaling.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035666","count":5},{"id":"GO:0070911","count":5},{"id":"GO:0051443","count":5},{"id":"GO:0051865","count":5},{"id":"GO:0050852","count":5}]},{"hash":"2269193026383777355","title":"Unknown","description":"These proteins are annotated with diverse GO terms spanning RNA processing (mRNA splicing, mRNA export), chromatin assembly, ubiquitination and protein turnover, cell cycle regulation, inflammatory signaling, glial apoptosis, and neural development. The terms do not converge on a single, coherent biological function or pathway, so there isn't a clear, representative label for the cluster.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000728","count":1},{"id":"GO:1904668","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0061641","count":1},{"id":"GO:0002534","count":1}]},{"hash":"267232785091740591","title":"Plant carbohydrate metabolism and sugar signaling","description":"This cluster centers on carbohydrate metabolism, especially starch and glycogen-related biosynthesis (amylopectin, starch) and related processes, with links to fatty acid biosynthesis and general signaling. The presence of circadian rhythm and responses to sucrose and nitrogen suggests regulation of this metabolic module by temporal and nutrient cues in plants. The terms collectively point to a metabolism-and-signaling theme, though no single, precise enzyme function dominates, so the label is a plausible, moderate-confidence match.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0005978","count":1},{"id":"GO:0007165","count":1},{"id":"GO:0019252","count":1},{"id":"GO:0005980","count":1},{"id":"GO:0010021","count":1}]},{"hash":"1134623024833553932","title":"Unknown","description":"There are no GO terms provided to guide a shared function, and with limited connections and no clear common annotation, a cohesive theme cannot be inferred. Therefore Unknown with None confidence.","confidence":"","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[]},{"hash":"62439077156860487","title":"RNA processing and ubiquitin-mediated degradation","description":"This cluster shows strong signals for mRNA processing and ubiquitin-dependent protein catabolic processes, including positive regulation of cytoplasmic mRNA processing body assembly, suggesting a link between RNA metabolism and proteostasis via ubiquitin signaling; obsolete chromatin terms are likely noise.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070537","count":1},{"id":"GO:0006397","count":1},{"id":"GO:0008583","count":1},{"id":"GO:1900425","count":1},{"id":"GO:0035871","count":1}]},{"hash":"2074487057003666553","title":"ER\u2013Golgi trafficking and secretion","description":"This cluster is dominated by GO terms for ER to Golgi transport, COPI-coated vesicles, and protein retention in the ER lumen, all central to the early secretory pathway. Wnt secretion and egg-laying regulation further point to secretory cargo processing and release, suggesting a cohesive theme around ER-Golgi trafficking and regulated secretion, with some developmental processes reflecting secreted signaling factors.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048042","count":2},{"id":"GO:0061357","count":2},{"id":"GO:0002121","count":2},{"id":"GO:0007311","count":2},{"id":"GO:0070863","count":2}]},{"hash":"1902597152209995241","title":"Central carbon metabolism and terpenoid biosynthesis","description":"GO terms cluster around core carbon flux\u2014glucose metabolism, glycolysis (GAP), PPP, and TCA\u2014together with terpenoid biosynthesis (terpenoid biosynthetic process), consistent with inputs to the DOXP/MEP pathway. The stress-response terms (cellular response to paraquat and chloramphenicol) likely reflect regulatory signals but do not override the central metabolic theme.","confidence":"High","size":5,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006006","count":2},{"id":"GO:0006099","count":2},{"id":"GO:0046166","count":2},{"id":"GO:0072756","count":2},{"id":"GO:0006098","count":2}]},{"hash":"546319508532689569","title":"Redox and Nitrosative Stress Response","description":"Most terms point to redox biology and inflammatory signaling (oxidation-reduction, nitrosative stress, LPS response, prostaglandin metabolism, and protein S-nitrosylation). A few outliers (fermentation, blood pressure regulation) are less central but still fit metabolic/inflammatory context, so the core theme is redox and nitrosative stress responses.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0032496","count":4},{"id":"GO:0006693","count":3},{"id":"GO:0046688","count":3},{"id":"GO:0006116","count":3}]},{"hash":"159079549837523042","title":"Glycolysis, TCA, and glyoxylate metabolism under stress","description":"This cluster centers on core carbon metabolism\u2014glycolysis, TCA cycle, glyoxylate cycle, and related pyruvate fermentation\u2014plus stress-responsive terms such as hypoxia and xenobiotic response, suggesting a metabolism-shift state under environmental stress.","confidence":"High","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":4},{"id":"GO:0006096","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0006097","count":3},{"id":"GO:0042493","count":3}]},{"hash":"1104435461387046017","title":"Neural stress response and development","description":"This cluster includes GO terms tied to RNA processing (mRNA export in response to heat, splicing), protein homeostasis (ubiquitin ligase activity, polyubiquitination), cell cycle control (checkpoint regulation, CENP-A chromatin assembly), inflammatory signaling (cytokine production), glial apoptosis, GPCR-mediated signaling, and brain development. The common thread appears to be neural-context stress responses coupled with developmental and regulatory processes affecting gene expression and protein turnover in neural cells. Confidence: Medium.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000728","count":2},{"id":"GO:1904668","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0061641","count":2},{"id":"GO:0002534","count":2}]},{"hash":"1028663775464891544","title":"ER-Golgi trafficking and mitosis","description":"Based on the GO terms, the cluster is enriched for COPII-coated vesicle budding and ER-Golgi transport (anterograde and retrograde), as well as mitotic spindle assembly and mitotic cell cycle, indicating involvement in secretory pathway dynamics linked to cell division. While ribosome biogenesis is also present, the strongest shared theme is ER-Golgi trafficking combined with mitotic processes, justifying this label.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090114","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0000278","count":2}]},{"hash":"952737148585640891","title":"Developmental morphogenesis and tissue remodeling","description":"The top GO terms cluster around basement membrane disassembly, epithelial tube branching in lung morphogenesis, and intramembranous ossification, all central to tissue remodeling during development. Additional terms point to regulatory and catabolic processes that support remodeling, and decidualization and thyroid hormone response may reflect broader developmental signaling contexts. While some terms (e.g., T cell cytotoxicity) are less directly related, the overall pattern supports proteins involved in developmental morphogenesis and extracellular matrix remodeling rather than a single narrow function.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034769","count":3},{"id":"GO:0051603","count":3},{"id":"GO:0050790","count":3},{"id":"GO:0097067","count":3},{"id":"GO:0060441","count":3}]},{"hash":"939995958630675091","title":"Germline Stem Cell and Meiosis Regulation","description":"This cluster centers on germline maintenance and meiotic processes (female germ-line stem cell population maintenance; meiosis I) and includes chromatin regulation and transcription/translation control (heterochromatin formation, regulation of transcription by RNA polymerase II, translation initiation complex assembly). The combination suggests a theme around germline cell fate, meiotic regulation, and chromatin-mediated gene expression, with some protein turnover aspects. The lack of interactions (edges) means the label is a best-fit high-level characterization rather than a tightly connected module.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007127","count":1},{"id":"GO:0048863","count":1},{"id":"GO:0006511","count":1},{"id":"GO:0075525","count":1},{"id":"GO:0090054","count":1}]},{"hash":"1998069653122215454","title":"Iron-Sulfur Cluster Assembly for Nitrogen Fixation","description":"The cluster shows strong signals for iron-sulfur (Fe-S) cluster biogenesis and nitrogen fixation (GO:0016226, GO:0009399), with additional protein maturation and translation terms suggesting a broader cellular context. The prominence of Fe-S cluster assembly and nitrogen fixation points to a functional group of proteins involved in assembling Fe-S clusters essential for nitrogenase and related maturation processes; the iron-handling term aligns with this theme. A concise label focusing on Fe-S cluster biogenesis in nitrogen fixation best captures the shared function among these proteins.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006880","count":1},{"id":"GO:0009399","count":1},{"id":"GO:0016226","count":1},{"id":"GO:0051604","count":1}]},{"hash":"2056120206519656525","title":"Embryonic patterning and proliferation control","description":"The GO terms cluster around embryonic development (anterior/posterior axis specification, limb development) and regulation of cell proliferation (negative regulation of fibroblast and neuroblast proliferation). While there are general terms about transcription and nuclear localization, the dominant signals point to developmental patterning and growth control, with a few meiosis-related terms likely incidental. Thus, the cluster best fits embryonic patterning and growth regulation, with Medium confidence due to some noise.","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042517","count":1},{"id":"GO:0051457","count":1},{"id":"GO:0006311","count":1},{"id":"GO:0048147","count":1},{"id":"GO:0008595","count":1}]},{"hash":"188579321161853305","title":"Xenobiotic chemical response","description":"The top GO terms point to responses to various exogenous chemicals (curcumin, catechin, mercury ion), suggesting a shared function in chemical stress response; cell adhesion is a more generic term and may be incidental in this small cluster. Thus, a concise label is Xenobiotic chemical response.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904643","count":1},{"id":"GO:0007155","count":1},{"id":"GO:0046689","count":1},{"id":"GO:1902168","count":1}]},{"hash":"2094247169667379532","title":"RNA transcription and preribosome assembly","description":"The terms center on RNA transcription processes (RNA-templated transcription; Pol II/III promoter initiation; transcription termination) and 90S preribosome assembly, suggesting a cohesive group involved in RNA biogenesis and ribosome-related transcription/processing activities.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001172","count":1},{"id":"GO:0090503","count":1},{"id":"GO:0034463","count":1},{"id":"GO:0000291","count":1},{"id":"GO:0010323","count":1}]},{"hash":"714774920430254686","title":"Lipid Biosynthesis and Lipid Metabolism","description":"The top terms cluster around lipid-related processes (unsaturated fatty acid biosynthesis, ergosterol and sphingolipid metabolism) and lipid-rich functions (myelin maintenance, sebaceous gland differentiation), suggesting a lipid metabolism theme. Some terms (mitochondrion inheritance, nitrate assimilation) are outliers, so the overall label has moderate confidence.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000001","count":5},{"id":"GO:0042128","count":5},{"id":"GO:0006809","count":5},{"id":"GO:0001949","count":5},{"id":"GO:0032286","count":5}]},{"hash":"309684204431202011","title":"Golgi-to-plasma membrane transport","description":"This cluster is characterized by the GO term Golgi to plasma membrane transport, pointing to proteins involved in vesicular trafficking along the secretory pathway from the Golgi to the cell surface. With five proteins and a single representative transport term, the common theme appears to be secretory vesicle trafficking to the plasma membrane.","confidence":"Medium","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006893","count":1}]},{"hash":"1462166900319214742","title":"Unknown","description":"The GO terms cover xenobiotic transport, diverse developmental processes across tissues, signaling via JAK-STAT, cell cycle regulation, and stress responses, with no single cohesive function tying all proteins together. Therefore there is no clear cluster theme.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":1},{"id":"GO:0034606","count":1},{"id":"GO:0021510","count":1},{"id":"GO:0043588","count":1},{"id":"GO:0034608","count":1}]},{"hash":"1269381288564390721","title":"Mitochondrial import and membrane permeability regulation","description":"Several GO terms point to mitochondria, notably regulation of mitochondrial membrane permeability and protein import into the mitochondrial matrix, suggesting a shared mitochondrial function among the proteins. While other terms touch on plant development and cell cycle, the strongest single theme is mitochondrial biology, leading to a mitochondria-centric cluster label with moderate confidence due to some annotations being less clearly related. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":1},{"id":"GO:2000134","count":1},{"id":"GO:0070940","count":1},{"id":"GO:1903740","count":1},{"id":"GO:0010867","count":1}]},{"hash":"2149874798702468278","title":"Unknown","description":"The top terms cover a broad set of functions from RNA processing and transcription regulation to chromatin modification, trafficking, signaling, and neuronal communication, with no single cohesive theme. Given there are no edges or connections among the proteins, there isn\u2019t a clear shared function tying these terms together, so Unknown with no confidence is appropriate.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0034968","count":2},{"id":"GO:0001881","count":2},{"id":"GO:0006355","count":2}]},{"hash":"991036610911684969","title":"Glycogen and alpha-glucan catabolism","description":"Two of the top GO terms clearly indicate breakdown of glycogen and alpha-glucan, pointing to a carbohydrate catabolic theme for this cluster. The remaining terms (PRPP biosynthesis and necroptotic process) do not align well with this theme, suggesting the connection is weak and may reflect annotation noise.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030980","count":1},{"id":"GO:0005980","count":1},{"id":"GO:0006015","count":1},{"id":"GO:0070266","count":1}]},{"hash":"436758703220215272","title":"RNA Polymerase II Transcription Initiation","description":"This cluster centers on the initiation of transcription by RNA Polymerase II, with terms referring to preinitiation complex assembly, promoter binding, transcription initiation at Pol II promoters, start-site selection, and DNA-templated transcription. While a couple of terms touch on related contexts (e.g., Pol III promoter initiation, viral transcription), the dominant theme is the assembly and regulation of transcription initiation machinery at promoters, suggesting these proteins act as initiation factors or regulators of Pol II transcription. Confidence in this labeling is High.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904798","count":1},{"id":"GO:0050434","count":1},{"id":"GO:0051123","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0070893","count":1}]},{"hash":"1423869337287233973","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by GO terms linked to ribosome assembly and biogenesis (ribosomal subunit biogenesis, ribosome biogenesis, ribosomal large/small subunit export from the nucleus), along with cytoplasmic translation and tRNA modification, indicating a core role in making and utilizing ribosomes. Additional terms related to cell cycle and division suggest a link to cell growth, while a single outlier term about salt-stress regulation is less central. Overall, the group likely represents proteins involved in ribosome production and protein synthesis machinery, with a possible connection to cell growth phases.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002181","count":2},{"id":"GO:1901001","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0042274","count":2},{"id":"GO:0006400","count":2}]},{"hash":"1063863591089027754","title":"ER-assisted secretory protein maturation","description":"Based on the top GO terms, the proteins are associated with the secretory pathway: protein folding in the endoplasmic reticulum, vesicle-mediated transport, and eventual protein secretion. This cluster appears to capture components of ER quality control and trafficking toward secretion, with magnesium transport being a less central, ancillary hint. Therefore, a label focusing on ER-assisted secretory maturation best reflects the common function.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009306","count":1},{"id":"GO:0016192","count":1},{"id":"GO:0034975","count":1},{"id":"GO:0015693","count":1}]},{"hash":"1072860336872251236","title":"Actin-driven membrane remodeling and signaling","description":"Top terms indicate actin-based structures (microspikes, filopodia) and endomembrane organization (Golgi, vesicle trafficking) together with TGF-\u03b2 signaling; this points to a function in actin-driven membrane remodeling with signaling and trafficking roles.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007183","count":1},{"id":"GO:0010256","count":1},{"id":"GO:1904562","count":1},{"id":"GO:0030035","count":1},{"id":"GO:0007179","count":1}]},{"hash":"1133527217023780763","title":"Unknown","description":"The associated GO terms span RNA processing (splicing and mRNA export), ubiquitination, chromatin assembly, inflammatory signaling, GPCR pathways, glial apoptosis, and brain development, with no single dominant function across the cluster.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000728","count":1},{"id":"GO:1904668","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0061641","count":1},{"id":"GO:0002534","count":1}]},{"hash":"1668650586232586322","title":"Post-transcriptional regulation and RNA silencing","description":"The proteins appear linked to mRNA processing steps (splicing, polyadenylation, stability, modification) and to translational control and ncRNA/miRNA-mediated gene silencing, suggesting a cluster focused on post-transcriptional regulation and RNA silencing rather than transcription initiation.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":2},{"id":"GO:0048025","count":2},{"id":"GO:0035278","count":2},{"id":"GO:0010610","count":2},{"id":"GO:0016556","count":2}]},{"hash":"23903277059096446","title":"Unknown","description":"The GO terms are highly diverse, including developmental processes in different tissues (cardiac, cuticle, kidney) and signaling-related activities (nuclear import, calcium release regulation, kinase activity modulation, and reactive oxygen species generation). With only five proteins and no observed edges, there isn\u2019t a coherent, single function tying the cluster together, so a precise, representative label cannot be inferred.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055003","count":1},{"id":"GO:0097274","count":1},{"id":"GO:0008365","count":1},{"id":"GO:1905205","count":1},{"id":"GO:0072286","count":1}]},{"hash":"22344463596470151","title":"NOD2-Driven Immune Signaling and Chemokine Production","description":"The top GO terms center on NOD2 signaling and regulation of inflammatory chemokines (MIP-1\u03b1 and CCL5), suggesting a cluster focused on innate immune sensing and chemokine-mediated responses. Other terms appear more scattered (epithelial polarity, spindle assembly, etc.) and may reflect multifunctional annotations, but the immune signaling and chemokine production theme is the strongest signal.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070431","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0071642","count":1},{"id":"GO:1901594","count":1},{"id":"GO:0086070","count":1}]},{"hash":"485819587541113791","title":"Multi-substrate membrane transporters","description":"The top GO terms are dominated by transmembrane transport across membranes for a variety of substrates (nitrate/nitrite, sodium, potassium, xenobiotics, arabinose, vitamins, etc.), indicating a shared function as membrane transporter proteins with broad substrate specificity. The telomerase holoenzyme assembly term appears as an outlier, but the overall signal points to solute transport activity rather than a nuclear telomere-maintenance process. This makes the label \u201cMulti-substrate membrane transporters\u201d a concise and representative name for the cluster.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1905323","count":2},{"id":"GO:0042128","count":1},{"id":"GO:0035725","count":1},{"id":"GO:0006855","count":1},{"id":"GO:0042891","count":1}]},{"hash":"1817406976480382839","title":"Mitotic regulation and signaling modulation","description":"The strongest theme is mitosis-related: mitotic cytokinesis checkpoint signaling, mitotic actomyosin contractile ring maturation, protein localization to kinetochore, and negative regulation of CDK activity, indicating cell-cycle control. The remaining terms (Notch signaling, circadian rhythm, habituation, and immune-related regulation) appear peripheral, suggesting broader or incidental connections. Overall, the cluster most plausibly centers on mitotic regulation with some signaling modulation.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0039563","count":4},{"id":"GO:0044878","count":4},{"id":"GO:1902406","count":4},{"id":"GO:0046959","count":4},{"id":"GO:0044387","count":4}]},{"hash":"701985997680974825","title":"ECM Remodeling and Angiogenesis","description":"The terms cluster around extracellular matrix organization, angiogenesis in wound healing, and endothelial cell migration, with supportive hints from adipogenesis and redox regulation, implying tissue remodeling with new vasculature. While a few terms (cytochrome complex assembly, oxidation) are broader, the central theme of ECM dynamics plus vascularization fits best.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045444","count":1},{"id":"GO:0030198","count":1},{"id":"GO:0018158","count":1},{"id":"GO:1902176","count":1},{"id":"GO:0060055","count":1}]},{"hash":"1347912879207417425","title":"Mitotic Kinetochore Localization and CDK Regulation","description":"Explanation: The top GO terms are strongly tied to mitosis and kinetochore processes (protein localization to kinetochore; regulation of CDK activity; mitotic cytokinesis checkpoint signaling; actomyosin ring maturation), indicating a cluster focused on mitotic progression and kinetochore function. Other terms appear incidental or broad, but the dominant theme is cell cycle control during mitosis.","confidence":"High","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0034501","count":4},{"id":"GO:0045736","count":4},{"id":"GO:0035729","count":3},{"id":"GO:0039563","count":2},{"id":"GO:0044878","count":2}]},{"hash":"1478622197269926804","title":"Neuronal development and synaptic vesicle transport","description":"The terms show a clear emphasis on brain development, synaptic vesicle exocytosis regulation, and dendritic transport of neurotransmitter receptor complexes, pointing to neuronal maturation and synaptic trafficking as the core function of this cluster. While a few terms relate to broader cytoskeletal processes, the strongest theme is neuronal development linked to synaptic transport.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0010796","count":2},{"id":"GO:0031384","count":2},{"id":"GO:2000300","count":2}]},{"hash":"1006121994669382401","title":"Actin Cytoskeleton Remodeling and Cell Migration","description":"This cluster is dominated by actin-myosin\u2013driven processes: mesenchyme migration, actomyosin contractile ring activity, cortical actin assembly, and skeletal muscle fiber adaptation, plus mitotic cytokinesis. While a few terms are peripheral or obsolete (e.g., histone-related terms), the core signal is actin cytoskeleton remodeling enabling movement and division.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090131","count":3},{"id":"GO:0043503","count":3},{"id":"GO:0016344","count":3},{"id":"GO:1904623","count":3},{"id":"GO:0009825","count":3}]},{"hash":"1664611267019355373","title":"DNA Repair and Nuclear Transport","description":"Proteins in this cluster show strong signals for DNA maintenance and nuclear organization, including global genome nucleotide-excision repair, protein localization to the nuclear pore, PML body organization, and histone H3-K4 methylation regulation. While there are hints of cytoskeletal and stress-related roles (cytoplasmic microtubule organization, heat acclimation), the dominant theme ties to nuclear repair and chromatin regulation, justifying this label.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0070911","count":4},{"id":"GO:0031122","count":4},{"id":"GO:0033132","count":4},{"id":"GO:0090204","count":4},{"id":"GO:0014070","count":4}]},{"hash":"1567938768164055281","title":"Fungal protein targeting and stress response","description":"The top GO terms cluster around SRP-dependent and post-translational protein targeting to membranes, and responses related to unfolded proteins, including negative regulation of inclusion body assembly and cellular heat response, suggesting a focus on protein handling and quality control. The presence of fungal-specific processes such as beta-glucan biosynthesis and karyogamy, alongside general processes like DNA replication, points to a fungal cellular context with overlapping roles in protein targeting and stress response. Taken together, the theme that best fits is fungal protein targeting plus stress/quality-control mechanisms, with ancillary mating and cell wall-related processes.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090084","count":2},{"id":"GO:0016226","count":2},{"id":"GO:0034620","count":2},{"id":"GO:0000742","count":2},{"id":"GO:0006260","count":2}]},{"hash":"956522232783760835","title":"Ubiquitin-Dependent Protein Degradation","description":"The top GO terms are dominated by ubiquitination and ubiquitin-dependent protein turnover (K29-linked ubiquitination, autoubiquitination, and MVB sorting\u2013mediated catabolic processes), suggesting the cluster centers on ubiquitin-mediated proteostasis, with RNA processing and cell-cycle references likely related regulatory links.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:2000235","count":2},{"id":"GO:0014809","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0010768","count":2}]},{"hash":"470200652612209116","title":"Hypoxia-responsive signaling and cell cycle regulation","description":"The cluster contains GO terms tied to hypoxia response, regulation of kinase and GTPase activities, autophosphorylation, and positive regulation of the mitotic cell cycle and proliferation, pointing to a cohesive theme of signaling pathways linking stress response to cell growth and division. Some terms (e.g., mRNA transport, cardiac myofibril assembly) are less central, but the dominant pattern is signaling plus cell cycle regulation.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071456","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0071902","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0000278","count":2}]},{"hash":"673913421836730527","title":"Nuclear transport and mitotic regulation","description":"The top GO terms point to nuclear localization and mitotic processes (NLS-mediated import, mitotic nuclear membrane reassembly), with additional signals related to transcription regulation, kinase activity, and broader growth/morphogenesis pathways. The terms are varied and only loosely cohesive, suggesting a cluster centered on nuclear transport and cell-cycle\u2013related signaling, but with peripheral involvement in growth and apoptosis. Overall, the link is plausible but not strong.","confidence":"Low","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007084","count":1},{"id":"GO:0045945","count":1},{"id":"GO:0097711","count":1},{"id":"GO:0001938","count":1},{"id":"GO:0060561","count":1}]},{"hash":"127595010109609641","title":"Unknown","description":"The listed GO terms are highly diverse and include obsolete chromatin modification, transcription regulation, endosome/receptor recycling, Rho signaling, glutamatergic synaptic transmission, calcium-channel-related activity, mitochondrial membrane permeability, and cell-cycle regulation. There is no clear, shared functional theme linking these four proteins, and the prevalence of obsolete terms reduces confidence in any specific biological link. Unknown cluster with no coherent unifying function.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034968","count":1},{"id":"GO:0001881","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0051036","count":1},{"id":"GO:0035023","count":1}]},{"hash":"2035641471096749336","title":"Cytoskeleton-Driven Cell Migration","description":"The top GO terms show ameboid-type cell migration, cell spreading/adhesion, and cytoskeletal/mitotic processes. While there are also terms related to phagosome maturation and signaling, the strongest signal across the cluster revolves around cell movement and the cytoskeletal regulation that drives adhesion and migration. This makes \u201cCytoskeleton-Driven Cell Migration\u201d a concise, representative label for the cluster.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1903215","count":4},{"id":"GO:0001667","count":4},{"id":"GO:0006878","count":4},{"id":"GO:0043316","count":4},{"id":"GO:1900026","count":4}]},{"hash":"2187849981032552777","title":"Unknown","description":"The GO terms for these four proteins are from very different biological contexts (muscle actin/myofibril assembly, cuticle development, kidney tubule development, nuclear import, and calcium signaling), and there\u2019s essentially no shared function or pathway tying them together. With only one edge and no cohesive theme, there isn\u2019t a meaningful label beyond Unknown.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055003","count":1},{"id":"GO:0097274","count":1},{"id":"GO:0008365","count":1},{"id":"GO:2001246","count":1},{"id":"GO:1905205","count":1}]},{"hash":"1575120324596118797","title":"Mitotic regulation and proteasome function","description":"The top GO terms point to cell cycle control (G1/S transition, mitotic DNA replication checkpoint signaling) and proteasomal protein catabolic processes, suggesting a role in coordinating cell division with protein turnover. Some energy and stress-related terms appear but are secondary to the core theme. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043666","count":2},{"id":"GO:0000082","count":2},{"id":"GO:0046034","count":1},{"id":"GO:0071712","count":1},{"id":"GO:0033314","count":1}]},{"hash":"2057227950427204633","title":"Wnt-driven EMT and organ development","description":"This cluster shows strong representation of developmental and EMT-related terms: mesenchymal cell proliferation in lung development, canonical Wnt signaling involved in promoting EMT, and diverse cell fate determinations (glial, endodermal) plus organ identity maintenance and cell cycle regulation. Together, these point to proteins involved in Wnt-regulated epithelial-to-mesenchymal transition during organogenesis. ","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0060916","count":4},{"id":"GO:0044334","count":4},{"id":"GO:0007403","count":4},{"id":"GO:0051211","count":4},{"id":"GO:0001711","count":4}]},{"hash":"764638858376483245","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071374","count":1},{"id":"GO:0090084","count":1},{"id":"GO:1901621","count":1},{"id":"GO:0006458","count":1},{"id":"GO:0010198","count":1}]},{"hash":"1688346807924829544","title":"Unknown","description":"The top GO terms span multiple, unrelated biological areas (nuclear export; pain perception; development; transcription; endosome transport; pseudohyphal growth; neural signaling and p53 regulation) with little cohesive function tying the proteins together. The absence of interactions (edges/triangles) further suggests the cluster is not functionally cohesive, so a single interpretable label cannot be confidently assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":3},{"id":"GO:0019233","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0006351","count":3},{"id":"GO:2000641","count":2}]},{"hash":"1922229110238737786","title":"Unknown","description":"The GO terms are spread across RNA processing (mRNA export, splicing), ubiquitination, chromatin assembly, cell cycle regulation, inflammatory signaling, glial apoptosis, and neural development, with no clear single function linking them all. This makes it hard to assign a cohesive, specific label beyond Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000728","count":2},{"id":"GO:1904668","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0061641","count":2},{"id":"GO:0002534","count":2}]},{"hash":"1073585673500541333","title":"Unknown","description":"The top GO terms are highly heterogeneous, spanning chromatin regulation, nucleotide biosynthesis, development, apoptosis, and cilium movement, with no clear shared function linking the proteins. Given the lack of a cohesive theme and no interactions, this cluster likely does not reflect a single biological module.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042464","count":1},{"id":"GO:0051568","count":1},{"id":"GO:1902176","count":1},{"id":"GO:0021591","count":1},{"id":"GO:0006228","count":1}]},{"hash":"1300953289072939760","title":"DNA replication and cell cycle","description":"The cluster is dominated by nuclear processes tied to DNA replication and cell cycle progression (DNA-templated transcription, DNA replication, centrosome cycle, G1/S transition, meiotic/mitotic cell cycle, and kinetochore localization), indicating a cohesive role in DNA replication and mitosis; the few terms related to neuronal signaling appear incidental.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0007098","count":2},{"id":"GO:0000082","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0034501","count":2}]},{"hash":"952384441843862787","title":"Metal and oxidative stress response","description":"This cluster is dominated by GO terms for cellular response to cadmium ion and to hydrogen peroxide, indicating a shared metal/oxidative stress response function. The other, lower-frequency terms (antibiotic biosynthetic and various fatty acid/metabolism processes) are less cohesive and may reflect broader metabolic capabilities or annotation noise, but the strongest signal points to stress response to metals and ROS.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071276","count":2},{"id":"GO:0070301","count":2},{"id":"GO:0017000","count":1},{"id":"GO:0019367","count":1},{"id":"GO:0051790","count":1}]},{"hash":"1649475397990396044","title":"Calcium signaling and ion transport regulation","description":"This cluster is dominated by GO terms about calcium handling (cytosolic Ca2+ concentration, Ca2+ release from Golgi), membrane repolarization, potassium ion transport, and regulation of muscle contraction and NFAT signaling, which together imply ion homeostasis and calcium-dependent signaling in muscle and neural contexts. A few terms are less directly connected (nerve formation, glucocorticoid regulation) but do not override the central theme.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0086009","count":1},{"id":"GO:0031947","count":1},{"id":"GO:0051481","count":1},{"id":"GO:0002028","count":1},{"id":"GO:0045988","count":1}]},{"hash":"2080909137256881385","title":"Endosomal/MVB Trafficking and Exosome Regulation","description":"The top GO terms center on endosomal/MVB biogenesis (multivesicular body assembly), SNARE-related vesicle fusion/disassembly, ER-to-Golgi transport, and regulation of exosomal secretion, with supporting protein ubiquitination signals and some cell-cycle context. This pattern points to vesicle trafficking and exosome biology as the shared theme of the cluster, making a focused label appropriate.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036258","count":2},{"id":"GO:0030225","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0035494","count":2},{"id":"GO:0016567","count":2}]},{"hash":"2199637537880075732","title":"Unknown","description":"The top GO terms are highly diverse (mitochondrial targeting, cell migration, copper homeostasis, T cell degranulation, adhesion/spreading, phagosome maturation, Wnt signaling, oligodendrocyte differentiation, and mitosis-related processes), with no single functional theme or shared pathway tying the proteins together. There are no edges to suggest interactions, so a cohesive cluster label cannot be assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903215","count":1},{"id":"GO:0001667","count":1},{"id":"GO:0006878","count":1},{"id":"GO:0043316","count":1},{"id":"GO:1900026","count":1}]},{"hash":"104688978859470726","title":"Ion Transport and Membrane Dynamics","description":"This cluster shows a clear emphasis on ion movement across membranes and related signaling, with terms like regulation of sodium ion transport, potassium ion export across the plasma membrane, monoatomic cation transmembrane transport, and release of sequestered calcium into the cytosol by the Golgi. While there are other divergent terms (lipopolysaccharide biosynthesis, stilbene catabolic process, nerve formation, epoxygenase P450 pathway, autophosphorylation), the dominant theme centers on membrane-associated ion transport. Confidence: Low.","confidence":"","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0086009","count":1},{"id":"GO:0009103","count":1},{"id":"GO:0002028","count":1},{"id":"GO:0046272","count":1},{"id":"GO:0021650","count":1}]},{"hash":"1142845473444764834","title":"ER Translocation and Secretory Trafficking","description":"These proteins are linked to SRP-dependent cotranslational targeting to the ER membrane, Sec-dependent transport of proteins, post-translational targeting to ER membranes, and ER-to-cytosol retrograde transport (ERAD). The presence of developmental GO terms is likely contextual rather than indicating core function. Overall, the cluster centers on targeting and trafficking proteins to the endoplasmic reticulum and through the secretory pathway.","confidence":"High","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006605","count":1},{"id":"GO:0039019","count":1},{"id":"GO:0043952","count":1},{"id":"GO:0031204","count":1},{"id":"GO:0006616","count":1}]},{"hash":"2188805741169077575","title":"RNA metabolism: processing, translation, and decay","description":"This cluster centers on RNA biology, with clear enrichment for translation (GO:0006412, GO:0006413), rRNA maturation and snoRNA processing, and multiple mRNA decay pathways (no-go, non-stop, RNase MRP-dependent), suggesting a cohesive group involved in RNA processing and protein synthesis with quality control. Some outlier terms may reflect pleiotropic annotations, but the core theme is coherent.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0030261","count":1},{"id":"GO:0000294","count":1},{"id":"GO:0034965","count":1},{"id":"GO:0048235","count":1}]},{"hash":"598282998793972753","title":"Lipid and small-molecule metabolism","description":"The GO terms are dominated by metabolism and turnover/biosynthesis of lipids and small organic molecules (menaquinone biosynthesis, carnitine and bile acid metabolism, fatty acid transport, and various organic acid catabolic processes). There are a couple of outliers (seed coat development, nonribosomal peptide activation) that are less related, but the majority point to lipid- and small-molecule metabolic functions, supporting this label.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009234","count":3},{"id":"GO:1902987","count":2},{"id":"GO:0010124","count":2},{"id":"GO:0009437","count":2},{"id":"GO:0043041","count":2}]},{"hash":"1881282600612425220","title":"Ribosome biogenesis and translation","description":"The top GO terms center on translation and ribosome assembly (translation, cytoplasmic translation, ribosome assembly) and rRNA processing (ITS2 cleavage). Additional terms about SRP-dependent cotranslational targeting to membranes and signal sequence recognition reinforce a ribosome-associated translation/membrane targeting theme, consistent with proteins involved in ribosome function, biogenesis, and early translation steps.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0006412","count":2},{"id":"GO:0042255","count":2},{"id":"GO:0000448","count":2},{"id":"GO:0006616","count":1}]},{"hash":"566387101768741255","title":"Glycolysis and ATP production","description":"This cluster centers on glycolytic flux and energy generation, highlighted by canonical glycolysis, pyruvate biosynthesis, and ATP biosynthetic processes. The presence of regulation-related terms (responses to cAMP, glucose, epinephrine, hypoxia, heat) suggests these proteins are jointly involved in metabolic control under stress, with a minor link to programmed cell death. Confidence: High","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042866","count":3},{"id":"GO:0051591","count":2},{"id":"GO:0012501","count":1},{"id":"GO:0001666","count":1},{"id":"GO:0009408","count":1}]},{"hash":"887998866436010628","title":"Unknown","description":"These terms encompass endosome transport, fungal growth, neural development and signaling, calcium responsiveness, dopaminergic neurotransmission, p53 pathway regulation, NK T cell differentiation, CNS neuron axonogenesis, and cartilage formation. The span across vastly different biological areas offers no single cohesive function linking all proteins, so a generic Unknown label with no confidence is most appropriate.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2000641","count":2},{"id":"GO:0007124","count":2},{"id":"GO:1901621","count":2},{"id":"GO:1904637","count":2},{"id":"GO:0001963","count":2}]},{"hash":"1103377984003994340","title":"RNA decay and stress granule regulation","description":"This cluster is enriched for P-body and stress granule assembly, deadenylation/decapping of mRNA, and repression of translation, alongside RIG-I/IFN signaling terms, pointing to a core role in post-transcriptional RNA regulation during cellular stress and antiviral responses.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0033962","count":2},{"id":"GO:0031087","count":2},{"id":"GO:0060340","count":2},{"id":"GO:0045947","count":2},{"id":"GO:0034063","count":2}]},{"hash":"328672844807735689","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning DNA repair, endosome transport, fungal growth, neural signaling and development, immune differentiation, and aging\u2014there is no single convergent function or pathway tying these proteins together, and zero edges suggest no detectable interactions. ","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:2000641","count":1},{"id":"GO:0007124","count":1},{"id":"GO:1901621","count":1},{"id":"GO:1904637","count":1}]},{"hash":"1571025354642096127","title":"DNA replication and mitotic cell cycle","description":"The terms are dominated by DNA replication and mitotic cell cycle, indicating a core involvement in cell division and genome duplication. Other terms (endosome transport, p53 signaling, development-related processes) are present but secondary, so the primary theme is cell cycle-related functions.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0000278","count":3},{"id":"GO:2000641","count":2},{"id":"GO:0007124","count":2},{"id":"GO:1901621","count":2}]},{"hash":"748874713158145469","title":"Dopaminergic signaling and neural development","description":"This cluster centers on neuronal processes: dopaminergic synaptic transmission and sensory perception of pain, along with neural development and patterning terms. Additional terms point to transcriptional regulation and intracellular trafficking, which are common in neural development and synaptic function. Some terms (like pseudohyphal growth) seem less related, but the dominant theme is neural signaling and development, giving moderate confidence in the label.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":4},{"id":"GO:0019233","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0007275","count":4},{"id":"GO:2000641","count":3}]},{"hash":"1608299815829075175","title":"Unknown","description":"The top GO terms cover a wide range of processes (neural development, dopaminergic signaling, immune differentiation, cartilage condensation, endosome transport, and signaling regulation) with no clear, unified theme, so a specific functional label is not supported.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":4},{"id":"GO:0007124","count":4},{"id":"GO:1901621","count":4},{"id":"GO:1904637","count":4},{"id":"GO:0001963","count":4}]},{"hash":"2008710375579409566","title":"Ribosome biogenesis and translation","description":"The top GO terms for this cluster are ribosomal large subunit assembly and translation, each with two proteins, which strongly points to involvement in protein synthesis machinery. Although other low-frequency terms appear (e.g., calcium-related processes and tRNA regulation), the dominant signal centers on ribosome assembly and translation, suggesting these four proteins are linked to the core protein synthesis pathway.","confidence":"High","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000027","count":2},{"id":"GO:0006412","count":2},{"id":"GO:1990927","count":1},{"id":"GO:2000235","count":1},{"id":"GO:0034351","count":1}]},{"hash":"441264267804313471","title":"Vacuolar protein processing","description":"The top GO term is vacuolar protein processing (GO:0006624), suggesting a shared function in maturation or handling of proteins within vacuoles. The cluster is small with few connections and only one annotation, indicating limited but coherent evidence for this process; the inclusion by ReCIPE adds more members but the core signal remains vacuolar processing.","confidence":"Medium","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006624","count":1}]},{"hash":"1501393715866961934","title":"Unknown","description":"There are four proteins but no edges, no enriched GO terms, and no top terms reported, giving no clear shared function to label this cluster.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1162651574540077652","title":"Viral modulation of host mRNA processing","description":"This cluster shows strong representation of mRNA splicing and processing terms (spliceosome-mediated splicing, alternative splicing, mRNA stability, polyadenylation). A few GO terms reference viral processes such as release, budding, and translation reinitiation, suggesting these proteins are host factors involved in RNA processing that can be exploited by viruses. The name emphasizes the core RNA-processing function with the accompanying viral interaction signals.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019076","count":1},{"id":"GO:1900363","count":1},{"id":"GO:0048025","count":1},{"id":"GO:0035278","count":1},{"id":"GO:0039702","count":1}]},{"hash":"1825410386759580544","title":"Unknown","description":"The GO terms are highly diverse, spanning endosome transport, pseudohyphal growth, neural patterning signaling, ionomycin response, dopaminergic synaptic transmission, p53 signaling, NK T cell differentiation, CNS axonogenesis, aging response, and cartilage condensation. There is no clear, cohesive functional theme linking these proteins, so a specific, interpretable label is not supported.","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2000641","count":1},{"id":"GO:0007124","count":1},{"id":"GO:1901621","count":1},{"id":"GO:1904637","count":1},{"id":"GO:0001963","count":1}]},{"hash":"1068689143721611906","title":"Nuclear Chromatin Organization and Ribosome Biogenesis","description":"The cluster shows a coherent emphasis on chromatin dynamics and assembly (nucleosome assembly, CENP-A\u2013containing chromatin, histone methylation regulation, nucleus organization, heterochromatin formation) together with nucleolar processes (ribosome biogenesis and rRNA transcription). While a few terms are peripheral (e.g., dosage compensation, fertilization), the dominant theme ties chromatin organization in the nucleus to ribosome production. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032147","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0007338","count":1},{"id":"GO:1901837","count":1},{"id":"GO:0051572","count":1}]},{"hash":"1334841623251079313","title":"Translation initiation and ribosome regulation","description":"The top GO terms are dominated by translation-related processes (initiation, preinitiation complex formation, ribosome disassembly, translational termination regulation, and positive regulation of cytoplasmic translation), suggesting a cluster centered on control of protein synthesis machinery. A few terms (mitochondrial autophagy, glial proliferation) are present but appear peripheral to the main theme. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043457","count":1},{"id":"GO:0000422","count":1},{"id":"GO:0010259","count":1},{"id":"GO:0014009","count":1},{"id":"GO:0046677","count":1}]},{"hash":"2063569863502612316","title":"Unknown","description":"There are no GO terms or functional connections among the proteins (Top Terms is empty; Edges 0), so there is no shared theme to define a function for this cluster. Without enrichment or interaction signals, the cluster cannot be labeled beyond Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1546249106180214687","title":"Unknown","description":"The GO terms for this cluster are highly diverse, including nucleotide biosynthesis (UTP/CTP/GTP), chromatin/epigenetic aspects (subtelomeric heterochromatin formation, histone methylation), developmental processes (ventricular system development, spermatid differentiation), epithelial cilium movement, and apoptosis regulation. With 0 edges and no clear shared function among the proteins, there is no coherent theme tying the proteins together, so a single representative function cannot be assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042464","count":1},{"id":"GO:0051568","count":1},{"id":"GO:1902176","count":1},{"id":"GO:0021591","count":1},{"id":"GO:0006228","count":1}]},{"hash":"116250847989278237","title":"Chromatin silencing and heterochromatin formation","description":"The top GO terms cluster around rDNA heterochromatin formation, regulation of nucleosome density, and chromatin silencing at telomeres, plus DNA methylation\u2013dependent heterochromatin formation and transcriptional regulation by RNA Pol II. These points indicate a common theme of epigenetic control of chromatin state and gene expression, i.e., heterochromatin formation and chromatin silencing. Additional terms about rRNA methylation and protein methylation suggest related chromatin-modifying or methyltransferase activities that can accompany such epigenetic regulation. Overall, the dominant signal is chromatin silencing/heterochromatin formation, with supplementary methylation-related processes.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":3},{"id":"GO:0060303","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0031940","count":2},{"id":"GO:0031167","count":2}]},{"hash":"839920580623233408","title":"Pol II Transcription Regulation Under Stress","description":"This cluster\u2019s top GO terms cluster around transcriptional regulation by RNA polymerase II, including initiation site selection and termination, with specific reference to oxidative-stress responses. While a couple terms touch on calcium signaling and development, the strongest signal is transcription control under stress, suggesting a cohesive core function. Confidence in this labeling is Moderate due to some peripheral annotations that are not strictly transcription-related.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0036091","count":3},{"id":"GO:0010880","count":2},{"id":"GO:0001178","count":2},{"id":"GO:0021553","count":2},{"id":"GO:2001229","count":2}]},{"hash":"1971740512367154174","title":"Diverse Cellular Stress Responses","description":"The top GO terms point to responses to a range of stressors (oxidative stress, radiation, hypoxia, chemical stress) and a DNA damage-related regulation, suggesting a cluster of proteins involved in general stress sensing/transduction rather than a single pathway. Some terms are obsolete or unrelated, but the common theme is cellular stress response.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033169","count":1},{"id":"GO:1990911","count":1},{"id":"GO:1904843","count":1},{"id":"GO:0071480","count":1},{"id":"GO:0000304","count":1}]},{"hash":"1376929026119322138","title":"Ion Transport and Membrane Potential Regulation","description":"The term set centers on sodium and potassium ion movement across the plasma membrane and on membrane potential dynamics (resting potential, stabilization, and action potential repolarization), with supporting hints from cAMP/cGMP signaling. This cohesive theme points to proteins involved in ion transport and electrical properties of the cell.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0098719","count":3},{"id":"GO:0071321","count":3},{"id":"GO:0010754","count":3},{"id":"GO:0071805","count":3},{"id":"GO:0098914","count":3}]},{"hash":"350983485645958768","title":"Ubiquitin-mediated cell cycle control","description":"This cluster is dominated by GO terms tied to ubiquitination (protein polyubiquitination; regulation of ubiquitin ligase activity) and mitotic regulation (establishment of mitotic spindle orientation; regulation of cell cycle checkpoint), suggesting a core function in ubiquitin-dependent control of the cell cycle and mitosis. Additional terms touch on nuclear processes (splicing, mRNA export, CENP-A chromatin assembly) that can accompany cell-cycle\u2013related chromatin and gene expression changes; some neuronal/glial terms may reflect broader regulatory roles or annotation noise. Overall, the common thread appears to be ubiquitin-mediated regulation of cell division. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":2},{"id":"GO:0000132","count":2},{"id":"GO:2000728","count":1},{"id":"GO:1904668","count":1},{"id":"GO:0050773","count":1}]},{"hash":"308743985901175134","title":"Meiosis-Cytokinesis Machinery","description":"The top GO terms are dominated by meiotic processes and cytokinesis (spermatocyte division, meiosis I/II cytokinesis, actomyosin contractile ring contraction, cell plate assembly), pointing to proteins involved in the machinery of cell division. A few other terms (endosome transport, cortical development, transcription regulation) appear but do not define the cluster; the core theme is meiosis-associated cytokinetic machinery.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048137","count":1},{"id":"GO:0000916","count":1},{"id":"GO:0007111","count":1},{"id":"GO:0000919","count":1},{"id":"GO:0007110","count":1}]},{"hash":"200128643371945111","title":"Unknown","description":"The listed GO terms are diverse (ATP metabolism, proteasomal protein catabolic processes, oxidative stress response, mitochondrial complex III assembly, chromatin assembly, transcription elongation) and there is no single, coherent function that clearly ties all four proteins together. Because of this heterogeneity, there isn't a reliable, specific label beyond Unknown.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046034","count":1},{"id":"GO:0071712","count":1},{"id":"GO:0033314","count":1},{"id":"GO:1901800","count":1},{"id":"GO:0034551","count":1}]},{"hash":"291632873441600639","title":"ECM remodeling and fibrinolysis regulators","description":"The GO terms point to extracellular proteolysis and ECM remodeling, with explicit mentions of fibrinolysis, negative regulation of plasminogen activation, and regulation of ECM constituent secretion. Other terms appear more peripheral (heat response, Purkinje cell differentiation, deglutamylation), so with only four proteins the theme is present but not strong; hence a Medium confidence. ","confidence":"Medium","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0018279","count":1},{"id":"GO:0010757","count":1},{"id":"GO:0009408","count":1},{"id":"GO:0002002","count":1},{"id":"GO:0003331","count":1}]},{"hash":"1037267256846320612","title":"Ubiquitin-regulated neural stress pathways","description":"The top GO terms cluster around ubiquitin-related regulation (ERAD pathway, ubiquitin ligase activity, polyubiquitination) with neural context (dendrite development, glial apoptosis) and stress-responsive processes (heat-stress mRNA export/splicing, cytokine production), suggesting a set of proteins tied to ubiquitin-mediated control of neural stress and development.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:2000728","count":2},{"id":"GO:1904668","count":2},{"id":"GO:0050773","count":2},{"id":"GO:0000398","count":2}]},{"hash":"42920381588821283","title":"Diverse Transmembrane Transporters","description":"The top GO terms point to transmembrane transport of a variety of substrates (glycine betaine, taurine, cobalt, molybdate, xenobiotics, monoatomic anions) and ceramide translocation, indicating a functional cluster of membrane proteins that mediate transport across membranes rather than a single substrate. While some terms like SOS response or cytochrome complex assembly are less directly tied, the dominant theme is broad substrate transport, supporting a label of diverse transporter activity. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":1},{"id":"GO:0031460","count":1},{"id":"GO:0099133","count":1},{"id":"GO:0006824","count":1},{"id":"GO:0009432","count":1}]},{"hash":"2273020289115308788","title":"Copper Ion Transport and Homeostasis","description":"The top GO terms cluster around copper handling\u2014import across the membrane, regulation of copper transmembrane transport, and intracellular copper ion homeostasis\u2014with an additional link to cisplatin response and xenobiotic transport, suggesting a cohesive copper transport/homeostasis functional group that may influence drug uptake.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0072719","count":1},{"id":"GO:0006855","count":1},{"id":"GO:0015680","count":1},{"id":"GO:1902311","count":1},{"id":"GO:0006878","count":1}]},{"hash":"150377255697887325","title":"Unknown","description":"The four proteins show a highly heterogeneous mix of GO terms (endosome transport regulation, pseudohyphal growth, dopaminergic synaptic transmission, cardiac cell communication, immune chemokine production, p53 signaling, ionomycin response, fatty acid oxidation regulation, etc.) with no clear shared biological process or pathway. There are no edges linking them, suggesting no cohesive functional theme for this cluster.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000641","count":1},{"id":"GO:0007124","count":1},{"id":"GO:0071642","count":1},{"id":"GO:1901621","count":1},{"id":"GO:1904637","count":1}]},{"hash":"930423016162980698","title":"Virus and Symbiont Interactions with Host","description":"This cluster centers on GO terms related to viral release from host cells, symbiont entry and suppression of host gene expression, indicating a theme around host\u2013microbe interactions. It also includes ubiquitin- and ERAD-related processes, suggesting a broader link to host protein degradation during infection. The mix of clearly related host\u2013pathogen interactions with ubiquitin degradation terms and some obsolete annotations means the theme is present but not uniformly cohesive, giving a Low confidence.","confidence":"Low","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019076","count":1},{"id":"GO:0033132","count":1},{"id":"GO:0051865","count":1},{"id":"GO:0014070","count":1},{"id":"GO:0046718","count":1}]},{"hash":"1852502144538035693","title":"Steroid Hormone Biosynthesis & Hormone-Dependent Development","description":"The top GO terms include androgen metabolic process, testosterone biosynthetic process, and brassinosteroid biosynthetic process, all pointing to steroid hormone production across different organisms. Developmental terms like mammary gland development and female gonad development further suggest hormone-regulated growth. While some terms are broader (methylation, macrophage chemotaxis), the strongest signal centers on steroid biosynthesis and hormone-driven development.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008209","count":2},{"id":"GO:1900087","count":2},{"id":"GO:0016132","count":2},{"id":"GO:0071615","count":2},{"id":"GO:0033076","count":2}]},{"hash":"1648703259760172090","title":"Unknown","description":"The GO terms associated with this small cluster are highly diverse, including stress responses (cadmium ion, heat), RNA processing (splicing, mRNA export), chromatin assembly, development processes (notochord, dendrite development), and cytokine production. There is no clear, single biological theme tying these proteins together, and the terms seem too heterogeneous to justify a specific, concise functional label. Therefore, I cannot assign a coherent cluster name beyond Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071276","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0050731","count":2},{"id":"GO:2000728","count":1},{"id":"GO:1904668","count":1}]},{"hash":"939772641163202745","title":"Unknown","description":"The GO terms are highly diverse: ion transport and membrane-related processes appear alongside neural development, immune differentiation, and even bacterial metabolism terms, with no single unifying function. Coupled with only a single edge and no triangles, there isn\u2019t a coherent pathway or process that clearly defines this cluster, so an Unknown label with no clear confidence is most appropriate.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0086009","count":1},{"id":"GO:0009103","count":1},{"id":"GO:0002028","count":1},{"id":"GO:0050884","count":1},{"id":"GO:0046272","count":1}]},{"hash":"1802752345561092589","title":"Ion Transport and Metal Homeostasis","description":"This cluster\u2019s strongest motif is ion handling across membranes: regulation of sodium transport, potassium export across the plasma membrane, and copper ion homeostasis, all pointing to membrane-associated ion transport and metal balance. The other terms appear more disparate (biosynthetic processes, nerve formation) and may reflect annotation noise, but the core theme remains ion/membrane physiology. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016311","count":1},{"id":"GO:0086009","count":1},{"id":"GO:0051479","count":1},{"id":"GO:0009103","count":1},{"id":"GO:0002028","count":1}]},{"hash":"448586530968749104","title":"Neural development and epigenetic regulation","description":"Though the cluster has diverse GO terms, several entries point to neural biology: neuron projection extension, dopamine biosynthesis/metabolism, suggesting neuronal development and neurotransmitter synthesis. In addition, GO terms about chromatin binding and histone methylation hint at epigenetic regulation linked to gene expression programs during differentiation. The remaining metabolic terms are broader, but do not contradict the neural/epigenetic theme.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046168","count":1},{"id":"GO:1990138","count":1},{"id":"GO:0009435","count":1},{"id":"GO:0035563","count":1},{"id":"GO:0010044","count":1}]},{"hash":"1443188323665822866","title":"Unknown","description":"The cluster lacks any GO terms or functional annotations in the Top Terms, so there is no clear shared function or process to name. With only a few proteins and basic connectivity, a confident, specific label cannot be assigned.","confidence":"","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[]},{"hash":"77993466292800976","title":"Unknown","description":"The GO terms are spread across tRNA wobble uridine modification, NAD+ biosynthesis, chromatin regulation, stem cell proliferation, neuron projection development, spliceosome-mediated splicing, and mitochondrial electron transport. With no single dominant biological theme tying these terms together, the cluster cannot be assigned a coherent, representative function. ","confidence":"","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0002098","count":2},{"id":"GO:0009435","count":1},{"id":"GO:0035563","count":1},{"id":"GO:2000648","count":1},{"id":"GO:0010976","count":1}]},{"hash":"1509800368933489318","title":"Unknown","description":"The top GO terms are highly diverse, spanning stress responses (cadmium, ozone), multiple tissue development (gonad, liver/hepatocytes, retina), lipid-derived oxylipin biosynthesis, and even plant-specific terpene oxidation. With no clear shared function or pathway across these terms and no interactions among proteins, there is no coherent theme to name the cluster beyond Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071276","count":2},{"id":"GO:0008585","count":2},{"id":"GO:0061370","count":2},{"id":"GO:0070365","count":2},{"id":"GO:0061298","count":2}]},{"hash":"1363937183989421577","title":"Unknown","description":"The GO terms are highly diverse (DNA replication/telomere maintenance alongside plant hormone signaling, immune/cytokine responses, xenobiotic response, and even bacterial motility), with no clear single shared function across the cluster.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006261","count":1},{"id":"GO:0009736","count":1},{"id":"GO:0033160","count":1},{"id":"GO:0035690","count":1},{"id":"GO:1905323","count":1}]},{"hash":"2202050701110185582","title":"Nuclear ubiquitin-regulated transcription and RNA processing","description":"This cluster centers on ubiquitin-related control of nuclear processes, including transcription, RNA splicing and export, and chromatin assembly. The presence of polyubiquitination and ubiquitin ligase activity terms suggests a core role of ubiquitin signaling influencing gene expression and nuclear RNA processing; additional terms reflect stress responses and cell fate regulation (apoptosis, necroptosis, TLR signaling) that often intersect with ubiquitin pathways. While some terms are peripheral, the dominant pattern points to ubiquitin-mediated regulation of nuclear gene expression and chromatin dynamics.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":2},{"id":"GO:0060544","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0043066","count":1},{"id":"GO:0034121","count":1}]},{"hash":"662412179450670750","title":"Protein post-translational modifications","description":"This cluster shows multiple GO terms related to protein modification and processing (sumoylation, ufmylation, lipidation) as well as RNA/tRNA modification, hinting at a shared theme of molecular modification and regulatory processes, even though there are few edges and a small protein set. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032447","count":1},{"id":"GO:0002143","count":1},{"id":"GO:0045892","count":1},{"id":"GO:1990592","count":1},{"id":"GO:0061504","count":1}]},{"hash":"665806205890126675","title":"Golgi-centered vesicle trafficking and vacuolar targeting","description":"This cluster\u2019s GO terms cluster around vesicle transport involving the Golgi, including ER-to-Golgi, intra-Golgi, endosome-to-Golgi retrograde transport, and Golgi-to-vacuole pathways, as well as vacuole fusion and macroautophagy. Together these terms point to a cohesive role in Golgi- and vacuole-associated vesicle trafficking and protein localization, with autophagic processes linked to vesicle dynamics.  ","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048280","count":1},{"id":"GO:0042147","count":1},{"id":"GO:0016236","count":1},{"id":"GO:1903076","count":1},{"id":"GO:0006891","count":1}]},{"hash":"215597086964108227","title":"Unknown","description":"The set of top GO terms includes animal development processes (asymmetric neuroblast division, mitotic cell cycle, maintenance of animal organ identity, male sex differentiation) alongside plant-specific and obsolete terms (cytokinin signaling, chlorophyll biosynthesis regulation, ubiquitin-dependent ERAD). There are no edges or interactions among the proteins (Edges: 0, Triangles: 0, Max Degree: 0), suggesting the proteins do not share a cohesive, unified function and the annotations appear noisy or cross-kingdom.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055059","count":2},{"id":"GO:0009736","count":2},{"id":"GO:0000278","count":2},{"id":"GO:1902325","count":2},{"id":"GO:0048496","count":2}]},{"hash":"1654281357844727094","title":"Innate antiviral response and ubiquitin-dependent proteolysis","description":"The top GO terms cluster around defense response to virus and innate immune response, with ubiquitin-dependent protein catabolic processes (ERAD), suggesting a shared role in antiviral signaling and protein turnover, even though there are no detected edges among the four proteins.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0060252","count":1}]},{"hash":"1387206317674740568","title":"NF-kappaB/TNF immune signaling regulation","description":"Most of the GO terms point to immune signaling and inflammatory regulation (positive regulation of canonical NF-kappaB signaling and TNF-mediated signaling), along with related control of cell death and antimicrobial responses. While a few terms touch on unrelated processes (neuronal vesicle transport, lymph node development, ERAD), the dominant theme across the cluster is immune signaling modulation.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:1903265","count":4},{"id":"GO:0043123","count":3},{"id":"GO:0060546","count":3},{"id":"GO:0050999","count":3}]},{"hash":"554349330720499383","title":"Ciliary transition zone in embryonic patterning","description":"The top GO terms indicate a focus on ciliary biology (non-motile cilium assembly; localization to the ciliary transition zone) and developmental patterning (neural tube patterning; embryonic digit morphogenesis). This suggests proteins involved in ciliogenesis and ciliary signaling that influence embryonic development, justifying a name centered on the ciliary transition zone and its developmental role.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021532","count":1},{"id":"GO:1905515","count":1},{"id":"GO:0042733","count":1},{"id":"GO:1904491","count":1}]},{"hash":"1292703448529832236","title":"Unknown","description":"The four proteins have GO terms that are highly diverse and disjoint, including endosome transport, fungal growth, Hedgehog-related neural patterning, calcium signaling, dopaminergic synaptic transmission, p53 signaling, NK T differentiation, CNS neuron axonogenesis, aging stress response, and cartilage condensation. With no clear shared function or theme, there is no coherent label beyond Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000641","count":1},{"id":"GO:0007124","count":1},{"id":"GO:1901621","count":1},{"id":"GO:1904637","count":1},{"id":"GO:0001963","count":1}]},{"hash":"201928883608284650","title":"Neuronal receptor trafficking and signaling","description":"This cluster prominently features terms tied to membrane trafficking and neuron signaling: receptor recycling, regulation of endosome size, Rho signaling, and glutamatergic synaptic transmission. These collectively point to endomembrane trafficking coupled with neuronal communication. The presence of transcription regulation and histone methylation terms could reflect multifunctional proteins or annotation noise, but they don\u2019t strongly redefine the main theme. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034968","count":1},{"id":"GO:0001881","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0051036","count":1},{"id":"GO:0035023","count":1}]},{"hash":"1458817019674733580","title":"Unknown","description":"There are no GO terms listed for this cluster, so there is no clear shared function or process to name. The available network metrics do not reveal a specific biological theme.","confidence":"","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[]},{"hash":"1146559437021365405","title":"Mitochondrial Membrane Regulation and Protein Import","description":"The top GO terms emphasize regulation of mitochondrial membrane permeability and protein import into the mitochondrial matrix, suggesting a mitochondria-centered function cluster. Other terms mentioning cell cycle regulation and lipid metabolism are present but appear less central to the core theme.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":4},{"id":"GO:2000134","count":4},{"id":"GO:0070940","count":4},{"id":"GO:1903740","count":4},{"id":"GO:0010867","count":4}]},{"hash":"2105020538049007971","title":"Glycolysis Regulation and Energy Metabolism","description":"The top terms are dominated by glycolytic processes and fructose/glucose metabolism, including both positive and negative regulation of glycolysis and related steps, suggesting a cluster tied to energy production and carbohydrate metabolism. Additional terms referencing mitophagy regulation and developmental or apoptotic contexts imply broader metabolic and mitochondrial regulatory roles rather than a single, precise pathway, supporting a label focused on glycolysis regulation and energy metabolism rather than a narrow function.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016311","count":2},{"id":"GO:0007585","count":2},{"id":"GO:0006000","count":2},{"id":"GO:1904024","count":2},{"id":"GO:0033133","count":2}]},{"hash":"1305956185842465401","title":"Unknown","description":"The top terms are highly heterogeneous, spanning epigenetic modification, trafficking, transcription regulation, endosome dynamics, signal transduction, synaptic transmission, calcium signaling, telomere maintenance, plant hormone signaling, and plant cell wall biogenesis, with several obsolete terms. There is no clear, single shared function to unify the cluster, so the label Unknown with no confidence is appropriate.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034968","count":1},{"id":"GO:0001881","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0051036","count":1},{"id":"GO:0035023","count":1}]},{"hash":"468600028807964619","title":"Unknown","description":"The listed GO terms span plant glucosinolate metabolism and a wide range of animal developmental and cell-cycle processes (hepatocyte differentiation, lymphangiogenesis, various differentiation pathways, endoreduplication, mRNA stabilization), with no single cohesive function or species context linking them all. Therefore there is no meaningful label beyond Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019760","count":1},{"id":"GO:0070365","count":1},{"id":"GO:0048146","count":1},{"id":"GO:0001946","count":1},{"id":"GO:0033301","count":1}]},{"hash":"1069360875097287651","title":"Actin cytoskeleton remodeling and migration","description":"The cluster\u2019s GO terms mainly point to actin-related processes (actin cortical patch assembly, actomyosin contractile ring contraction, mitotic cytokinesis) and cell movement (mesenchyme migration, skeletal muscle fiber adaptation). This suggests a cohesive theme centered on actin cytoskeleton dynamics driving cell migration and division, with a few unrelated or historical terms present. Confidence: Medium","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090131","count":1},{"id":"GO:0043503","count":1},{"id":"GO:0016344","count":1},{"id":"GO:1904623","count":1},{"id":"GO:0009825","count":1}]},{"hash":"1532031876658484529","title":"Cellular Stress Response","description":"The cluster shows GO terms such as response to heat (GO:0009408) and response to ischemia (GO:0002931), plus regulation of reactive oxygen species and apoptotic processes, which together suggest a stress-related, cellular maintenance module. Some terms are obsolete or unrelated (e.g., toxin transport, Cajal body localization), but the prevalent signals point to a stress response function rather than a single specialized pathway.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1901998","count":3},{"id":"GO:1904871","count":3},{"id":"GO:1903427","count":3},{"id":"GO:0002931","count":3},{"id":"GO:0052212","count":3}]},{"hash":"421261874736443923","title":"Actin Cytoskeleton Remodeling and Cell Migration","description":"This cluster is dominated by GO terms related to the actin cytoskeleton and cell movement, including mesenchyme migration, actin cortical patch assembly, and actomyosin contractile ring\u2013driven cytokinesis, as well as skeletal muscle fiber adaptation. While a couple of terms are unrelated (serine biosynthesis, obsolete annotations), the overall pattern points to dynamic cytoskeletal remodeling and cellular migration/division. The label accordingly reflects the core function of the cluster.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006564","count":2},{"id":"GO:0090131","count":1},{"id":"GO:0043503","count":1},{"id":"GO:0016344","count":1},{"id":"GO:1904623","count":1}]},{"hash":"672003668942090390","title":"Skeletal muscle and nervous system development","description":"Based on the top GO terms, the dominant signal is sarcomere organization and skeletal muscle fiber development, indicating a muscle-structure\u2013related cluster. The presence of substantia nigra development and nervous system development terms adds a neural development dimension, suggesting some members may also engage in neural development pathways. The remaining terms (kinetochore localization, chromatin modification, adenosine biosynthesis, etc.) appear less representative for a small cluster and likely reflect broader cellular processes. Overall, the cluster most plausibly reflects skeletal muscle development with a secondary nervous system development component.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045214","count":3},{"id":"GO:0048741","count":3},{"id":"GO:0021762","count":3},{"id":"GO:0007399","count":2},{"id":"GO:0010719","count":2}]},{"hash":"1071002874929528281","title":"Neuronal microtubule dynamics and dendritic transport","description":"The terms cluster around microtubule cytoskeleton regulation and organization, including depolymerization, spindle polarity, and kinetochore attachments, together with neuron-specific processes like dendritic transport and neuron projection maintenance, suggesting a function centered on microtubule-based neuronal structure and cargo movement. A plant-related chloroplast movement term appears as an outlier but does not overturn the overall theme.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010938","count":3},{"id":"GO:0001560","count":3},{"id":"GO:0032487","count":3},{"id":"GO:0098971","count":3},{"id":"GO:0009904","count":3}]},{"hash":"1326909977318100616","title":"DNA Damage Response and Kinetochore Regulation","description":"The strongest signals are about DNA repair and mitosis: localization to the kinetochore, intra-S checkpoint signaling, and processing of DNA double-strand breaks via SDSA. These converge on cell-cycle control and genome maintenance. The other terms (EMT regulation, glucocorticoid signaling, hypertrophy, cocaine response) are more peripheral, likely reflecting broader stress-related regulation but do not define a single cohesive function.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0034501","count":3},{"id":"GO:0010719","count":2},{"id":"GO:0046086","count":2},{"id":"GO:1905205","count":2},{"id":"GO:0010791","count":2}]},{"hash":"387395081215620600","title":"Unknown","description":"The top terms cover diverse processes (cardiac myofibril assembly, cuticle development, kidney tubule development, nuclear import, calcium signaling, kinase regulation). There is no single shared function linking these proteins; the GO terms appear to reflect disparate roles rather than a coherent pathway.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055003","count":2},{"id":"GO:0097274","count":2},{"id":"GO:0008365","count":2},{"id":"GO:2001246","count":2},{"id":"GO:1905205","count":2}]},{"hash":"1561239704436489106","title":"Microtubule Dynamics and Neuronal Transport","description":"This cluster is driven by GO terms pointing to microtubule-based processes: mitotic spindle assembly and kinetochore attachment indicate spindle dynamics; anterograde dendritic transport and neuron projection maintenance reflect microtubule-dependent transport and structural maintenance in neurons. Additional terms like chloroplast movement also involve microtubule activity, suggesting a broad microtubule-dynamics theme across contexts. Confidence: Medium","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":2},{"id":"GO:0010938","count":1},{"id":"GO:0000743","count":1},{"id":"GO:0001560","count":1},{"id":"GO:0032487","count":1}]},{"hash":"1325173001785975618","title":"Mitotic Regulation and Cytokinesis","description":"The top GO terms are dominated by mitotic processes: localization to the kinetochore, regulation of CDK activity, mitotic cytokinesis checkpoint signaling, and maturation of the actomyosin contractile ring. These point to a coherent theme around cell division control. Some terms (Notch signaling, circadian rhythm, habituation, and JAK-STAT suppression) are broader or context-specific annotations, but they do not outweigh the core mitotic focus. Confidence reflects this core-to-periphery mix.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034501","count":3},{"id":"GO:0045736","count":3},{"id":"GO:0039563","count":2},{"id":"GO:0044878","count":2},{"id":"GO:1902406","count":2}]},{"hash":"1890478028758093160","title":"Neuronal glutamine metabolism and dopaminergic signaling","description":"The GO terms emphasize glutamine metabolism and dopaminergic synaptic transmission, pointing to neuronal metabolism and neurotransmission; oxidative stress and inflammatory response also fit neuronal stress contexts, though several terms are obsolete or non-specific. This combination best suggests a neural signaling/metabolic theme, despite some noise.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":1},{"id":"GO:0007338","count":1},{"id":"GO:0006954","count":1},{"id":"GO:0001963","count":1},{"id":"GO:0045560","count":1}]},{"hash":"185158279012340393","title":"Microtubule Cytoskeleton and Neuronal Projection Maintenance","description":"The GO terms cluster around microtubule dynamics and cytoskeletal organization, with specific emphasis on neuronal projections, dendritic transport, and cerebellar/neuronal structure, along with spindle/kinetochore MT interactions. This suggests a core function in MT-based cytoskeleton maintenance and neuronal projection upkeep.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010938","count":1},{"id":"GO:0000743","count":1},{"id":"GO:0001560","count":1},{"id":"GO:0032487","count":1},{"id":"GO:0098971","count":1}]},{"hash":"956092582867778092","title":"Unknown","description":"There are 3 proteins with 3 connecting edges and a single triangle, but no GO terms or functional annotations are provided to bind them to a common function, so no meaningful label can be assigned.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[]},{"hash":"1574864650900293157","title":"ECM remodeling and cell adhesion signaling","description":"These proteins cluster around extracellular matrix remodeling and adhesion-related signaling, evidenced by terms like extracellular matrix disassembly, regulation of cell adhesion molecule production, and protein kinase C signaling, with some supporting roles in protease activity regulation. While a few terms are obsolete or tangential, the core theme points to ECM remodeling and adhesion processes.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045541","count":1},{"id":"GO:0052547","count":1},{"id":"GO:0070528","count":1},{"id":"GO:0022617","count":1},{"id":"GO:0060355","count":1}]},{"hash":"2257642703810488766","title":"Actin Cytoskeleton Dynamics","description":"A set of terms centers on actin filament organization, cortical patches, contractile ring formation, cytokinesis, and actin-myosin\u2013driven movement and muscle adaptation, suggesting the proteins in this cluster largely participate in actin cytoskeleton remodeling and contractile processes. A couple of terms (e.g., meiotic chromosome movement) are less directly aligned but do not outweigh the dominant actin-centric theme.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090131","count":1},{"id":"GO:0043503","count":1},{"id":"GO:0016344","count":1},{"id":"GO:1904623","count":1},{"id":"GO:0009825","count":1}]},{"hash":"1828093659015488403","title":"Oocyte Maturation and Meiotic DNA Repair","description":"The top terms point to meiotic recombination and double-strand break repair via homologous recombination, along with ovarian follicle development and oocyte maturation. There are also DNA damage response signals (camptothecin/cisplatin) and transcription-related activity, suggesting these proteins function in meiosis-linked DNA repair and maturation of oocytes. This cohesive theme justifies a label centered on meiosis, DNA repair, and oocyte development.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0072757","count":1},{"id":"GO:0001541","count":1},{"id":"GO:0000709","count":1},{"id":"GO:0072719","count":1}]},{"hash":"1938171480706896150","title":"Unknown","description":"The top GO terms are highly diverse, spanning positive regulation of cell size, placenta development, glucose metabolism, transcription, signaling (cytokinin), endosome transport, yeast pseudohyphal growth, and even cocaine response. There is no single cohesive function or pathway tying these annotations together across the three proteins, suggesting this cluster does not reflect a specific, shared biological role.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045793","count":2},{"id":"GO:0001890","count":2},{"id":"GO:0006006","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0033160","count":2}]},{"hash":"2080823943736917189","title":"Unknown","description":"The top GO terms span endosomal transport, yeast pseudohyphal growth, Hedgehog-related neural patterning, calcium signaling, dopaminergic synaptic transmission, p53 signaling, NK T cell differentiation, neuron axonogenesis, oxidative stress responses, and cartilage condensation, showing no clear, single shared function tying all three proteins together. This absence of a cohesive theme supports labeling the cluster as Unknown. ","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":3},{"id":"GO:0007124","count":3},{"id":"GO:1901621","count":3},{"id":"GO:1904637","count":3},{"id":"GO:0001963","count":3}]},{"hash":"1441239989286401197","title":"Cell migration and division machinery","description":"These terms cluster around movement and cell-cycle related processes, including ameboidal migration, cell spreading, spindle/kinetochore dynamics, and phagosome maturation, with additional signaling and differentiation terms. The dominant theme appears to be cytoskeletal remodeling and vesicular trafficking linked to motility and division, despite some divergent terms.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1903215","count":3},{"id":"GO:0001667","count":3},{"id":"GO:0006878","count":3},{"id":"GO:0043316","count":3},{"id":"GO:1900026","count":3}]},{"hash":"978889842938659933","title":"Ribosome Biogenesis and Translation","description":"Top terms indicate a core link to ribosome assembly and protein synthesis, with rRNA processing (ITS1 cleavage) and translation being prominent. While several carbohydrate metabolism terms appear, they are less represented and likely incidental. Overall, the cluster appears to reflect ribosome biogenesis and translation functions.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0000023","count":1},{"id":"GO:0005978","count":1}]},{"hash":"182756757531823921","title":"Unknown","description":"The GO terms are highly diverse, spanning endosomal transport, fungal morphogenesis, neural development and signaling, calcium response, p53-mediated regulation, immune differentiation, neuron axonogenesis, and cartilage condensation. There is no single cohesive function that ties these proteins together, so a precise label cannot be assigned.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":3},{"id":"GO:0007124","count":3},{"id":"GO:1901621","count":3},{"id":"GO:1904637","count":3},{"id":"GO:0001963","count":3}]},{"hash":"1554818218673152023","title":"Unknown","description":"The terms span vascular development, DNA replication/transcription, ion transport, energy synthesis, and bacterial flagellum-related functions, with little overlap. There is no clear shared function uniting the proteins, so I label this cluster Unknown.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043536","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006814","count":1}]},{"hash":"222778239823819570","title":"Ubiquitin-Regulated Immune Signaling","description":"The top terms cluster around ubiquitination and regulatory signaling pathways (protein ubiquitination, autoubiquitination, NF-kappaB signaling, necroptosis regulation) with immune-related processes (V(D)J recombination) and additional signaling contexts (NOS activity regulation, Wnt catabolic process, synaptic vesicle transport). This suggests the proteins collectively participate in ubiquitin-mediated regulation of diverse signaling pathways, particularly related to immunity, rather than a single cohesive function. Confidence: Medium","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043123","count":2},{"id":"GO:0046621","count":2},{"id":"GO:0033151","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0038018","count":2}]},{"hash":"1042318528115975806","title":"Unknown","description":"Top GO terms point to a highly diverse set of functions, including transcription, nuclear transport regulation, endosomal trafficking, fungal pseudohyphal growth, Hedgehog-related signaling, calcium signaling, dopaminergic synaptic transmission, p53 pathway regulation, NK T cell differentiation, and CNS neuron axonogenesis. This wide dispersion suggests there is no single coherent function tying the proteins together, so a meaningful label cannot be assigned beyond Unknown.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0046826","count":3},{"id":"GO:2000641","count":2},{"id":"GO:0007124","count":2},{"id":"GO:1901621","count":2}]},{"hash":"1556348971995865518","title":"Unknown","description":"GO terms for this cluster are highly diverse, including neural development (axonogenesis, dopaminergic synaptic transmission, neural tube patterning) but also endosomal transport, immune differentiation, aging-related, and cartilage condensation terms. The lack of a single cohesive function across all three proteins means there isn\u2019t a reliable, representative label to assign.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":3},{"id":"GO:0007124","count":3},{"id":"GO:1901621","count":3},{"id":"GO:1904637","count":3},{"id":"GO:0001963","count":3}]},{"hash":"836214209392794013","title":"PKC signaling and ECM remodeling","description":"Proteins in this cluster are linked by signaling and regulatory processes that govern adhesion and extracellular matrix dynamics, highlighted by PKC signaling, regulation of protease activity, and extracellular matrix disassembly, with additional support from regulation of adhesion molecule production. While some terms seem tangential (developmental or obsolete processes), the dominant theme is signaling-driven control of cell\u2013matrix interactions and proteolytic remodeling.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045541","count":3},{"id":"GO:0052547","count":3},{"id":"GO:0070528","count":3},{"id":"GO:0022617","count":3},{"id":"GO:0060355","count":3}]},{"hash":"725577726075187695","title":"Neural development and signaling","description":"The terms point to neural development and neuronal signaling, notably CNS neuron axonogenesis, neural tube patterning regulation of Hedgehog signaling, and dopaminergic synaptic transmission. Endosomal transport and ionomycin-responsive calcium signaling align with neuronal signaling machinery, while unrelated terms like pseudohyphal growth and cartilage condensation suggest some annotation noise. Overall, the core theme is neural development and neurotransmission.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2000641","count":2},{"id":"GO:0007124","count":2},{"id":"GO:1901621","count":2},{"id":"GO:1904637","count":2},{"id":"GO:0001963","count":2}]},{"hash":"903509966829099522","title":"Unknown","description":"The GO terms are highly diverse, covering energy metabolism, ER-associated degradation, proteasome regulation, mitochondrial assembly, oxidative stress response, chromatin assembly, and transcriptional elongation, with no cohesive functional theme linking them. This makes it hard to assign a meaningful, specific label beyond Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046034","count":1},{"id":"GO:0071712","count":1},{"id":"GO:0033314","count":1},{"id":"GO:1901800","count":1},{"id":"GO:0034551","count":1}]},{"hash":"1815633986603658325","title":"Actin cytoskeleton remodeling","description":"The top GO terms cluster around actin dynamics and cell shape, including actin polymerization, branching, and assembly of filopodia, ruffles, and podosomes, as well as cell spreading, polarity maintenance, and junction assembly. These together indicate a coordinated program of actin cytoskeleton remodeling that shapes cell morphology and adhesion.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900026","count":2},{"id":"GO:0097178","count":2},{"id":"GO:0034260","count":2},{"id":"GO:0046847","count":2},{"id":"GO:0071963","count":2}]},{"hash":"896340777752688017","title":"Unknown","description":"This tiny cluster shows no cohesive biological theme; the top GO terms span proteasome core assembly, various stress responses (salt, cadmium), and multiple signaling pathways (Wnt/PCP, NF-kappaB, TNF, TCR, Fc-epsilon). With only three proteins and scattered terms, there isn't a common function that ties them together, so a single representative label is not supported.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0080129","count":1},{"id":"GO:0009651","count":1},{"id":"GO:0060071","count":1},{"id":"GO:0038095","count":1},{"id":"GO:0050852","count":1}]},{"hash":"360514588440745187","title":"DNA Repair and Immune Signaling","description":"The proteins show enrichment for base-excision repair, DNA ligation, and double-strand break repair via NHEJ, pointing to a DNA damage response role, while accompanying terms suggest immune-related processes (inflammatory response, somatic hypermutation, lymph node development) and regulatory ubiquitin-related deubiquitination. The mix indicates a functional link between DNA repair and immune signaling, though a few terms are less cohesive, likely reflecting pleiotropy. ","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006286","count":2},{"id":"GO:0007435","count":2},{"id":"GO:0006954","count":2},{"id":"GO:0061674","count":2},{"id":"GO:0006288","count":2}]},{"hash":"293645454235697476","title":"Unknown","description":"The GO terms are very heterogeneous, spanning nuclear RNA processing (splicing, mRNA export), chromatin assembly (CENP-A), ubiquitin-related regulation, cell cycle checkpoints, and various signaling and inflammatory processes. There is no clear, single functional theme tying these terms together for this cluster, so a precise label isn\u2019t supported. ","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070208","count":2},{"id":"GO:2000728","count":1},{"id":"GO:1904668","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0061641","count":1}]},{"hash":"2172906140771345780","title":"Unknown","description":"The Top Terms section is empty, so there is no GO-based signal to define a shared function for these proteins. With only 3 proteins and 3 edges (triangle count 1, max degree 2), there is insufficient functional evidence to assign a meaningful label.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[]},{"hash":"854392907184330946","title":"Neural development kinase signaling","description":"These proteins show a consistent signal for nervous system development and neuron projection development (GO:0007399, GO:0010976), along with protein autophosphorylation, suggesting kinase-based regulation in neural growth/signaling. Some other terms (nucleotide biosynthesis, responses to glucose/fatty acids) appear but likely represent noise or shared metabolic roles rather than the core neural function. With a small cluster of 3 proteins and phosphorylation-related terms as the strongest link, this label captures the main theme.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":2},{"id":"GO:0061508","count":2},{"id":"GO:0006186","count":2},{"id":"GO:0071398","count":2},{"id":"GO:0010976","count":2}]},{"hash":"1402178848302019270","title":"Unknown","description":"The GO terms are widely diverse and do not point to a single coherent function for this small cluster; they cover developmental regulation across different tissues, chromatin-related processes, and even plant-specific processes, with minimal connectivity (one edge, no triangles). As a result, it's not possible to assign a meaningful shared function label.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048742","count":1},{"id":"GO:0097421","count":1},{"id":"GO:0043985","count":1},{"id":"GO:0061246","count":1},{"id":"GO:0045600","count":1}]},{"hash":"2149752298329984600","title":"Unknown","description":"The GO terms are spread across endosomal transport regulation, neural development and signaling, immune differentiation, calcium response, and cartilage formation, with no single cohesive function tying the proteins together. There isn\u2019t a clear shared theme to justify a more specific label, so Unknown is appropriate.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":3},{"id":"GO:0007124","count":3},{"id":"GO:1901621","count":3},{"id":"GO:1904637","count":3},{"id":"GO:0001963","count":3}]},{"hash":"604604551631256344","title":"Unknown","description":"The top GO terms show a broad mix of endosomal transport, neural development, signaling, immune differentiation, and cartilage formation, with no single cohesive function tying the proteins together. This lack of a unifying theme supports labeling the cluster Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000641","count":3},{"id":"GO:0007124","count":3},{"id":"GO:1901621","count":3},{"id":"GO:1904637","count":3},{"id":"GO:0001963","count":3}]},{"hash":"1264466952250548026","title":"Unknown","description":"The top GO terms span many unrelated processes (mitochondrial targeting, migration, copper homeostasis, degranulation, phagosome maturation, Wnt signaling, differentiation, and mitosis), showing no cohesive function; with no edges, a precise label cannot be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903215","count":1},{"id":"GO:0001667","count":1},{"id":"GO:0006878","count":1},{"id":"GO:0043316","count":1},{"id":"GO:1900026","count":1}]},{"hash":"1139875655233383721","title":"Neuronal development and signaling","description":"This cluster shows several nervous-system\u2013related terms, including CNS projection neuron axonogenesis, dopaminergic synaptic transmission, and neural tube patterning, suggesting a core focus on neuronal development and signaling. Additional terms related to endosome transport and calcium signaling align with neuronal trafficking and signaling in neurons, while a few terms pertain to non-neural processes, indicating some heterogeneity. Overall, the strongest theme is neural development and signaling.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000641","count":1},{"id":"GO:0007124","count":1},{"id":"GO:1901621","count":1},{"id":"GO:1904637","count":1},{"id":"GO:0001963","count":1}]},{"hash":"821695889393092381","title":"Neural Development and Signaling","description":"Top GO terms cluster around nervous system processes, including pain perception, dopaminergic synaptic transmission, and CNS neuron axonogenesis, plus neural tube patterning. While a few terms touch on endosomal transport, ionomycin response, and NK T cell differentiation, the dominant theme is neural development and neurotransmission, suggesting the proteins function together in neural signaling and development.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019233","count":2},{"id":"GO:0007275","count":2},{"id":"GO:2000641","count":1},{"id":"GO:0007124","count":1},{"id":"GO:1901621","count":1}]},{"hash":"1499494175844623255","title":"Unknown","description":"The top terms are a mix of immune-related processes (platelet maturation, B cell proliferation, dendritic cell cytokine regulation, TLR signaling) and unrelated developmental/neuro/kinase terms (lung connective tissue development, otolith morphogenesis, cellular response to dopamine, regulation of protein kinase activity). There is no clear, single function tying these few proteins together, so a coherent label cannot be assigned.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0036345","count":1},{"id":"GO:0002730","count":1},{"id":"GO:1903215","count":1},{"id":"GO:1902499","count":1},{"id":"GO:0002322","count":1}]},{"hash":"614572552480739431","title":"Unknown","description":"These three proteins do not share a coherent functional theme based on the top GO terms. The terms span immune signaling (TLR pathways, B cell proliferation), neural/dopaminergic response, tissue development (lung connective tissue), and developmental morphogenesis (otolith morphogenesis), plus regulatory processes (protein kinase activity, autoubiquitination). With no edges and no consistent functional signal, there is no clear label to assign.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002730","count":1},{"id":"GO:1903215","count":1},{"id":"GO:1902499","count":1},{"id":"GO:0002322","count":1},{"id":"GO:1903351","count":1}]},{"hash":"255871240058805734","title":"Cytoskeletal organization and spindle assembly","description":"The listed GO terms cluster around cytoskeletal dynamics and spindle apparatus formation: actomyosin contractile ring, actin filament bundle assembly, regulation of cell shape, centrosome localization, and meiotic spindle localization, plus chromosome movement in meiosis. Together, these point to roles in organizing the cytoskeleton and the spindle during cell division or meiosis. Some terms appear as outliers (e.g., histamine response, cardiac myofibril assembly), but the core signal is cytoskeletal/spindle related.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055003","count":1},{"id":"GO:0060292","count":1},{"id":"GO:0007292","count":1},{"id":"GO:0071519","count":1},{"id":"GO:0008360","count":1}]},{"hash":"2082545583071129506","title":"Unknown","description":"There are no shared GO terms or connections (Top Terms is empty and there are no edges or triangles), so a common function cannot be inferred from the data available. The cluster label is Unknown to reflect this lack of evidence.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"47103136121240441","title":"Unknown","description":"There are no GO terms or functional signals provided for this cluster (Edges: 0, Top Terms: empty), so no common function can be inferred. The mention of ReCIPE re-additions suggests curation rather than functional annotation, leaving the cluster without a representative theme.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"562064661414401139","title":"Ubiquitin-Dependent Protein Turnover and Signaling","description":"The GO terms point to a common thread of ubiquitin-mediated protein degradation, including ubiquitin-dependent proteolysis (ERAD, general protein catabolism, autoubiquitination) and histone ubiquitination, linked to regulation of signaling pathways (TNF, JNK) and receptor turnover (Wnt). While a few terms touch on chromatin or immune-related processes, the dominant theme ties ubiquitin-dependent turnover to signaling control.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046621","count":2},{"id":"GO:0033151","count":2},{"id":"GO:0038018","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0030433","count":2}]},{"hash":"1412343989703027993","title":"Renin-angiotensin system and kidney regulation","description":"The top GO terms are dominated by renin-angiotensin\u2013related processes (blood volume regulation, angiotensin maturation, aldosterone production) and kidney development (mesonephros), pointing to renal function and hormonal regulation of cardiovascular physiology as the core theme. Some terms touch on unrelated areas, but the prevailing pattern supports a kidney/RAS-focused cluster label.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002016","count":1},{"id":"GO:0070305","count":1},{"id":"GO:0016540","count":1},{"id":"GO:0019886","count":1},{"id":"GO:0002003","count":1}]},{"hash":"2109938362698153713","title":"Protein glycosylation","description":"This cluster shows enrichment for glycosylation-related processes (N-linked and O-linked glycosylation), suggesting a shared involvement in protein glycosylation pathways. The magnesium transport term appears unrelated and the small cluster with a single edge provides limited evidence, so the label is plausible but not strongly supported. ","confidence":"Low","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0018279","count":1},{"id":"GO:0035269","count":1},{"id":"GO:0015693","count":1}]},{"hash":"627257814809126626","title":"Thermosensory signaling and ionic membrane potential regulation","description":"The top GO terms cluster around temperature-related responses (thermosensory behavior, diet-induced thermogenesis, response to capsazepine) and neural excitability (sodium ion import, regulation of membrane potential). Although there are a couple of development terms, the dominant signal points to proteins involved in sensing temperature and regulating neuronal membrane potential, i.e., thermosensory signaling and ionic control in neurons.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071642","count":1},{"id":"GO:1901594","count":1},{"id":"GO:0098719","count":1},{"id":"GO:0040040","count":1},{"id":"GO:0071651","count":1}]},{"hash":"407573070032379003","title":"Central carbon metabolism","description":"The Top Terms include succinyl-CoA metabolic process, the TCA cycle, and acetyl-CoA biosynthetic process, which together point to core energy/central carbon metabolism as the main shared function of this cluster. The other terms (neuroblast division, cytokinin signaling, chlorophyll regulation, etc.) appear less coherent with metabolism and may reflect annotation noise. Thus, the strongest, most representative theme is central carbon metabolism, albeit with limited support from non-metabolic terms.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006104","count":1},{"id":"GO:0006099","count":1},{"id":"GO:0006085","count":1},{"id":"GO:0055059","count":1},{"id":"GO:0009736","count":1}]},{"hash":"1079747755177571965","title":"Neuronal Synaptic Signaling and Trafficking","description":"The top GO terms cluster around synaptic transmission (glutamatergic and dopaminergic) and neuronal communication, with additional hints of endosomal transport and general cellular signaling. This suggests a theme of proteins involved in neuronal signaling and vesicle trafficking, rather than a single specific pathway. Confidence: Medium","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007118","count":2},{"id":"GO:0035249","count":2},{"id":"GO:2000641","count":1},{"id":"GO:0007124","count":1},{"id":"GO:0071642","count":1}]},{"hash":"1122807763880297853","title":"Histone demethylation and chromatin regulation","description":"Top terms are dominated by histone demethylation (H3-K4/9/27) and chromatin-related processes (chromosome condensation, chromatin binding, RITS complex localization), pointing to epigenetic regulation of gene expression as the cluster\u2019s core function. Some brain development terms appear but likely reflect broader developmental contexts rather than a specific activity of these proteins. High","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021555","count":1},{"id":"GO:0033169","count":1},{"id":"GO:0034630","count":1},{"id":"GO:0060763","count":1},{"id":"GO:0035563","count":1}]},{"hash":"2246627229418065621","title":"Unknown","description":"The terms are highly diverse (dephosphorylation, membrane repolarization, various biosynthetic and transport processes, neuromuscular and neural development, immune differentiation, and catabolic processes) with no coherent functional theme linking the proteins. There are no edges or clusters connecting annotations, so no specific common function can be inferred.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016311","count":1},{"id":"GO:0086009","count":1},{"id":"GO:0051479","count":1},{"id":"GO:0009103","count":1},{"id":"GO:0002028","count":1}]},{"hash":"376338428514109420","title":"Oxidative stress response and ER protein folding","description":"The top GO terms point to cellular response to oxidative stress and protein folding in the endoplasmic reticulum, along with redox-related processes such as deglutathionylation. This suggests the cluster comprises proteins involved in managing oxidative stress and maintaining protein quality through ER-associated folding and redox regulation.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0033158","count":1},{"id":"GO:0034599","count":1},{"id":"GO:1903206","count":1},{"id":"GO:0018401","count":1}]},{"hash":"594746851428372200","title":"Lung morphogenesis and basement membrane remodeling","description":"The strongest consistent theme among the top GO terms is epithelial tube branching involved in lung morphogenesis and basement membrane disassembly, which together point to a developmental module focused on lung tissue remodeling. Other terms like memory or T cell cytotoxicity appear less connected to this core function, and the small network supports a narrowly focused cluster.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034769","count":1},{"id":"GO:0051603","count":1},{"id":"GO:0050790","count":1},{"id":"GO:0097067","count":1},{"id":"GO:0060441","count":1}]},{"hash":"1635558877346939362","title":"Calcium-Driven Immune and Neural Signaling","description":"The cluster's top GO terms cluster around calcium signaling, including calcium-regulated lysosome exocytosis, store-operated calcium channel activation, and cellular responses to calcium. Immune-related terms (B and T cell signaling) and neural-related terms (dendrite extension, glial apoptosis regulation) suggest calcium-dependent signaling is a unifying theme across immune and neural contexts, despite some outlier terms (lipid and tRNA processing). This makes calcium-centric signaling a concise, representative label.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1990927","count":1},{"id":"GO:2000235","count":1},{"id":"GO:0034351","count":1},{"id":"GO:0002322","count":1},{"id":"GO:0002692","count":1}]},{"hash":"1540858371665113769","title":"Unknown","description":"The terms include basement membrane disassembly and epithelial tube branching in lung morphogenesis, plus neuropeptide catabolic processes, autophagy regulation, memory, thyroid hormone response, and cytotoxicity. This mix does not reveal a single coherent functional theme for the cluster, so the label Unknown with confidence None.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034769","count":1},{"id":"GO:0051603","count":1},{"id":"GO:0050790","count":1},{"id":"GO:0097067","count":1},{"id":"GO:0060441","count":1}]},{"hash":"1385899058326040160","title":"Amino acid catabolism and NAD precursor biosynthesis","description":"The top GO terms are dominated by amino acid catabolic processes (glycine, L-alanine, L-tryptophan, L-kynurenine) and a related biosynthetic step (quinolinate biosynthesis) that feeds NAD production, suggesting a shared theme around amino-acid breakdown and NAD cofactor biosynthesis. A few terms (Notch signaling, mitochondrial tRNA thio-modification) seem less connected, indicating some noise or multifunctional proteins. ","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019265","count":1},{"id":"GO:0019805","count":1},{"id":"GO:0018283","count":1},{"id":"GO:0019448","count":1},{"id":"GO:0007219","count":1}]},{"hash":"1721107001574094609","title":"Iron Transport and Homeostasis","description":"The top terms point to iron metabolism, including detoxification of iron ions, iron transport, and siderophore-iron import, indicating a coherent theme of iron handling. A few outliers (e.g., chromosome condensation, regulation of proliferation) likely reflect annotation noise or unrelated functions, but the dominant signal supports iron homeostasis as the cluster\u2019s main function.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990461","count":1},{"id":"GO:0006880","count":1},{"id":"GO:0097286","count":1},{"id":"GO:1904234","count":1},{"id":"GO:1904231","count":1}]},{"hash":"1587704325651514050","title":"Unknown","description":"The GO terms are very diverse, spanning redox/detoxification (oxidation-reduction, cellular oxidant detoxification), multiple catabolic pathways (beta-ketoadipate, stilbene, glucuronoside, prostaglandin), plus cell adhesion, host-symbiont entry, locomotory behavior, and insulin regulation. There is no clear, cohesive function that ties these terms together, so a single interpretable label cannot be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0007155","count":2},{"id":"GO:0042952","count":2},{"id":"GO:1905344","count":2}]},{"hash":"1385340179792464607","title":"Amino acid and nucleotide metabolism","description":"This cluster includes GO terms spanning peptide catabolic processes and proteolysis (protein turnover) alongside amino acid biosynthetic pathways (arginine, lysine) and purine nucleobase metabolic processes, plus related catabolic routes (ureide/allantoin). The mix suggests a broader metabolic/turnover theme rather than a single specific function, making \"Amino acid and nucleotide metabolism\" a concise, representative label. The calcium-transport-related lysosome exocytosis term is less central but can connect to vesicle-mediated turnover, supporting a metabolism/turnover theme.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043171","count":1},{"id":"GO:0019877","count":1},{"id":"GO:0009442","count":1},{"id":"GO:0019878","count":1},{"id":"GO:0006526","count":1}]},{"hash":"1652053822128919900","title":"Chromatin Organization and Histone Modification","description":"All four proteins are annotated with GO terms centered on chromatin biology: chromatin organization, DNA replication-dependent chromatin assembly, subtelomeric heterochromatin formation, and histone acetylation. Together, these suggest a chromatin-associated group, likely involving histone chaperones or chromatin modifiers active during DNA replication and heterochromatin formation. The label aims to be concise and representative of this shared function.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006348","count":1},{"id":"GO:0006335","count":1},{"id":"GO:0006336","count":1},{"id":"GO:0016573","count":1}]},{"hash":"1477922783247862011","title":"Unknown","description":"No common GO terms or network connections are observed (0 edges, 0 triangles). Although ReCIPE added 20 proteins, there is still no consistent function linking the proteins, so a specific label cannot be assigned. Therefore, the cluster is Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"261726862985306835","title":"Ubiquitin-Mediated Immune Signaling","description":"The top GO terms cluster around protein ubiquitination (including autoubiquitination) and immune-related regulation, such as negative regulation of RIG-I signaling, adaptive immune response, and NF-kappaB pathway modulation. This suggests the proteins participate in ubiquitin-dependent control of innate and adaptive immune signaling routes, rather than a single enzymatic function. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0039536","count":2},{"id":"GO:0002250","count":2},{"id":"GO:0043123","count":1},{"id":"GO:0046621","count":1}]},{"hash":"1327904723918457471","title":"Unknown","description":"The dataset provides no GO terms or functional signals to connect the proteins; Top Terms are empty. With only one edge and no shared process or function evident, there isn't a clear theme to label the cluster.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[]},{"hash":"2238368420623522795","title":"Ubiquitin-mediated NF-kB signaling and protein turnover","description":"The top GO terms cluster around ubiquitination (protein ubiquitination, autoubiquitination), ERAD, and sumoylation, with several entries related to NF-kappaB and TNF signaling, plus a Wnt receptor catabolic process. This suggests a shared theme of ubiquitin-dependent regulation of signaling pathways and protein turnover, despite a few peripheral terms like V(D)J recombination and NOS regulation. ","confidence":"High","size":3,"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:1903265","count":3},{"id":"GO:0016925","count":2},{"id":"GO:0043123","count":2}]},{"hash":"521967395874226075","title":"Ubiquitin-Dependent Signaling and Regulation","description":"The set of GO terms shows a strong emphasis on ubiquitin biology\u2014positive regulation of ubiquitin-protein transferase activity, protein autoubiquitination, and free ubiquitin chain polymerization\u2014with immune signaling terms (TRIF-dependent TLR and T cell receptor signaling) suggesting regulation of signaling pathways via ubiquitination. A few terms relate to DNA repair or neuronal development but are less central to the cluster's core theme, which is ubiquitin-mediated control of signaling.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035666","count":1},{"id":"GO:0070911","count":1},{"id":"GO:0051443","count":1},{"id":"GO:0051865","count":1},{"id":"GO:0050852","count":1}]},{"hash":"1604037588236502817","title":"Nuclear transcriptional regulation under oxidative stress","description":"The top GO terms point to repression of RNA Pol II-driven transcription, plus nuclear transport and redox-related processes such as deglutathionylation and cellular oxidative stress response. This suggests a theme where transcriptional control in the nucleus is linked to redox signaling and oxidative stress, making a concise label around nuclear transcriptional regulation in redox contexts appropriate, even though some terms are obsolete.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0033158","count":1},{"id":"GO:0034599","count":1},{"id":"GO:0055114","count":1},{"id":"GO:1903206","count":1}]},{"hash":"960871557410439091","title":"Glycolysis and glucose metabolism","description":"The top terms are dominated by glycolytic and glucose/fructose metabolic processes (glycolytic process, fructose metabolic process, negative regulation of glycolytic process, and negative regulation of glucose catabolic to lactate via pyruvate), suggesting the cluster centers on energy metabolism through glycolysis. Some terms about brain development or mitophagy are present but appear less central. This makes the glycolysis/glucose metabolism theme the most representative.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016311","count":1},{"id":"GO:0007585","count":1},{"id":"GO:0006000","count":1},{"id":"GO:1904024","count":1},{"id":"GO:0033133","count":1}]},{"hash":"1705188869791555636","title":"Membrane Transporters and Stress Response","description":"The top GO terms point to diverse membrane-based transport activities (glycine betaine, taurine, cobalt ion, monoatomic anion, xenobiotic) plus lipid-related movement (ceramide translocation) and even cytochrome complex assembly, all suggesting membrane-associated transport and respiratory processes, with SOS response highlighting a stress-adaptation angle. The cluster thus seems centered on membrane transport and related stress responses, though the signals are varied, giving a Moderate level of confidence.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0031460","count":2},{"id":"GO:0099133","count":2},{"id":"GO:0006824","count":2},{"id":"GO:0099040","count":2}]},{"hash":"1689965514872358508","title":"Glycolysis and terpenoid biosynthesis","description":"The top GO terms cluster around central carbon metabolism, notably glycolytic process and terpenoid (isoprenoid) biosynthesis, with additional glyoxylate-related metabolism. A few outlier neuronal development terms appear among the list, suggesting possible annotation noise. Overall, the proteins seem linked to metabolic pathways for energy production and terpenoid precursor synthesis, justifying a metabolism-focused label.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046487","count":1},{"id":"GO:0016114","count":1},{"id":"GO:0052865","count":1},{"id":"GO:0061732","count":1},{"id":"GO:0005999","count":1}]},{"hash":"665070393124951975","title":"Ribosome biogenesis and translation regulation","description":"This cluster centers on ribosome production and protein synthesis. It is enriched for translation and ribosome assembly terms (translation, ribosome assembly, preribosome large subunit assembly) as well as positive regulation of ribosome biogenesis and negative regulation of translation, indicating a cohesive set of proteins involved in ribosome biogenesis and control of translation. Some transcription-related terms are present, and a response to antibiotic term may reflect ribosome-associated processes, but the dominant theme remains ribosome biogenesis and translation regulation.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0090070","count":1},{"id":"GO:1902626","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0006353","count":1}]},{"hash":"743864495819093003","title":"Unknown","description":"No GO terms are reported for this cluster, so I cannot identify a common function. With only 3 proteins and 3 edges, there is insufficient functional signal to assign a meaningful label.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[]},{"hash":"1841512653053892443","title":"Brain energy metabolism and development","description":"The cluster shows core metabolic processes (glycolysis, TCA cycle, glucose metabolism, and pyruvate-to-acetyl-CoA regulation) alongside neural development terms (pyramidal neuron development, cerebellar cortex development, olfactory bulb mitral cell layer development), suggesting proteins involved in brain energy metabolism in the context of neural differentiation and brain region development. Confidence: Medium","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":1},{"id":"GO:0021860","count":1},{"id":"GO:0046487","count":1},{"id":"GO:0061732","count":1},{"id":"GO:0009083","count":1}]},{"hash":"858325283385436411","title":"Translation regulation and immune signaling","description":"The terms cluster around post-transcriptional control: translational elongation and negative regulation of cytoplasmic translation, plus RNA processing processes (snoRNA splicing, deadenylation-independent decay, and pre-mRNA cleavage). There are also immune/stress signaling cues (p38 MAPK cascade, glucocorticoid response) and cues for immune cell differentiation (T cell/T cell proliferation, monocyte differentiation). This suggests a cluster focused on how gene expression is controlled at the RNA level in immune and stress contexts.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000766","count":1},{"id":"GO:0045647","count":1},{"id":"GO:0038066","count":1},{"id":"GO:0034247","count":1},{"id":"GO:0042129","count":1}]},{"hash":"1973042966818443016","title":"Antiviral innate immunity with NF-kB signaling and autophagy","description":"The top GO terms point to antiviral defense and inflammatory signaling, including canonical NF-kB activation, defense response to virus, and innate immune response, with autophagy also represented. Additional terms indicate host suppression of viral processes and broader immune signaling, suggesting a cohesive role in innate antiviral defense and related cellular quality-control mechanisms.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043123","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0046597","count":2},{"id":"GO:0032897","count":2},{"id":"GO:0031664","count":2}]},{"hash":"1710059141999134257","title":"Cilium and flagellum assembly and movement","description":"The GO terms clustered around cilium/axoneme biology, including sperm flagellum motility, epithelial cilium movement, axoneme assembly, and regulation of cilium movement. The presence of tubulin PTMs (polyglycylation and polyglutamylation) further ties these proteins to microtubule-based motility in cilia/flagella, especially in sperm. This cohesive theme points to cilium/flagellum structure and motility as the core function of the cluster.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0003353","count":2},{"id":"GO:0030516","count":2},{"id":"GO:0018094","count":2},{"id":"GO:0018095","count":2},{"id":"GO:0007288","count":2}]},{"hash":"61434286302385911","title":"Unknown","description":"The two top GO terms do not reveal a coherent shared function for the cluster: one describes tail-anchored membrane protein insertion into the ER, the other a plant-specific root hair elongation process. With such sparse and disparate terms, there isn\u2019t a clear common function to label the cluster. ","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071816","count":1},{"id":"GO:0048767","count":1}]},{"hash":"367876573081285903","title":"mRNA Splicing and Decay Regulation","description":"Genes in this cluster cluster around post-transcriptional RNA processing: spliceosome-mediated splicing, regulation of splicing, mRNA stability and decay surveillance, and RNA silencing, indicating a cohesive theme of mRNA maturation and quality control. Some developmental terms appear but are not central to the core function. ","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":2},{"id":"GO:0006378","count":2},{"id":"GO:1900363","count":1},{"id":"GO:0048025","count":1},{"id":"GO:0035278","count":1}]},{"hash":"812521603359071467","title":"Post-transcriptional RNA regulation","description":"This cluster is enriched for GO terms related to mRNA processing, splicing, modification, stability, and translation control (including alternative splicing, miRNA-mediated silencing, and EIF4F complex assembly), pointing to post-transcriptional regulation of gene expression.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":2},{"id":"GO:0048025","count":2},{"id":"GO:0035278","count":2},{"id":"GO:0010610","count":2},{"id":"GO:0016556","count":2}]},{"hash":"2252265179580043426","title":"Unknown","description":"The Top Terms are empty and there are no edges or triangles connecting the three proteins, so there is no clear shared function to define a label. Unknown is appropriate when no GO-term signal or network connectivity is evident.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1659908856110927254","title":"Mitochondrial membrane regulation and matrix import","description":"The top GO terms are dominated by mitochondrial-specific processes, notably regulation of mitochondrial membrane permeability and protein import into the mitochondrial matrix, pointing to a shared mitochondrial function. Some other terms touch lipid metabolism and cell-cycle regulation, which can be connected to mitochondrial signaling, but the core signal remains mitochondrial membrane dynamics and import. Confidence: High","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":1},{"id":"GO:2000134","count":1},{"id":"GO:0070940","count":1},{"id":"GO:1903740","count":1},{"id":"GO:0010867","count":1}]},{"hash":"988373731456458668","title":"Unknown","description":"Top Terms are empty and there are no edges or shared annotations to define a common function, despite multiple proteins listed. Without any cohesive functional signal, a meaningful label cannot be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1133473142099256372","title":"Mitochondrial calcium signaling in insulin secretion","description":"The GO terms highlight mitochondrial calcium handling (calcium import into the mitochondrion; positive regulation of mitochondrial calcium ion concentration) alongside positive regulation of insulin secretion, suggesting these proteins function together in a mitochondrial calcium\u2013dependent pathway that promotes insulin release.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032024","count":1},{"id":"GO:0051561","count":1},{"id":"GO:0036444","count":1},{"id":"GO:0035786","count":1}]},{"hash":"751841662075377743","title":"Sterol Metabolism and Cholesterol Homeostasis","description":"The cluster\u2019s GO terms cluster around sterol biosynthesis, sterol transport, cholesterol response, and lipid trafficking (including ER-Golgi ceramide transport and nuclear pore localization), with a note on insulin signaling regulation. This points to a cohesive lipid/sterol metabolism theme, making cholesterol homeostasis a fitting label.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071397","count":1},{"id":"GO:0046628","count":1},{"id":"GO:0015918","count":1},{"id":"GO:0034727","count":1},{"id":"GO:0090204","count":1}]},{"hash":"915235509257196063","title":"Telomere maintenance and chromatin assembly","description":"The terms strongly point to nuclear/chromatin biology: telomere-associated processes (telomeric D-loop disassembly, regulation of protein localization to telomere), nucleosome assembly, and DNA structural features like G-quadruplex formation, plus transcription-related activities (snRNA transcription). Plant-specific signals (cytokinin pathway) and osmotic stress response appear secondary but do not override the core chromatin/telomere theme. This supports a label focused on telomere maintenance and chromatin dynamics.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0061820","count":3},{"id":"GO:0009736","count":3},{"id":"GO:1901347","count":3},{"id":"GO:0072362","count":3},{"id":"GO:0006334","count":3}]},{"hash":"1757598914752063157","title":"Unknown","description":"There are no GO terms or functional signals provided for this cluster (no edges, no triangles, and an empty Top Terms list), so there is no basis to infer a shared function. Therefore a reliable label cannot be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]}]