[{"hash":"2008324902013083412","title":"Chloroplast Translation and Photosynthesis","description":"This cluster is dominated by terms tied to chloroplast functions: translation and translational termination, photosynthesis and nonphotochemical quenching, and the respiratory electron transport chain, all pointing to chloroplast gene expression and energy metabolism. A few terms (e.g., viral genome replication) are outliers, but the core signal supports a chloroplast-centric module. ","confidence":"Medium","size":29,"edges":358,"triangles":2619,"max_degree":28,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0051301","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0010196","count":4},{"id":"GO:0015979","count":4}]},{"hash":"1889197376753354729","title":"Steroid and retinoid metabolism with development","description":"The cluster\u2019s top GO terms center on steroid hormone biosynthesis/metabolism (glucocorticoid, C21-steroid, androgen), retinoic acid biosynthesis, and lipid-related processes (very long-chain fatty acids, melanin biosynthesis, phylloquinone/acetoin catabolism) along with a developmental term (lung development). This pattern suggests a cohesive metabolic module coordinating steroid and retinoid signaling with developmental or tissue-specific processes, even though some terms are peripheral. Confidence in a coherent theme is Medium.","confidence":"","size":29,"edges":352,"triangles":2493,"max_degree":28,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0042376","count":28},{"id":"GO:0045150","count":28},{"id":"GO:0042761","count":28},{"id":"GO:0030324","count":28},{"id":"GO:0002138","count":28}]},{"hash":"2032672225188575269","title":"Diverse small-molecule catabolism","description":"The top GO terms are dominated by catabolic and metabolic processes for a variety of small organic molecules (alkaloids, retinoic acid, bile acids, triglycerides), indicating the cluster is centered on broad detoxification/metabolism of diverse compounds rather than a single pathway.","confidence":"Medium","size":29,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046232","count":10},{"id":"GO:0033280","count":10},{"id":"GO:0009822","count":9},{"id":"GO:0006641","count":9},{"id":"GO:0071615","count":9}]},{"hash":"1112674360083061461","title":"Ribosome Biogenesis and Translation","description":"The majority of enriched GO terms center on ribosome production and function (ribosome biogenesis, translation, cytoplasmic translation, SSU-rRNA maturation, ribosomal subunit export), indicating this cluster mainly reflects components involved in assembling and operating ribosomes; a few terms like cell cycle and cell septum assembly are peripheral.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0000055","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0000462","count":4},{"id":"GO:0090529","count":3}]},{"hash":"590030997809617233","title":"Mitotic spindle and chromosome dynamics","description":"This cluster is dominated by GO terms related to mitosis and microtubule function: mitotic spindle assembly, microtubule-based movement, microtubule severing, cell division, and CENP-A\u2013chromatin assembly\u2014all core to chromosome segregation. A few terms (ER/Golgi transport, ubiquitin-dependent ERAD, TGF-beta response) are less directly tied but may reflect broader cell-cycle coordination. Overall, the proteins likely participate in mitotic machinery and chromosome dynamics.","confidence":"High","size":29,"edges":16,"triangles":5,"max_degree":5,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0090307","count":7},{"id":"GO:0051260","count":6},{"id":"GO:0030433","count":6},{"id":"GO:0007018","count":6},{"id":"GO:0006351","count":5}]},{"hash":"1332691502767625797","title":"DNA Repair and Telomere Maintenance","description":"The cluster is dominated by GO terms tied to genome stability: mismatch repair, regulation of the cell cycle, and especially telomerase-related processes (telomerase holoenzyme assembly and telomere maintenance via telomerase). This suggests the proteins function together in DNA repair and telomere maintenance pathways, despite some outliers (e.g., placenta development, xenobiotic response) that may reflect broader or incidental annotations.","confidence":"High","size":29,"edges":224,"triangles":664,"max_degree":26,"top_function":"protein folding","top_go_terms":[{"id":"GO:0071157","count":9},{"id":"GO:0006298","count":9},{"id":"GO:0006457","count":9},{"id":"GO:1903660","count":8},{"id":"GO:0033160","count":8}]},{"hash":"1188753479171535941","title":"Wnt Regulation, Immune Signaling, and Proteolysis","description":"The cluster is enriched for both positive and negative regulation of canonical Wnt signaling, plus immune signaling pathways (T cell receptor and Fc-epsilon receptor signaling) and proteolysis-related processes (SCF-dependent ubiquitin-protein degradation and APC-dependent catabolic processes). This combination suggests a coherent module where signal transduction intersects with protein turnover, especially in immune-related contexts and cell-cycle regulation.","confidence":"High","size":29,"edges":183,"triangles":587,"max_degree":26,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0090090","count":9},{"id":"GO:0050852","count":9},{"id":"GO:0090263","count":9},{"id":"GO:0051436","count":9},{"id":"GO:0010950","count":8}]},{"hash":"857229497949668030","title":"Transcription Regulation and RNA Processing","description":"The top GO terms cluster around gene expression control and RNA maturation, including negative regulation of transcription by RNA polymerase II, DNA-templated transcription, translation, regulation of alternative mRNA splicing via spliceosome, and box C/D snoRNP/snoRNA assembly, highlighting a theme of transcriptional control and RNA processing; ancillary terms like viral process and ER protein folding fit within broader cellular housekeeping. ","confidence":"Medium","size":29,"edges":8,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0045454","count":3},{"id":"GO:0034975","count":3},{"id":"GO:0006412","count":2}]},{"hash":"755887213601946082","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0090615","count":3},{"id":"GO:0090617","count":3},{"id":"GO:0042793","count":3},{"id":"GO:1905639","count":3},{"id":"GO:1900865","count":3}]},{"hash":"2210197352720338338","title":"Vesicle trafficking and cytoskeletal remodeling","description":"Most terms point to vesicle trafficking, exocytosis, and endosome\u2013lysosome transport, together with small GTPase\u2013regulated cytoskeletal remodeling (cell migration, podosome, dendritic spine development). This suggests a theme of membrane trafficking coupled to actin dynamics, despite some liver-specific annotations that may reflect broader secretory pathway roles. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051131","count":2},{"id":"GO:0097284","count":1},{"id":"GO:0045956","count":1},{"id":"GO:1902824","count":1},{"id":"GO:0007264","count":1}]},{"hash":"1672694123662617731","title":"ABA signaling and cuticle biosynthesis in plants","description":"The top GO terms cluster around abscisic acid-activated signaling, regulation of wax and cutin biosynthesis, and plant development (floral meristem growth, multicellular development), with contributions from transcriptional regulation. This points to a coherent plant-specific theme: hormone signaling (ABA) coordinating development and construction of the cuticle, including wax and cutin biosynthetic processes. An outlier term about host-mediated activation of viral replication is present but does not redefine the cluster\u2019s core function.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":4},{"id":"GO:0009738","count":3},{"id":"GO:0044829","count":2},{"id":"GO:0007275","count":2},{"id":"GO:1904276","count":2}]},{"hash":"97941277645832635","title":"TLR Signaling and Antigen Presentation","description":"The top GO terms are centered on innate immune signaling (defense response to virus, innate immune response, TLR4 and TLR10 signaling, I-kappaB phosphorylation) and processes related to dendritic cell function and MHC class I biosynthesis, all pointing to Toll-like receptor\u2013mediated immune activation and antigen presentation; a few neuronal terms may reflect multifunctional proteins but do not override the main immune theme. ","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051607","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0006469","count":3},{"id":"GO:0045345","count":2},{"id":"GO:0002730","count":2}]},{"hash":"1210201269007486852","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090617","count":7},{"id":"GO:0042793","count":7},{"id":"GO:1905639","count":7},{"id":"GO:1900865","count":7},{"id":"GO:0010019","count":7}]},{"hash":"1428154885051237482","title":"Endomembrane trafficking and autophagy regulation","description":"The top terms point to a cohesive theme around intracellular membrane dynamics: endomembrane system organization, regulation of endosome size, and autophagosome assembly, with related vesicle trafficking such as synaptic transmission. The presence of transcription regulation and intron splicing terms likely reflects multifunctional proteins or annotations rather than a core function of the entire cluster. Overall, the dominant signal is membrane trafficking and autophagy-related processes.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0000372","count":1},{"id":"GO:0000373","count":1},{"id":"GO:0035023","count":1},{"id":"GO:0035249","count":1}]},{"hash":"1695177426030496659","title":"Plant transcriptional regulation & chromatin remodeling","description":"The cluster's top terms cluster around DNA-templated transcription and its regulation, along with chromatin remodeling, with several terms pointing to plant hormone signaling (gibberellin, cytokinin, salicylic acid) and secondary cell wall biogenesis. This suggests a set of proteins involved in transcriptional control modulated by plant hormone cues and chromatin state. Some terms (pituitary gland development, neuron maturation) appear less relevant to plants and may reflect broader or cross-species annotations, but the core theme is plant transcription regulation and chromatin remodeling.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0006355","count":6},{"id":"GO:1901348","count":6},{"id":"GO:0009739","count":5},{"id":"GO:0009751","count":5}]},{"hash":"1512532598815102151","title":"Nuclear DNA replication and transcription with export","description":"The top terms are dominated by nuclear processes: DNA replication (GO:0006260) and DNA-templated transcription (GO:0006351), along with protein export from the nucleus (GO:0006611) and its regulation. While other terms touch on ER polarization, viral response, and regeneration, the core theme centers on nuclear gene expression and nuclear-cytoplasmic transport, justifying this label.","confidence":"High","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006260","count":27},{"id":"GO:0046826","count":27},{"id":"GO:0006351","count":27},{"id":"GO:0043277","count":26},{"id":"GO:0046641","count":26}]},{"hash":"1478431640016912763","title":"Cell Wall Biosynthesis and Remodeling","description":"There are several GO terms centered on cell wall processes: peptidoglycan biosynthetic process, cell wall organization, and cell wall modification, pointing to a core theme of cell envelope biosynthesis and remodeling. Additional terms reference regulatory pathways (Rho signaling, transcription regulation) and sporulation, which can accompany cell wall changes in microbes or fungi. Some terms (lung development, obsolete oxidation-reduction) seem outliers or noisy annotations. Overall, the cluster appears best described by cell wall biosynthesis/remodeling, with a few functionally divergent annotations.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0008360","count":2},{"id":"GO:0030324","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0030435","count":2}]},{"hash":"1543518435339965983","title":"Ubiquitin-Proteasome Regulation of Growth and Development","description":"These proteins cluster around ubiquitin-dependent proteolysis, including SCF-dependent proteasomal degradation and polyubiquitination, pointing to a core role in targeted protein turnover. The co-occurrence of circadian rhythm regulation and developmental processes (oocyte maturation, neural tube closure) suggests proteolysis coordinating timing and developmental milestones, with additional links to growth control and cytoskeletal dynamics (microtubule polymerization). In short, the cluster centers on ubiquitin-proteasome\u2013mediated regulation of growth, timing, and developmental processes.","confidence":"High","size":29,"edges":15,"triangles":1,"max_degree":7,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0042787","count":12},{"id":"GO:0031146","count":11},{"id":"GO:0000209","count":8},{"id":"GO:0008285","count":8},{"id":"GO:0042752","count":8}]},{"hash":"1141461466431474421","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:1905639","count":6},{"id":"GO:1900865","count":6},{"id":"GO:0042793","count":6},{"id":"GO:0031425","count":6},{"id":"GO:0016554","count":6}]},{"hash":"277362865080967784","title":"Cytokinin-Driven Hormone Signaling and Leaf Formation","description":"The cluster shows strong enrichment for cytokinin-activated signaling, with additional responses to salicylic acid, gibberellin, and jasmonic acid, plus developmental processes like leaf formation and vegetative growth, indicating a coherent plant hormone signaling and leaf development module. Some terms (e.g., viral process) may be unrelated noise, but the dominant theme is plant hormone signaling coupled with leaf development.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":14},{"id":"GO:0009751","count":10},{"id":"GO:0009739","count":10},{"id":"GO:1903770","count":9},{"id":"GO:1900386","count":9}]},{"hash":"1681191265156136212","title":"Spinal cord development and synaptic plasticity","description":"This cluster is driven by GO terms explicitly tied to neural development (spinal cord development) and synaptic plasticity, with supportive terms indicating neural transcription, protein turnover (ubiquitination/SCF proteasomal degradation), and intracellular trafficking\u2014collectively pointing to neural development and synaptic function as the core theme.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0016567","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0031146","count":2}]},{"hash":"1964534500400712847","title":"Mitochondrial lipid metabolism and energy production","description":"This cluster is dominated by GO terms for mitochondrial ATP synthesis and multiple lipid-related processes (cardiolipin and phosphatidylcholine remodeling, triglyceride biosynthesis, CDP-diacylglycerol biosynthesis, platelet activating factor biosynthesis), pointing to a cohesive theme of mitochondrial lipid metabolism fueling energy production. Immune signaling terms (IL-2 production, T cell death regulation) may reflect metabolic regulation in immune cells but are secondary to the lipid/mitochondrial core. ","confidence":"High","size":28,"edges":124,"triangles":292,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0042775","count":13},{"id":"GO:0019432","count":12},{"id":"GO:0070970","count":12},{"id":"GO:0035965","count":12},{"id":"GO:0036151","count":12}]},{"hash":"522206307406583478","title":"Plant organellar RNA processing and editing","description":"Most top GO terms indicate chloroplast/plastid RNA processing, chloroplast RNA modification, plastid transcription, and mitochondrial mRNA modification/editing, pointing to regulation of organellar gene expression in plants. A few terms (seed dormancy, UV-C response) are less central, but the dominant signal is RNA metabolism in chloroplasts and mitochondria.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0071494","count":2},{"id":"GO:0042793","count":2},{"id":"GO:1905639","count":2},{"id":"GO:1900865","count":2}]},{"hash":"2186137408021364931","title":"Unknown","description":"The top GO terms are highly diverse, including photosynthesis, iron homeostasis, nuclear export, nonphotochemical quenching, bacterial biosynthesis, stress responses, and development across both plant and animal contexts. There is no coherent functional theme tying these terms together, so a specific label cannot be assigned. ","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":3},{"id":"GO:0006879","count":2},{"id":"GO:0000056","count":2},{"id":"GO:0010196","count":2},{"id":"GO:0019251","count":1}]},{"hash":"47013710142306674","title":"Zinc Ion Transport and Homeostasis","description":"This cluster is dominated by GO terms directly related to zinc biology: zinc ion transmembrane transport, response to zinc ion, intracellular zinc ion homeostasis, and regulation of zinc import. The mention of cadmium/iron/cobalt transporter-related terms likely reflects shared metal transport pathways, but the strongest signals are zinc-specific transport and homeostasis, making this a coherent zinc-centric cluster.","confidence":"High","size":28,"edges":61,"triangles":90,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0071577","count":9},{"id":"GO:0070574","count":9},{"id":"GO:0010043","count":8},{"id":"GO:0071584","count":8},{"id":"GO:0006882","count":8}]},{"hash":"139114558216691819","title":"Neural development and sensory signaling","description":"This cluster is dominated by terms related to nervous system development and sensory function, including Schwann cell development, visual perception, excitatory postsynaptic potential, and cranial morphogenesis. Though a few terms reference cell cycle processes (kinetochore localization, G2/M transition), the prominent theme centers on neural development and sensory signaling rather than cell division. ","confidence":"Medium","size":28,"edges":49,"triangles":22,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0014044","count":22},{"id":"GO:0034501","count":22},{"id":"GO:0043065","count":22},{"id":"GO:0007601","count":22},{"id":"GO:0010800","count":22}]},{"hash":"136882884097887677","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0031426","count":6},{"id":"GO:0016554","count":6},{"id":"GO:0031425","count":6},{"id":"GO:1905639","count":6},{"id":"GO:1900865","count":6}]},{"hash":"312404192494544649","title":"Bacterial secretion system and bacteriocin transport","description":"The top GO terms cluster around secretion and export across membranes, notably protein secretion by the Type I secretion system, bacteriocin transport/immunity, and peptide export. This points to a cohesive set of proteins involved in exporting bacteriocins and related peptides in bacteria, with broader membrane transport roles for xenobiotics and vitamins as supporting context.","confidence":"High","size":28,"edges":67,"triangles":52,"max_degree":17,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006855","count":25},{"id":"GO:0035461","count":24},{"id":"GO:0042883","count":17},{"id":"GO:0046677","count":17},{"id":"GO:0030253","count":17}]},{"hash":"2186080424335680115","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:1901621","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0097428","count":1},{"id":"GO:0045454","count":1}]},{"hash":"59569692091771330","title":"Ribosome Biogenesis and Translation","description":"The top GO terms are dominated by translation and ribosome-related processes (translation; ribosome biogenesis; maturation of SSU-rRNA; ribosomal subunit biogenesis), indicating a core function in ribosome assembly and protein synthesis. A few other terms (DNA repair, iron transport, cell septum assembly) are less representative and may reflect multifunctionality or annotation noise. Overall, the cluster centers on ribosome production and translation.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0042254","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0090529","count":1}]},{"hash":"569285747645851233","title":"Stress-Responsive Metabolism","description":"The terms include both biosynthetic processes (thiamine and quinolinate biosynthesis) and responses to various stimuli (cytokinin signaling, lipopolysaccharide, aluminum, xenobiotic, selenium), suggesting proteins involved in metabolic pathways that are modulated by environmental stress rather than a single dedicated function. The presence of neurotransmitter regulation terms broadens to general signaling roles, reinforcing a theme of metabolism tied to stress/response rather than a unique pathway.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":6},{"id":"GO:0032496","count":5},{"id":"GO:0009228","count":5},{"id":"GO:0010044","count":5},{"id":"GO:0019805","count":5}]},{"hash":"3742201552420498","title":"Nuclear RNA Processing and Ribosome Biogenesis","description":"This cluster centers on RNA maturation and transport: mRNA splicing, export, and decay pathways, plus maturation of rRNA (5.8S/LSU) and tricistronic transcripts, which points to a nuclear RNA processing and ribosome assembly module. The presence of protein\u2013protein interactions and centrosome maintenance suggests broader nuclear/polysome assembly roles, while the dsRNA response term is a less central but related stress-linked RNA pathway.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071360","count":3},{"id":"GO:0071169","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0006406","count":2}]},{"hash":"312637385421844716","title":"Embryonic organogenesis and innate immune signaling","description":"The top GO terms point to embryonic organ development (cranial skeleton, placenta, thymus) as well as immune-related responses (interferon-beta production, lipopolysaccharide response, interleukin-12 response), with supporting signals from DNA replication and stress responses like cadmium exposure. This suggests a cluster of proteins involved in developmental processes that are linked to innate immune and cellular stress signaling, rather than a single narrow function.","confidence":"Medium","size":28,"edges":122,"triangles":188,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048701","count":23},{"id":"GO:0006260","count":23},{"id":"GO:0000187","count":17},{"id":"GO:0001890","count":17},{"id":"GO:0048538","count":17}]},{"hash":"537006145812960403","title":"Developmental signals and nuclear transport","description":"Most represented terms point to organ development and neural differentiation (lung induction, midbrain dopaminergic neuron differentiation, renal inner medulla development), suggesting a developmental signaling theme. The presence of nuclear transport (NLS-bearing protein import into nucleus) and cytoskeletal/chromatin related terms indicates roles in nucleus\u2013cytoplasm dynamics and cell structure, which are common in developing cells. Therefore this label captures the core theme of the cluster.","confidence":"Medium","size":28,"edges":299,"triangles":2083,"max_degree":25,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0006607","count":17},{"id":"GO:0043547","count":17},{"id":"GO:0010909","count":16},{"id":"GO:0060492","count":16},{"id":"GO:1904948","count":16}]},{"hash":"492869268161236132","title":"Unknown","description":"The top GO terms show photosynthesis and leaf development, hinting at a plant-related theme, but many terms are obsolete or pertain to processes in other organisms (peroxisome import, bud neck organization, Wnt catabolic process, X chromosome inactivation). This mix indicates no single cohesive function characterizes the entire protein set, so no confident, unified label can be assigned.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":3},{"id":"GO:0018298","count":3},{"id":"GO:0048366","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006950","count":1}]},{"hash":"1048913056408118615","title":"Glutamatergic Synapses and Cerebellar Function","description":"The top GO terms center on glutamatergic synaptic transmission, including neuromuscular aspects, along with cerebellar granule cell differentiation and related behavioral phenotypes (memory, locomotion, ethanol response), suggesting a cohesive module of proteins involved in excitatory synaptic signaling and cerebellar neuron development/function.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035249","count":1},{"id":"GO:0001967","count":1},{"id":"GO:0065009","count":1},{"id":"GO:0007274","count":1},{"id":"GO:0051967","count":1}]},{"hash":"1724548174405185883","title":"Unknown","description":"The top GO terms span plant hormone signaling, secondary metabolite biosynthesis, immune signaling, metabolism, and basic cellular processes with no consistent shared function or pathway, and the network shows no edges or interactions. Consequently, there isn\u2019t a coherent cluster-level function to name.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0009938","count":4},{"id":"GO:1901599","count":3},{"id":"GO:0071357","count":3},{"id":"GO:0090526","count":3},{"id":"GO:0051291","count":3}]},{"hash":"81027638807900986","title":"Unknown","description":"The top terms span a highly diverse set of functions (heart electrophysiology, GPCR signaling, response to mercury, endocytosis, neural differentiation, cell division, pain perception, multicellular processes, innate immune signaling, adipocyte differentiation) with no clear common theme. Because there is no single overarching function that accounts for the majority of proteins, a concise, representative label cannot be confidently assigned.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0098907","count":4},{"id":"GO:0007205","count":4},{"id":"GO:0046689","count":4},{"id":"GO:0048549","count":3},{"id":"GO:0021707","count":3}]},{"hash":"1874355462059500050","title":"Unknown","description":"The top GO terms span immune clearance, T cell regulation, placental development, nuclear transport, ER organization, antiviral response, organ regeneration, meiotic DNA processing, self-tolerance, and hormone secretion\u2014showing no single coherent function; thus there is no clear theme to name the cluster.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043277","count":28},{"id":"GO:0046641","count":28},{"id":"GO:0060709","count":28},{"id":"GO:0006611","count":28},{"id":"GO:0061167","count":28}]},{"hash":"1498506163094486456","title":"Plant cell wall polysaccharide biosynthesis","description":"The top GO terms cluster around biosynthesis and modification of plant cell wall components (homogalacturonan, glucuronoxylan, mucilage) and related sugar metabolism, as well as protein O-linked glycosylation, suggesting a coherent theme of polysaccharide production and glycosylation linked to cell wall/extracellular matrix processes. The chloroplast movement terms seem less central to this core, but do appear in the set, so the label focuses on the dominant shared function. ","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009904","count":1},{"id":"GO:0009903","count":1},{"id":"GO:0016266","count":1},{"id":"GO:0010289","count":1},{"id":"GO:0005978","count":1}]},{"hash":"31318802755429015","title":"Cell wall biogenesis and epithelial polarity","description":"The Top Terms cluster around cell wall biosynthesis and organization (chitin, cellulose, plant-type secondary cell walls; UDP-glucose metabolism; general cell wall organization), suggesting a shared role in building extracellular carbohydrate structures. Additionally, several terms pertain to epithelial development and adhesion (follicle cell adhesion and maintenance of follicular epithelium polarity), pointing to a theme of tissue organization and polarity in development. Some terms reflect cross-kingdom defense (salicylic acid signaling) and infection structure formation, but the strongest concurrent signal is cell wall biogenesis combined with epithelial polarity. ","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0075015","count":2},{"id":"GO:0006031","count":2},{"id":"GO:0030244","count":2},{"id":"GO:0001744","count":2},{"id":"GO:0007299","count":2}]},{"hash":"129062055221335305","title":"Plant growth, reproduction, and defense","description":"This cluster\u2019s top GO terms are largely plant-focused, including defense response to fungus, pollination, and sexual reproduction, along with growth-related processes like plant-type cell wall loosening and metabolism (glucose homeostasis). While a non-plant term (learning or memory) appears among them, the overall theme points to plant development, reproduction, and defense functions.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050832","count":5},{"id":"GO:0007611","count":2},{"id":"GO:0042593","count":2},{"id":"GO:0015690","count":2},{"id":"GO:0009856","count":2}]},{"hash":"1457931198558279577","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010019","count":5},{"id":"GO:0031426","count":5},{"id":"GO:0016554","count":5},{"id":"GO:0090615","count":5},{"id":"GO:0070129","count":5}]},{"hash":"1805856306278087330","title":"Plant developmental transcription regulators","description":"The GO terms point to transcriptional control (DNA-templated transcription and its regulation) governing plant development, with specific processes like root hair growth, seed dormancy/germination responses, shoot formation, and gibberellin response, suggesting a set of transcription-related regulators shaping plant development.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0048768","count":1},{"id":"GO:0009956","count":1},{"id":"GO:0090610","count":1},{"id":"GO:0006355","count":1}]},{"hash":"1559054189663415789","title":"DNA Damage Response and Cell Division","description":"The top GO terms point to mitotic/cell cycle regulation (G2/M transition, mitotic cell cycle, cell division) alongside DNA maintenance processes (regulation of DNA repair, SOS response, mRNA stabilization, division septum assembly). This suggests a cohesive theme where proteins coordinate DNA damage responses with cell division and cytokinesis across contexts, making a concise label like \"DNA Damage Response and Cell Division\" appropriate. Confidence: Medium","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":1},{"id":"GO:1905287","count":1},{"id":"GO:0045792","count":1},{"id":"GO:0048255","count":1},{"id":"GO:0051301","count":1}]},{"hash":"2288390984890881326","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":28,"triangles":2,"max_degree":26,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:1905639","count":19},{"id":"GO:1900865","count":19},{"id":"GO:0042793","count":19},{"id":"GO:0031425","count":19},{"id":"GO:0016554","count":19}]},{"hash":"1924933640606096583","title":"Heavy metal transport and detoxification","description":"This cluster is characterized by enrichment for metal ion transport and detoxification terms (copper, zinc, cadmium, mercury), copper homeostasis, and mercury response, suggesting a coherent role in cellular metal ion handling and detoxification.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060003","count":2},{"id":"GO:0050787","count":2},{"id":"GO:0071577","count":2},{"id":"GO:0070574","count":2},{"id":"GO:0046689","count":2}]},{"hash":"1125917065168298605","title":"Mitochondrial energy metabolism and nucleotide biosynthesis","description":"This cluster centers on mitochondrial-related energy production (cristae formation, proton motive force-driven ATP synthesis) and nucleotide metabolism (UMP salvage, uridine biosynthetic process, guanine catabolic process), with an additional link to riboflavin biosynthesis. While a couple terms (centrosome cycle, antibiotic response) are less clearly connected, the dominant themes point to energy metabolism and nucleotide pathways.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007098","count":2},{"id":"GO:0042407","count":1},{"id":"GO:0035786","count":1},{"id":"GO:0015986","count":1},{"id":"GO:0099132","count":1}]},{"hash":"152211831079290701","title":"Chloroplast Photosynthesis and Light Response","description":"The top GO terms cluster around photosynthesis and light-related processes: light harvesting in photosystems I and II, responses to various light conditions (far red, high/low light, UV-A), and nonphotochemical quenching, indicating a cohesive group of chloroplast photosynthetic machinery and light-regulated function.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":6},{"id":"GO:0018298","count":6},{"id":"GO:0009768","count":3},{"id":"GO:1904964","count":3},{"id":"GO:0010218","count":3}]},{"hash":"1686387607338004527","title":"Unknown","description":"The Top Terms are a mix of redox/ detoxification and metabolic processes (oxidation-reduction, redox homeostasis, lipid and ubiquinone regulation) alongside development and transcription (spinal cord development, DNA-templated transcription, cell division). This broad, heterogeneous set shows no single coherent function characterizing the entire cluster, making a precise, unified label inappropriate.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0000920","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0021510","count":2}]},{"hash":"545502830983011154","title":"Chloroplast/mitochondrial Protein Import and Photosynthesis","description":"The cluster\u2019s GO terms cluster around import of proteins into chloroplasts and mitochondria (chloroplast stroma, mitochondrial matrix, inner membrane) and the process of photosynthesis, with supporting redox-related processes. Some outliers appear (obsolete terms, unrelated traits), but the dominant theme is organelle protein targeting coupled with photosynthetic energy metabolism.","confidence":"Medium","size":27,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0045037","count":2},{"id":"GO:0045039","count":2},{"id":"GO:0032094","count":2}]},{"hash":"898963606700843117","title":"Plant development and jasmonate-regulated flavonoid biosynthesis","description":"The top GO terms point to plant-specific processes: leaf formation, vegetative growth, jasmonic acid response, and flavonol (flavonoid) biosynthesis, suggesting a coherent theme of plant development and secondary metabolism, despite no observed network edges.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903770","count":2},{"id":"GO:1900386","count":2},{"id":"GO:0010338","count":2},{"id":"GO:0006351","count":2},{"id":"GO:1905615","count":2}]},{"hash":"1133060126733080948","title":"Chromatin Regulation and Transcription","description":"This cluster centers on regulation of DNA-templated transcription and chromatin-related processes (negative regulation of chromatin binding, protein deneddylation, and desumoylation), suggesting a nuclear regulatory module that modulates transcription and chromatin state; some placental development terms appear as less central associations.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060702","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0060712","count":2},{"id":"GO:1904333","count":2}]},{"hash":"2221117915102189979","title":"Neural development and transcriptional regulation","description":"This cluster's top GO terms point to developmental processes (mushroom body development; multicellular organism development) and broad transcriptional control (DNA-templated transcription and its regulation), complemented by regulatory signaling (positive regulation of TOR signaling; positive regulation of GTPase activity) and intraciliary transport, suggesting a set of proteins involved in neural development and its upstream transcriptional and signaling regulation. The terms cohere around developmental regulation rather than a single enzymatic function, though some terms are somewhat diverse, so the label captures the central theme with moderate confidence.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000186","count":1},{"id":"GO:0035735","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0032008","count":1},{"id":"GO:0071230","count":1}]},{"hash":"561358449421843107","title":"Nuclear Transcription Regulation","description":"The cluster\u2019s top GO terms are dominated by DNA-templated transcription, transcription termination, and regulation of transcription, pointing to a core theme of nuclear transcription control. A few outliers (antibiotic biosynthetic process, ubiquitin-related deubiquitination, immunoglobulin production, infection structure formation) likely reflect annotation noise or multi-function proteins. Overall, the name captures the central shared function.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006353","count":2},{"id":"GO:0090503","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0017000","count":2}]},{"hash":"2012018535973730924","title":"Oocyte meiosis and early development","description":"The cluster is dominated by terms related to oocyte maturation and female meiosis I (spindle assembly) along with ubiquitin-proteasome\u2013mediated protein turnover, histone demethylation, and microtubule dynamics, plus several early neural/developmental processes (neural tube closure, third ventricle development). This suggests proteins coordinating meiosis/oogenesis with early developmental events and cell-cycle regulation.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":17},{"id":"GO:0001556","count":14},{"id":"GO:0070544","count":14},{"id":"GO:0046785","count":14},{"id":"GO:0021993","count":14}]},{"hash":"1146793193588028240","title":"Transcription Regulation and Vacuole Inheritance","description":"The cluster is dominated by GO terms related to DNA-templated transcription and regulation of transcription, suggesting a core role in nuclear gene expression control. The presence of vacuole inheritance and budding growth terms points to coordination with cell division and organelle partitioning, consistent with yeast-like systems. While there are some outliers and obsolete terms, the strongest signals revolve around transcriptional regulation and organelle inheritance, justifying a label reflecting these themes.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000011","count":2},{"id":"GO:0007118","count":2},{"id":"GO:0010252","count":2},{"id":"GO:0061408","count":2}]},{"hash":"135598047742722812","title":"Unknown","description":"The top GO terms are very heterogeneous, spanning nutrient and antibiotic responses, defense to bacteria, developmental processes (neural tube closure, nodulation), and various transport roles. This lack of a single cohesive function or pathway across the cluster suggests the proteins do not share a common, interpretable theme, so a specific, representative label cannot be confidently assigned.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007584","count":4},{"id":"GO:0046677","count":4},{"id":"GO:0050830","count":3},{"id":"GO:0001843","count":3},{"id":"GO:0001403","count":3}]},{"hash":"609852104629999100","title":"Plant Hormone Biosynthesis and Fruit Ripening","description":"The terms are dominated by plant hormone biosynthesis and metabolism (ethylene, gibberellin, auxin catabolic, salicylic acid catabolic) together with fruit ripening and related secondary metabolism (proanthocyanidin, poly-hydroxybutyrate biosynthetic) and oxidative stress\u2013related cell death, indicating a coherent theme of hormone-regulated fruit development in plants.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":13},{"id":"GO:0009835","count":6},{"id":"GO:0042619","count":5},{"id":"GO:0009852","count":5},{"id":"GO:0009693","count":5}]},{"hash":"2032155087765957981","title":"Plant cell wall biosynthesis and pollen development","description":"The cluster is dominated by GO terms for plant cell wall biogenesis (primary and secondary), cellulose biosynthesis, and related carbohydrate metabolism (UDP-glucose, rhamnogalacturonan I). The inclusion of cell plate assembly and pollen germination links reinforces a cohesive theme around plant cell wall construction and pollen-related development.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":6},{"id":"GO:0009834","count":5},{"id":"GO:0030244","count":4},{"id":"GO:0009846","count":4},{"id":"GO:0000919","count":4}]},{"hash":"1182368632074666715","title":"Lipid and Aromatic Metabolism","description":"The top GO terms cluster around lipid signaling (regulation of endocannabinoid signaling; triglyceride catabolic processes) and the catabolism or biosynthesis of aromatic/secondary metabolites (strigolactone, beta-ketoadipate, stilbene, phenylpropionate, antibiotic biosynthesis), plus detoxification processes. This suggests a theme of lipid-associated signaling coupled with aromatic compound metabolism, spanning multiple organisms, hence the chosen label. ","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:2000124","count":10},{"id":"GO:0019433","count":10},{"id":"GO:1901601","count":9},{"id":"GO:0019380","count":9},{"id":"GO:0098869","count":9}]},{"hash":"1617808967994752244","title":"DNA replication and Golgi-ER trafficking","description":"This cluster\u2019s top GO terms span core genome maintenance (DNA replication, cell division, mRNA export) and fundamental protein handling/trafficking (protein retention in Golgi, ER-to-Golgi transport, proteasome regulatory particle assembly) along with basic energy metabolism (ATP processes). The combination suggests a group of proteins tied to essential cellular machinery governing genome replication and protein sorting/processing, rather than a single specialized pathway. Hence, a label that reflects both nucleic acid-related functions and Golgi-ER trafficking best captures the overarching themes.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0045053","count":5},{"id":"GO:0000733","count":5},{"id":"GO:0070682","count":5},{"id":"GO:0006888","count":5}]},{"hash":"1310187757552461164","title":"Unknown","description":"The top terms span trafficking (ER-Golgi transport), meiosis/mitosis (ascospore formation, meiotic checkpoint signaling, kinetochore attachment), adhesion, immune regulation (T cell homeostasis and cytotoxicity), and metabolism, with no clear single theme tying all proteins together. This diversity makes it hard to assign a cohesive function label, so Unknown with None confidence.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0030437","count":2},{"id":"GO:0051315","count":2},{"id":"GO:0007155","count":2},{"id":"GO:0070262","count":1}]},{"hash":"1065633022326221247","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":21},{"id":"GO:0090617","count":21},{"id":"GO:0042793","count":21},{"id":"GO:1905639","count":21},{"id":"GO:1900865","count":21}]},{"hash":"533623223731528064","title":"DNA-Templated Transcription Regulation","description":"The cluster most strongly features terms about DNA-templated transcription and its regulation (GO:0006351, GO:0006355), which suggests the shared function is transcriptional control at the DNA level. While a few other terms touch on mitochondrial import, membrane regulation, or even photosynthesis, those appear ancillary or noisy in this set. The lack of edges indicates no direct interactions within the cluster, but the core signal remains transcription-related.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0015074","count":1},{"id":"GO:0010867","count":1},{"id":"GO:2000134","count":1}]},{"hash":"1941666093347762435","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042793","count":23},{"id":"GO:1905639","count":23},{"id":"GO:1900865","count":23},{"id":"GO:0031425","count":23},{"id":"GO:0016554","count":23}]},{"hash":"87171138629696516","title":"Multicellular Development and Tissue-Specific Signaling","description":"The top GO terms cluster around development-related processes (multicellular organism development, angiogenesis, retinal cone cell development) and tissue-specific signaling activities (regulation of atrial cardiac muscle cell action potential, response to cAMP, cytoskeleton-dependent transport, and protein dephosphorylation). While several terms point to broad developmental roles, others suggest specialized tissue contexts, indicating a theme of development coupled with tissue-specific signaling rather than a single uniform function. Edges are absent, which suggests a broad, diverse set of roles rather than a tightly connected module; the label aims to reflect the overarching developmental and tissue-specific signaling theme.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0033555","count":1},{"id":"GO:0043129","count":1},{"id":"GO:0051591","count":1}]},{"hash":"920428179355317286","title":"Translation Initiation Machinery","description":"This cluster is driven by GO terms for translational initiation, translation, and formation of cytoplasmic translation initiation complex, suggesting involvement in protein synthesis initiation. The other single-count terms (cell cycle and differentiation related) are likely incidental, so the core signal points to translation initiation. ","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006413","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0001732","count":1},{"id":"GO:0030890","count":1},{"id":"GO:0048102","count":1}]},{"hash":"775233454774255221","title":"Multi-tissue development and differentiation","description":"The top GO terms span muscle, neural, pancreas and kidney development, plus circadian entrainment and plant-specific development, indicating a broad developmental/differentiation theme rather than a single pathway.","confidence":"","size":26,"edges":325,"triangles":2600,"max_degree":25,"top_function":null,"top_go_terms":[{"id":"GO:2000820","count":24},{"id":"GO:2000323","count":23},{"id":"GO:0007518","count":23},{"id":"GO:0048658","count":23},{"id":"GO:0009649","count":23}]},{"hash":"971115584479906459","title":"Pigmentation and skin development signaling","description":"The top GO terms emphasize pigmentation and skin development within a multicellular context, suggesting a core theme of epidermal differentiation and pigment cell biology. Supporting signaling and cytoskeletal remodeling terms (GTPase and kinase regulation, autophosphorylation, and Arp2/3-mediated actin nucleation) indicate coordinated regulation of pathways essential for skin morphogenesis and pigmentation, with additional terms like mRNA transport and mitotic cell cycle reflecting general cellular activity in proliferative skin tissue.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":9},{"id":"GO:0071902","count":8},{"id":"GO:0043473","count":8},{"id":"GO:0031954","count":8},{"id":"GO:0007275","count":8}]},{"hash":"351313510292853716","title":"Mitochondrial energy and metabolite transport","description":"The top terms converge on transport of energy-related molecules and metabolites across membranes, especially mitochondrial ADP/ATP and phosphate transport, TPP cofactor transport, and amino acid (glycine) import, with one oblique mitochondrial maintenance term. This suggests a coherent theme of mitochondrial/metabolite transport governing energy metabolism.","confidence":"High","size":26,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":5},{"id":"GO:0035435","count":5},{"id":"GO:1990544","count":4},{"id":"GO:0097421","count":4},{"id":"GO:0032869","count":4}]},{"hash":"442296726202016755","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by GO terms tied to translation and ribosome assembly (translation, translational initiation, cytosolic ribosome assembly, ribosome biogenesis, and rRNA processing), indicating proteins involved in the protein synthesis machinery; additional terms about responses to antibiotics/cycloheximide suggest translation stress, and macroautophagy can relate to ribosome turnover. Overall, the common theme is the ribosome and translation apparatus.","confidence":"High","size":26,"edges":155,"triangles":441,"max_degree":25,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":19},{"id":"GO:0046677","count":6},{"id":"GO:0042273","count":4},{"id":"GO:0046898","count":4},{"id":"GO:0006413","count":3}]},{"hash":"1177716410441960678","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0090615","count":7},{"id":"GO:0090617","count":7},{"id":"GO:1905639","count":7},{"id":"GO:1900865","count":7},{"id":"GO:0042793","count":7}]},{"hash":"849250353411304866","title":"Plant development and jasmonate response","description":"This cluster highlights plant-specific processes such as leaf formation, vegetative growth, and responses to jasmonic acid, along with regulation of transcription and flavonol biosynthesis, suggesting a theme around growth and defense signaling in plants. Some terms (e.g., viral process, apoptosis) point to stress responses, but the core pattern fits plant development and jasmonate-regulated metabolism.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0006355","count":5},{"id":"GO:0006103","count":4},{"id":"GO:0006915","count":4},{"id":"GO:1903770","count":4}]},{"hash":"1000956799378619584","title":"Unknown","description":"The top GO terms span very diverse biological contexts (plant hormone signaling, ion transport, brain and root development, lipid biosynthesis, chromatin remodeling, and sensory processes) with little cohesive function tying them together. This mix across kingdoms and processes suggests no single interpretable cluster theme, so an Unknown label is appropriate.","confidence":"","size":26,"edges":44,"triangles":10,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0009736","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0022037","count":2},{"id":"GO:0046513","count":2},{"id":"GO:0007601","count":2}]},{"hash":"999554265709292452","title":"Unknown","description":"The Top Terms cover transcription, plant hormone biosynthesis/response (strigolactone), pigment catabolism (chlorophyll), vitamin biosynthesis (menaquinone), lipid signaling (prostaglandin, endocannabinoid), and a post-translational modification (C-terminal demethylation), indicating no single cohesive function tying all proteins together.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:1902348","count":3},{"id":"GO:1905344","count":3},{"id":"GO:0009086","count":3},{"id":"GO:1901601","count":3}]},{"hash":"568900323115438897","title":"Membrane amino acid transport and osmoregulation","description":"The Top Terms point to membrane transport of amino acids (D-serine, L-lysine, L-arginine, carnitine) and processes related to cell volume regulation and hypotonic salinity response. While other terms (cell shape regulation, macrophage activation, mitotic cycle) appear, the dominant signal is transporter activity at the plasma membrane tied to osmotic balance, justifying a transport- and osmoregulation-focused label.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008360","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0006884","count":1},{"id":"GO:0042942","count":1},{"id":"GO:0071477","count":1}]},{"hash":"481773054714485631","title":"Ribosome biogenesis and translation","description":"The top GO terms show a strong emphasis on ribosome production and function, including maturation of SSU-rRNA, ribosomal small subunit assembly, and ribosome biogenesis, along with translation. This points to a core role in assembling and using ribosomes for protein synthesis. A few additional terms (brain development, somatic stem cell maintenance, nucleotide-excision repair) appear but are less central to this cluster's main theme.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0031134","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0006289","count":2}]},{"hash":"170230703153261790","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0071630","count":1},{"id":"GO:0010198","count":1},{"id":"GO:0034975","count":1},{"id":"GO:0006986","count":1}]},{"hash":"1822677829631719449","title":"Metabolism and Detoxification","description":"This cluster shows a mix of catabolic and biosynthetic processes (triglyceride, stilbene, 3-phenylpropionate and strigolactone metabolism/biogenesis) along with cellular oxidant detoxification and related stress responses. While one term relates to endocannabinoid signaling, the prevailing pattern is diverse small-molecule metabolism and redox detoxification rather than a single specific pathway, suggesting a broad metabolic/detox role.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:2000124","count":6},{"id":"GO:0019433","count":6},{"id":"GO:1901601","count":5},{"id":"GO:0019380","count":5}]},{"hash":"317379424232076470","title":"Regulated vesicle trafficking and endosome-lysosome transport","description":"This cluster centers on vesicle dynamics and cargo routing, highlighted by terms for synaptic vesicle exocytosis regulation, endosome-to-lysosome transport, and melanosome transport, as well as multivesicular body size regulation. The brain development term supports neuronal relevance, while additional regulatory terms suggest modulation of trafficking and protein turnover. Collectively, they point to a cohesive function in controlled vesicle trafficking and degradation pathways.","confidence":"High","size":26,"edges":39,"triangles":4,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000300","count":10},{"id":"GO:0010796","count":10},{"id":"GO:0031384","count":10},{"id":"GO:0007420","count":9},{"id":"GO:0008333","count":6}]},{"hash":"744739253444478894","title":"T cell signaling and immune tolerance","description":"The cluster is strongly defined by immune-related GO terms, especially the T cell receptor signaling pathway (GO:0050852) with 23 proteins, along with related functions such as regulation of T cell proliferation (positive and negative), tolerance induction to self antigen, Fc receptor\u2013mediated inhibitory signaling, and apoptotic cell clearance. This combination points to a cohesive theme centered on T cell activation, regulation, and immune tolerance, with additional notes on adhesion/ECM regulation that may reflect downstream modulatory processes. ","confidence":"High","size":26,"edges":14,"triangles":0,"max_degree":4,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0050852","count":23},{"id":"GO:0008285","count":23},{"id":"GO:0043277","count":22},{"id":"GO:0046641","count":22},{"id":"GO:0002651","count":22}]},{"hash":"1382007332424089663","title":"Innate Immune Signaling and IFN-\u03b2 Production","description":"The top GO terms indicate a cohesive innate immune theme: positive regulation of interferon-\u03b2 production, defense against Gram-positive bacteria, responses to dsRNA, and lipopolysaccharide signaling and response, pointing to pathogen sensing and antiviral/antibacterial signaling pathways. Some neural development terms appear but are secondary to the dominant immune signal, so the cluster likely represents components of innate immune sensing and interferon-mediated responses.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045359","count":16},{"id":"GO:0050830","count":16},{"id":"GO:0043330","count":16},{"id":"GO:0045087","count":16},{"id":"GO:0051965","count":15}]},{"hash":"1719908043620065129","title":"Ubiquitination and Protein Degradation","description":"The top GO terms are dominated by ubiquitination-related processes (protein ubiquitination, K48-linked ubiquitination, autoubiquitination) and ubiquitin-dependent degradation pathways (ERAD, proteasomal catabolism). Peroxisomal matrix import is also listed, which can relate to protein trafficking linked to ubiquitin signaling, and immune signaling terms (RIG-I regulation, adaptive immune response) reflect ubiquitin's role in immune pathways. Together these terms point to a cohesive theme: protein turnover and quality control via the ubiquitin-proteasome system, with related regulatory roles in immunity and trafficking.","confidence":"High","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051865","count":7},{"id":"GO:0016558","count":7},{"id":"GO:0030433","count":7},{"id":"GO:0042787","count":7},{"id":"GO:0039536","count":6}]},{"hash":"746149390853192873","title":"Developmental transcriptional regulation","description":"The cluster centers on DNA-templated transcription and RNA polymerase II activity, with accompanying calcium-responsive signaling and diverse development-related processes (muscle differentiation, primitive streak formation, floral meristem determinacy, seed growth, and cartilage development), suggesting a cohesive theme of transcriptional control during development.","confidence":"High","size":26,"edges":309,"triangles":2270,"max_degree":25,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":10},{"id":"GO:0071277","count":9},{"id":"GO:0006366","count":7},{"id":"GO:2001016","count":6},{"id":"GO:0090009","count":6}]},{"hash":"1353948009010281703","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006281","count":3},{"id":"GO:0051123","count":3},{"id":"GO:0010606","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0002107","count":2}]},{"hash":"1126287290325851070","title":"DNA-Templated Transcription Regulation","description":"This cluster is dominated by GO terms for DNA-templated transcription and its regulation (GO:0006351 and GO:0006355), suggesting a core function in transcriptional control, likely including transcription factors or co-regulators. Secondary terms include proteolysis and various metabolic pathways, but they appear less represented, so the primary theme remains transcription regulation.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0006355","count":4},{"id":"GO:0006508","count":3},{"id":"GO:1905344","count":3}]},{"hash":"277195421032510781","title":"Neuronal development and axon guidance signaling","description":"The cluster\u2019s top GO terms center on nervous system development, axon extension, ephrin receptor signaling, focal adhesion dynamics, and ERK signaling, all core to neuronal growth and axon guidance. Immune-related terms appear less central and may reflect shared signaling modules rather than primary immune functions, so the dominant theme is neural development and axon guidance. High","confidence":"","size":26,"edges":39,"triangles":26,"max_degree":16,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051893","count":19},{"id":"GO:0050852","count":19},{"id":"GO:0048013","count":19},{"id":"GO:0045773","count":19},{"id":"GO:0043304","count":19}]},{"hash":"1065959274567621463","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0090615","count":26},{"id":"GO:0090617","count":26},{"id":"GO:0042793","count":26},{"id":"GO:1905639","count":26},{"id":"GO:1900865","count":26}]},{"hash":"1763058488001076612","title":"Pectin Metabolism and Cell Wall Remodeling","description":"The cluster's top terms are dominated by mucilage pectin biosynthesis, cell wall modification, and pectin catabolic processes, pointing to a shared role in pectin metabolism and cell wall remodeling. Some peripheral terms (visual perception, synapse-related processes, apoptosis) appear as outliers or cross-annotations and do not reflect the cluster's core function.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048358","count":7},{"id":"GO:0042545","count":7},{"id":"GO:0045490","count":7},{"id":"GO:0006508","count":3},{"id":"GO:0007601","count":3}]},{"hash":"256838676657438471","title":"Bacterial membrane transporters and antibiotic stress","description":"The top GO terms show diverse membrane transport activities (molybdate, methionine, thiamine, teichoic acid, glycerophosphodiesters, bacteriocin, phospholipid translocation) plus SOS and antibiotic response, suggesting a cluster of membrane transport proteins linked to stress responses in bacteria (likely gram-positive given teichoic acid and bacteriocin transport terms). This coherence supports a label focused on transport functions with antibiotic/ stress signaling.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":4},{"id":"GO:0015689","count":4},{"id":"GO:0045796","count":3},{"id":"GO:0001407","count":3},{"id":"GO:0043213","count":3}]},{"hash":"982378000928716121","title":"Autophagy and Intracellular Transport","description":"The top GO terms point strongly to autophagy-related processes (ribophagy, cytoplasm-to-vacuole targeting pathway) and vesicle/intracellular protein transport, supported by lipid signaling involved in membrane trafficking. While a few terms (transcription regulation, cell division) are less clearly connected, the dominant themes are autophagy and intracellular transport. ","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000060","count":2},{"id":"GO:0034517","count":2},{"id":"GO:0032534","count":2},{"id":"GO:0048015","count":2},{"id":"GO:0006654","count":2}]},{"hash":"25283706670378350","title":"Ubiquitination and TNF-NF-\u03baB Signaling","description":"The cluster is dominated by ubiquitin-related processes (ubiquitin-dependent proteolysis, autoubiquitination, and various ubiquitination linkages) and TNF/NF-\u03baB signaling terms, suggesting a cohesive role in ubiquitin-mediated regulation of inflammatory signaling and antiviral responses.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":11},{"id":"GO:0051865","count":10},{"id":"GO:1903265","count":9},{"id":"GO:0036205","count":9},{"id":"GO:0085020","count":9}]},{"hash":"770339843567438464","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009113","count":1},{"id":"GO:0070329","count":1},{"id":"GO:0006541","count":1},{"id":"GO:0006189","count":1},{"id":"GO:0046892","count":1}]},{"hash":"1208156986575660046","title":"Unknown","description":"The proteins show a scattered mix of GO terms, including nucleotide catabolism, snoRNA processing, transcription, and isoprenoid biosynthesis, with no clear shared function or strong enrichment, and no edges linking them; therefore a single cohesive label cannot be assigned.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0015967","count":1},{"id":"GO:0045337","count":1},{"id":"GO:0050992","count":1},{"id":"GO:1901909","count":1}]},{"hash":"1084593943821081851","title":"Cell division and microtubule regulation","description":"The top GO terms prominently include mitotic cell cycle, cell division, chromosome segregation, and regulation of microtubule polymerization or depolymerization, which collectively point to the machinery of cell division. While there are additional terms related to transport and extracellular signaling that appear in the set, they are represented by fewer proteins and do not define the cluster as clearly. Therefore, this label best captures the likely common function among the majority of terms.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071934","count":1},{"id":"GO:0015768","count":1},{"id":"GO:0035426","count":1},{"id":"GO:1902047","count":1},{"id":"GO:0061299","count":1}]},{"hash":"2256056947952560017","title":"Ubiquitin-Proteasome System Proteolysis","description":"Top GO terms dominated by ubiquitin-dependent protein catabolic processes, SCF-dependent proteasomal ubiquitin-mediated degradation, and protein polyubiquitination indicate the cluster centers on ubiquitin-proteasome\u2013driven proteolysis. The presence of circadian rhythm regulation and oocyte maturation hints at broader regulatory roles of this degradation pathway in timing and development. Some obsolete terms reflect historical annotations but do not change the core theme. ","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":13},{"id":"GO:0031146","count":10},{"id":"GO:0000209","count":9},{"id":"GO:0042752","count":9},{"id":"GO:0051436","count":8}]},{"hash":"312383982403174140","title":"Diverse Development and Secretory Transport","description":"The terms show a loose theme of development across different tissues (lens, kidney/proximal tubule, brain/lateral ventricle) alongside secretory and transport activities (saliva secretion, excretion, potassium transport) and signaling (response to cAMP). Because the proteins appear unconnected (no edges) and the terms span multiple unrelated processes, the label reflects a broad, cross-tissue mix rather than a single cohesive function, yielding a moderate level of confidence.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0002088","count":5},{"id":"GO:0071805","count":5},{"id":"GO:0072014","count":4},{"id":"GO:0021670","count":4}]},{"hash":"1802009907854913065","title":"Metabolism and Adipocyte Differentiation","description":"The cluster\u2019s top GO terms center on small-molecule metabolism (formate catabolic, dicarboxylic acid, methylamine, L-serine, pyridoxine biosynthesis) and excretion, with an additional term for white fat cell differentiation. While some terms are obsolete or plant-specific, the dominant pattern is metabolic processing, with a tangential link to adipocyte differentiation. This supports a label focusing on metabolism with an adipogenesis angle.","confidence":"Medium","size":25,"edges":300,"triangles":2300,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0007588","count":2},{"id":"GO:0042183","count":2},{"id":"GO:0050872","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0043648","count":2}]},{"hash":"704946408625980981","title":"GABA shunt and amino acid metabolism","description":"The top GO terms are dominated by amino-acid related catabolic and biosynthetic processes, especially GABA catabolism, the GABA shunt, putrescine catabolism, and proline-related synthesis. This points to a cluster enriched in neurotransmitter and amino-acid metabolism pathways, with a few developmental terms likely representing broad expression annotations rather than a shared developmental program. Overall, a concise label capturing GABA- and amino-acid metabolism best represents the cluster.","confidence":"Medium","size":25,"edges":299,"triangles":2277,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0006537","count":17},{"id":"GO:0009447","count":15},{"id":"GO:0009450","count":15},{"id":"GO:0055129","count":15},{"id":"GO:0006540","count":13}]},{"hash":"2113036668571908180","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042793","count":5},{"id":"GO:1905639","count":5},{"id":"GO:1900865","count":5},{"id":"GO:0031425","count":5},{"id":"GO:0016554","count":5}]},{"hash":"1195780519340586380","title":"Post-transcriptional RNA processing and translation machinery","description":"The cluster\u2019s top GO terms center on mRNA processing (splicing, RNA modification, export) and components of the translation apparatus (translation initiation, ribosome biogenesis, translation), suggesting a cohesive group involved in post-transcriptional gene expression and protein synthesis. This supports naming the cluster as post-transcriptional RNA processing and translation machinery.","confidence":"High","size":25,"edges":164,"triangles":699,"max_degree":20,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0031047","count":5},{"id":"GO:0048026","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0002188","count":5}]},{"hash":"51682889080303210","title":"RNA metabolism and translation","description":"Top GO terms cluster around protein synthesis (translation in cytoplasm and mitochondria) and RNA processing/degradation (RNA hydrolysis and mRNA catabolic processes), suggesting a cohesive group of proteins involved in RNA metabolism and the translation machinery. Some terms are marked obsolete, but they still reflect the same functional theme. ","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0090502","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0042619","count":2},{"id":"GO:0002181","count":1}]},{"hash":"912154159275818775","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":59,"triangles":61,"max_degree":19,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0090617","count":5},{"id":"GO:0042793","count":5},{"id":"GO:1905639","count":5},{"id":"GO:1900865","count":5}]},{"hash":"481835918222622115","title":"Unknown","description":"The top GO terms are highly diverse, covering development in multiple organs (kidney proximal tubule, lens, brain ventricle), excretion, fungal ascospore formation, salivary secretion, and various cellular processes (cAMP response, hydrogen peroxide transport, endosomal acidification). There is no clear common function or pathway linking these terms, and the network has no edges or connections (Max Degree 0, Edges 0), suggesting the proteins do not share a cohesive biological role. Therefore, this cluster is best labeled Unknown with None confidence.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072014","count":1},{"id":"GO:0002088","count":1},{"id":"GO:0021670","count":1},{"id":"GO:0046878","count":1},{"id":"GO:0030437","count":1}]},{"hash":"583369098792989042","title":"Transcriptional regulation of multi-tissue differentiation","description":"The cluster prominently features transcription by RNA polymerase II and multiple differentiation-related terms (myoblast/skeletal muscle differentiation, osteoblast differentiation, astrocyte differentiation, and development in other tissues), along with regulation of signaling pathways that influence these processes (androgen receptor and glucocorticoid signaling). This pattern points to a common theme: control of gene expression guiding differentiation across diverse tissues, rather than a single tissue-specific function.","confidence":"High","size":25,"edges":297,"triangles":2233,"max_degree":24,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":18},{"id":"GO:0045668","count":16},{"id":"GO:0060766","count":16},{"id":"GO:2001016","count":15},{"id":"GO:2000323","count":14}]},{"hash":"456464616694957619","title":"Transcription and Cell Cycle Regulation","description":"This cluster centers on transcriptional control and cell cycle progression, with strong signals for DNA-templated transcription, RNA Pol II\u2013mediated transcription regulation, and the G1/S transition. Additional terms point to growth-related processes and stress responses (liver regeneration, insulin signaling regulation, Leydig differentiation, and ER unfolded protein response), suggesting a broader regulatory network that coordinates gene expression with proliferation and differentiation. Overall, the core theme is transcription regulation coupled to cell cycle and growth signaling.","confidence":"High","size":25,"edges":153,"triangles":384,"max_degree":22,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":11},{"id":"GO:0030968","count":10},{"id":"GO:0006351","count":9},{"id":"GO:0000411","count":8},{"id":"GO:0097421","count":8}]},{"hash":"1820871059598228113","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2}]},{"hash":"576223118330420361","title":"Broad cellular processes (translation and organelle assembly)","description":"The top terms span translation, rRNA export, mitochondrial assembly, spindle organization, vesicle transport, and various developmental processes, indicating involvement in fundamental cellular machinery and general development rather than a single pathway. Thus, a concise label of Broad cellular processes captures the overarching theme of core protein synthesis, organelle assembly, and basic cell functions.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006407","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0033108","count":1},{"id":"GO:0000001","count":1},{"id":"GO:1904970","count":1}]},{"hash":"490129321597175968","title":"RNA Splicing and Ribosome Biogenesis","description":"The top GO terms are dominated by RNA processing: mRNA splicing via spliceosome and generation of catalytic spliceosome, plus maturation of SSU-rRNA. These point to a core theme of RNA processing machinery and ribosome assembly, with other terms like ubiquitination and DNA integration as peripheral functions. This name reflects the cluster\u2019s central RNA-processing role and is representative of its function.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002023","count":1},{"id":"GO:0009749","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0032929","count":1},{"id":"GO:0040016","count":1}]},{"hash":"2193335919152962287","title":"RNA Splicing and Processing Machinery","description":"The cluster is enriched for spliceosome-related terms (spliceosomal tri-snRNP complex assembly, RNA splicing, mRNA processing), indicating a core theme around RNA splicing and processing. Other terms (stress response, T cell differentiation) are present but seem less central to the main function.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901001","count":2},{"id":"GO:0051245","count":2},{"id":"GO:0046688","count":1},{"id":"GO:0000244","count":1},{"id":"GO:0006397","count":1}]},{"hash":"163766919829687327","title":"Developmental Epigenetic Regulation","description":"The top GO terms point to histone modification (H3-K27 methylation, H3/H4 acetylation) and DNA-templated transcription, alongside developmental processes (multicellular development, skin development, seminiferous tubule development). This implies a cluster of proteins involved in chromatin modification that governs gene expression during development, with some noise from obsolete terms or unrelated functions.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0061087","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0072520","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0043982","count":3}]},{"hash":"1856331603343051475","title":"Nuclear transcription and export regulation","description":"The top GO terms cluster around DNA-templated transcription, regulation of DNA binding, and regulation of protein export from the nucleus, pointing to a cohesive theme of nuclear gene expression control and transport. Redox-related terms suggest a secondary layer of regulation possibly tied to cellular stress responses, but the dominant signal remains nuclear transcription and transport. The absence of interaction edges does not undermine the coherence of this functional grouping, given the GO term enrichment. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0043388","count":3},{"id":"GO:0046826","count":3},{"id":"GO:0098869","count":3}]},{"hash":"1022669502667615233","title":"Plant Hormone Signaling and Cell Wall Dynamics","description":"The top terms point to multiple plant hormone responses (cytokinin, gibberellin, salicylic acid) along with processes tied to cell wall biogenesis and remodeling (secondary cell wall biogenesis, cellulose catabolic process), and signaling pathways at the cell surface. Although some terms (e.g., response to cocaine, antibiotic biosynthetic process) may be noise, the cohesive theme is hormone-regulated signaling influencing cell wall development/remodeling.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009736","count":4},{"id":"GO:1901348","count":4},{"id":"GO:0042220","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0006334","count":3}]},{"hash":"1097620727217976975","title":"Ubiquitin-Proteasome Regulation of Meiosis and Oocyte Maturation","description":"This cluster is driven by ubiquitin-dependent protein degradation (SCF-dependent proteasomal pathways) and contains strong signals for meiotic/oocyte processes, such as spindle assembly in female meiosis I and oocyte maturation, plus microtubule polymerization linked to meiotic spindle dynamics. While some developmental terms appear, the dominant theme is proteostasis controlling meiosis and oocyte maturation.","confidence":"High","size":25,"edges":174,"triangles":592,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":17},{"id":"GO:0042752","count":17},{"id":"GO:0031146","count":16},{"id":"GO:0008285","count":15},{"id":"GO:0001556","count":14}]},{"hash":"700092007373371449","title":"Unknown","description":"The listed GO terms span DNA integration, miRNA silencing, signaling pathways (semaphorin-plexin, dopamine receptor), cytoskeletal organization, and wound healing. They do not converge on a single biological function, so a specific label isn\u2019t reliably representational.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":2},{"id":"GO:1905000","count":1},{"id":"GO:0035278","count":1},{"id":"GO:2000637","count":1},{"id":"GO:0042068","count":1}]},{"hash":"1275847287367512603","title":"Placental development and placental vascular signaling","description":"The enriched GO terms predominantly point to placenta development and vascularization (maternal placenta development, embryonic placenta-related glycogen cell differentiation, labyrinthine layer blood vessel development) with supporting signaling pathways (insulin receptor signaling, Rho/Ras/JNK regulation). Some terms (glutamatergic synaptic transmission, cell cycle) appear less connected, suggesting a mix of signals but a core placenta-related theme.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0035249","count":3},{"id":"GO:0000086","count":2},{"id":"GO:0001893","count":2},{"id":"GO:0060709","count":2}]},{"hash":"1744561325394203834","title":"Ubiquitin-Dependent NF-\u03baB/JNK Signaling","description":"The terms converge on ubiquitin-mediated protein turnover and inflammatory signaling: ubiquitination (including autoubiquitination and K6-linked ubiquitination), NF-\u03baB activation (I\u03baB phosphorylation, NIK activity), JNK cascade regulation, and TNF-mediated signaling. This points to a cohesive cluster of proteins that regulate inflammatory signaling through ubiquitin modification rather than unrelated processes.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":15},{"id":"GO:1903762","count":11},{"id":"GO:0051865","count":11},{"id":"GO:0007250","count":11},{"id":"GO:1901253","count":11}]},{"hash":"212180176097754455","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0010019","count":4},{"id":"GO:0031426","count":4},{"id":"GO:0016554","count":4},{"id":"GO:0090615","count":4},{"id":"GO:0070129","count":4}]},{"hash":"1294703749610048300","title":"Plant developmental transcription regulators","description":"This cluster is driven by GO terms centered on DNA-templated transcription and regulation of transcription, plus tissue- and process-specific development terms such as protoxylem development, root cap development, sieve element enucleation, fruit dehiscence, callus formation, and leaf senescence. The combination suggests a group of transcription-regulatory proteins coordinating plant organ formation and differentiation, rather than a network-based interaction module (no edges/triangles). ","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0090709","count":3},{"id":"GO:0010047","count":3},{"id":"GO:0090059","count":3},{"id":"GO:0006355","count":3}]},{"hash":"1274675842385248226","title":"Telomere maintenance and DNA replication","description":"These terms cohere as telomere maintenance, chromatin remodeling, and DNA replication/cell cycle processes, indicating a cluster of factors coordinating telomere integrity with replication and transcription.","confidence":"High","size":25,"edges":5,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0035390","count":3},{"id":"GO:0009736","count":3},{"id":"GO:0071919","count":3}]},{"hash":"1422303629427007639","title":"Unknown","description":"The top GO terms are diverse across immune (antigen processing via MHC II), plant defense (systemic acquired resistance), plant and animal hormone signaling (ABA, renin-angiotensin), proteolysis, and stress responses, with no single cohesive theme uniting all proteins.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019886","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0080163","count":2},{"id":"GO:0009738","count":2},{"id":"GO:0043086","count":2}]},{"hash":"916285620510813748","title":"Lung and Skeletal Muscle Development","description":"The most frequent GO terms are lung development and skeletal muscle fiber development, suggesting a tissue-development theme. Although there are accompanying terms for calcium signaling and various metabolic processes, the prominent developmental terms guide the label toward tissue development rather than a single pathway.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0030324","count":3},{"id":"GO:0005513","count":3},{"id":"GO:0005979","count":3},{"id":"GO:0048741","count":3}]},{"hash":"250554099019200831","title":"Neural development and organ differentiation","description":"This cluster shows multiple development-related GO terms, especially neural lineage specification (cerebral cortex GABAergic interneuron differentiation; spinal cord motor neuron cell fate specification; spinal cord oligodendrocyte cell fate specification; subpallium neuron fate commitment). Additional terms indicate broader organ development (endocrine pancreas development; bronchiole development) and general transcription/ signaling. The dominant theme is developmental differentiation, primarily neural, with some cross-tissue differentiation.","confidence":"Medium","size":25,"edges":298,"triangles":2255,"max_degree":24,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":17},{"id":"GO:0071277","count":10},{"id":"GO:2001016","count":10},{"id":"GO:0009737","count":9},{"id":"GO:0031018","count":9}]},{"hash":"2264328388419347458","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090615","count":8},{"id":"GO:0090617","count":8},{"id":"GO:0042793","count":8},{"id":"GO:1905639","count":8},{"id":"GO:1900865","count":8}]},{"hash":"1079389405547568138","title":"Lipid and ubiquinone biosynthesis regulation","description":"This cluster is dominated by GO terms for lipid homeostasis and the regulation of ubiquinone biosynthesis, including regulation of tocopherol cyclase activity, suggesting a core theme around lipid/quinone metabolism and its control. Other terms (DNA transcription, sporulation, antibiotic biosynthesis) appear less consistently and may reflect broader or pleiotropic annotations, but the strongest shared signal is lipid and ubiquinone biosynthesis regulation. ","confidence":"Medium","size":25,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055088","count":4},{"id":"GO:1902171","count":4},{"id":"GO:1901006","count":4},{"id":"GO:0010795","count":4},{"id":"GO:0021692","count":4}]},{"hash":"1054869092467675157","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0090615","count":2},{"id":"GO:0090617","count":2},{"id":"GO:0042793","count":2}]},{"hash":"558786770489460788","title":"Plant RNAi and Pol II Promoter Regulation","description":"Cluster centers on plant RNA silencing pathways (siRNA/ta-siRNA, RNAi antiviral response, DNA methylation) and transcription initiation/promoter regulation (RNA polymerase II preinitiation complex assembly, start-site selection). The combination suggests a cohesive plant regulatory module linking RNA silencing to transcription control.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051123","count":2},{"id":"GO:0010199","count":1},{"id":"GO:0048441","count":1},{"id":"GO:0009616","count":1},{"id":"GO:0080188","count":1}]},{"hash":"1580232812282867459","title":"Nuclear Transcription Regulation","description":"Based on the top GO terms, the cluster is dominated by DNA-templated transcription and regulation of RNA polymerase II activity, plus negative regulation of nuclear processes, pointing to a nuclear transcription-control theme. Some neural signaling terms appear but likely represent noise or cross-domain annotations; overall, the function centers on transcriptional regulation in the nucleus.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0009834","count":4},{"id":"GO:0046826","count":3},{"id":"GO:1903026","count":3},{"id":"GO:0006915","count":2}]},{"hash":"1930512758183309153","title":"Unknown","description":"The terms are highly diverse and largely non-overlapping (bacterial cell division with FtsZ, neuron migration, microtubule organization, mRNA tail processing, and unrelated obsolete processes), and the cluster has no edges or strong shared functions, making a single meaningful biological label unreliable.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043093","count":2},{"id":"GO:0006808","count":2},{"id":"GO:0051568","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0000289","count":2}]},{"hash":"987386957139805118","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:1905012","count":2},{"id":"GO:1905004","count":2},{"id":"GO:0019619","count":2},{"id":"GO:0046874","count":2}]},{"hash":"2243911253301223572","title":"Ribosome and Translation Machinery","description":"The top terms are dominated by translation-related processes (GO:0006412), ribosomal large subunit assembly, and even mitochondrial translation initiation, indicating the cluster centers on ribosome function and protein synthesis. Secondary connections to transcription regulation suggest some transcription-associated components, but the primary signature remains translation machinery. ","confidence":"High","size":24,"edges":274,"triangles":1981,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0046677","count":3},{"id":"GO:0071480","count":2},{"id":"GO:0000027","count":2},{"id":"GO:0006355","count":2}]},{"hash":"918707270155703177","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":243,"triangles":1407,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0090615","count":2},{"id":"GO:0090617","count":2},{"id":"GO:0042793","count":2},{"id":"GO:1905639","count":2}]},{"hash":"579444797562395903","title":"Multiorgan Development and Differentiation","description":"This cluster connects to developmental processes across many organs (pituitary, inner ear, forebrain, pancreas, pharyngeal system, gonads, uterus, ureteric buds) and includes regulatory transcription activity, indicating a broad developmental/differentiation program rather than a single tissue-specific function.","confidence":"Medium","size":24,"edges":58,"triangles":44,"max_degree":17,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0021983","count":8},{"id":"GO:0042472","count":7},{"id":"GO:0021902","count":7},{"id":"GO:0003309","count":7},{"id":"GO:0060037","count":7}]},{"hash":"1258847632513662878","title":"Unknown","description":"Explanation: GO terms span neural development, immune signaling, metabolism, and cell-cycle processes, with no single dominant theme, so a cohesive, intuitive label cannot be assigned.","confidence":"","size":24,"edges":17,"triangles":9,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0050830","count":17},{"id":"GO:0071333","count":16},{"id":"GO:0048679","count":15},{"id":"GO:0008286","count":15},{"id":"GO:0021697","count":15}]},{"hash":"65368967712269517","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":5},{"id":"GO:0090617","count":5},{"id":"GO:1905639","count":5},{"id":"GO:1900865","count":5},{"id":"GO:0042793","count":5}]},{"hash":"1654923390313146043","title":"Neuronal vesicle trafficking","description":"The cluster shows enrichment for regulation of synaptic vesicle exocytosis, endosome-to-lysosome transport, and melanosome transport, plus brain development, pointing to a cohesive group involved in intracellular vesicle trafficking with neural relevance. While other terms appear (gene expression regulation, androgen receptor signaling), the vesicle trafficking theme is the strongest signal.","confidence":"Medium","size":24,"edges":50,"triangles":18,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010796","count":7},{"id":"GO:0031384","count":7},{"id":"GO:2000300","count":6},{"id":"GO:0007420","count":6},{"id":"GO:0008333","count":4}]},{"hash":"835449019869565626","title":"Bacterial LPS and exopolysaccharide biosynthesis","description":"This cluster centers on lipopolysaccharide and exopolysaccharide biosynthetic processes (LPS, O antigen, colanic acid, dTDP-rhamnose, galactose metabolism) and related precursors, strongly indicating a shared role in constructing bacterial cell envelopes; peripheral terms like PHB biosynthesis and photosynthesis are less central but fit within broader bacterial metabolism.","confidence":"High","size":24,"edges":4,"triangles":0,"max_degree":3,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0055114","count":9},{"id":"GO:0042619","count":7},{"id":"GO:0097171","count":6},{"id":"GO:0009243","count":6},{"id":"GO:0006541","count":6}]},{"hash":"152289431604924309","title":"Plant Hormone Signaling and Vegetative Growth","description":"These proteins are enriched for multiple plant hormone signaling terms (cytokinin-activated signaling, responses to salicylic acid, gibberellin, and jasmonic acid) and developmental processes (leaf formation and positive regulation of vegetative growth), suggesting a cohesive cluster focused on hormone-mediated growth and development in plants.","confidence":"High","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":10},{"id":"GO:0009751","count":9},{"id":"GO:0009739","count":9},{"id":"GO:1903770","count":8},{"id":"GO:1900386","count":8}]},{"hash":"2264469235288531567","title":"Plant cell wall biogenesis","description":"Top GO terms emphasize plant-type primary and secondary cell wall biogenesis, cellulose biosynthetic process, cell wall organization, and pectin metabolism, indicating proteins involved in building and remodeling the plant cell wall, with pollen germination as supporting context. Therefore, a concise label is Plant cell wall biogenesis.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000919","count":2},{"id":"GO:0009846","count":2},{"id":"GO:0030244","count":2},{"id":"GO:0009833","count":2},{"id":"GO:0010400","count":2}]},{"hash":"1053478897446589244","title":"Multi-tissue development and differentiation","description":"The top GO terms span various tissue development and differentiation processes (epithalamus, myoblasts, pancreas, ureter) and include TGF-beta signaling and hormone responses, suggesting a regulatory, multicellular development theme rather than a single function. Given the heterogeneity, the cluster appears to reflect general developmental regulation across tissues rather than a shared pathway.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021538","count":1},{"id":"GO:0048545","count":1},{"id":"GO:0045662","count":1},{"id":"GO:0071560","count":1},{"id":"GO:0010909","count":1}]},{"hash":"1552658050721961201","title":"Developmental Signaling and Differentiation","description":"The top GO terms point to development and signaling processes, including forebrain development, keratinocyte differentiation, and key growth pathways (Wnt and Hippo), along with apoptosis and cell-cycle related terms like DNA replication. This pattern suggests a cluster of proteins involved in developmental signaling and cell fate decisions rather than a single, tightly linked function.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006915","count":8},{"id":"GO:0030216","count":8},{"id":"GO:0090263","count":8},{"id":"GO:0060044","count":8},{"id":"GO:0035329","count":8}]},{"hash":"1813523864395736668","title":"Developmental Transcriptional Regulation","description":"The dominant GO terms point to transcriptional control (DNA-templated transcription, RNA Pol II regulation, miRNA transcription) intertwined with developmental processes (vitellogenesis, eyelid development, TGF-\u03b2 production) and calcium signaling, suggesting a cohesive theme of gene expression regulation during development and signaling rather than a single pathway.","confidence":"Medium","size":24,"edges":256,"triangles":1625,"max_degree":23,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007296","count":10},{"id":"GO:0071277","count":10},{"id":"GO:0006351","count":7},{"id":"GO:0009737","count":7},{"id":"GO:0000183","count":6}]},{"hash":"1637732040996673706","title":"Core cell growth and division machinery","description":"The dominant GO terms point to fundamental cellular processes: ribosome biogenesis, RNA splicing, mRNA capping, and assembly of pre-replicative complexes for DNA replication, all of which are essential for cell growth and division. The presence of plant-related terms like pectin biosynthesis and auxin transport suggests additional growth-related remodeling, but the core theme remains core cellular maintenance during proliferation.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0008380","count":2},{"id":"GO:0006370","count":2},{"id":"GO:0006267","count":2}]},{"hash":"1175349858042498585","title":"TLR-Driven Innate Immune Signaling","description":"These proteins cluster around Toll-like receptor signaling (TLR4/7/10) and downstream cytokine production, including regulation of interferon-\u03b1/\u03b2, inflammatory responses, and dendritic cell cytokine output, with a note on MyD88-independent pathways; together they point to innate immune sensing and antimicrobial peptide responses. This makes \"TLR-Driven Innate Immune Signaling\" a concise, representative label for the cluster.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0002730","count":3},{"id":"GO:0034142","count":3},{"id":"GO:0034166","count":3},{"id":"GO:0045356","count":3},{"id":"GO:0034154","count":3}]},{"hash":"1979334496452244796","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0090617","count":7},{"id":"GO:0042793","count":7},{"id":"GO:1905639","count":7},{"id":"GO:1900865","count":7},{"id":"GO:0031426","count":7}]},{"hash":"1043695433202202450","title":"Fungal sporulation and cell cycle regulation","description":"The top terms converge on ascospore formation, mitotic cell cycle control (G1/S transition), spindle\u2013kinetochore attachment, and nuclear migration during mating/conjugation, with exocytosis aligning to spore release processes. This points to a coordinated fungal developmental program that links cell cycle regulation to sporulation and meiosis, rather than a single generic pathway. ","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030437","count":3},{"id":"GO:0000082","count":2},{"id":"GO:0051315","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0071157","count":2}]},{"hash":"1983805066710854062","title":"Unknown","description":"The top GO terms cover immune, developmental, endocrine, and cellular processes with little overlap, and there are no edges among proteins, so there is no cohesive theme to label the cluster beyond Unknown.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043277","count":24},{"id":"GO:0046641","count":24},{"id":"GO:0060709","count":24},{"id":"GO:0006611","count":24},{"id":"GO:0061167","count":24}]},{"hash":"1992378575394707031","title":"Unknown","description":"The top terms span development, transcription, stress responses, hormone signaling, and immune/neural signaling with no single cohesive function, and with no edges connecting proteins, making a specific, representative label unlikely.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0034198","count":3},{"id":"GO:0000082","count":3},{"id":"GO:0006349","count":3}]},{"hash":"2159077340106783663","title":"ABA-Driven Plant Development and Cuticle Biosynthesis","description":"The cluster centers on transcriptional regulation in plant development (DNA-templated transcription, regulation of transcription) with concrete developmental processes (floral meristem growth, bract development, seed development) and ABA signaling, plus epidermal/epicuticular biosynthesis (wax and cutin). This suggests a cohesive module of ABA-responsive developmental control coupled to cuticle formation. ","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:0007275","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0009738","count":4},{"id":"GO:0048316","count":4}]},{"hash":"1439305618908452899","title":"Placental trophoblast development and gene regulation","description":"The cluster shows strong signals for placental structures (spongiotrophoblast and labyrinthine layer development) alongside diverse gene-regulatory processes (DNA-templated transcription, mRNA processing, miRNA turnover, chromatin regulation, and post-translational modifications), suggesting a cohesive module around placental/trophoblast differentiation and its transcriptional control. ","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006378","count":2},{"id":"GO:0010587","count":2},{"id":"GO:0060712","count":2},{"id":"GO:1904333","count":2}]},{"hash":"245346376504278358","title":"ER-Golgi trafficking and cytoskeletal transport","description":"This cluster centers on vesicle transport between the endoplasmic reticulum and Golgi, including retrograde and ER-to-Golgi routes, plus microtubule-based movement. Additional terms like peptidyl-serine dephosphorylation and positive regulation of GTPase activity suggest regulatory control of transport and cytoskeletal dynamics; TORC1 signaling and mRNA transport may modulate trafficking processes. The preponderance of vesicle trafficking and cytoskeleton terms indicates a cohesive function in intracellular transport and protein sorting.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070262","count":5},{"id":"GO:0038202","count":5},{"id":"GO:0051028","count":5},{"id":"GO:0006890","count":5},{"id":"GO:0043547","count":5}]},{"hash":"876059246452528114","title":"Neuronal development and synaptic regulation","description":"Top terms center on neuronal development and plasticity (nerve branching, axonal fasciculation, and long-term synaptic regulation). The presence of DNA-templated transcription and its regulation suggests coordinated gene expression during development, while Golgi-to-plasma membrane transport and rRNA maturation reflect essential cellular machinery. Lipid homeostasis and tocopherol regulation may relate to membrane dynamics in neurons; antibiotic response appears as an outlier. Overall, the cluster represents neuronal development and synaptic regulation.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000172","count":2},{"id":"GO:0007413","count":2},{"id":"GO:0048169","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2}]},{"hash":"1884345311884838658","title":"Developmental transcriptional and epigenetic regulation","description":"The set centers on developmental gene regulation and growth control, with GO terms for placenta morphogenesis, liver regeneration, and negative regulation of cell proliferation, plus transcriptional and epigenetic modifiers (DNA-templated transcription and histone lysine methylation). This points to a cohesive theme of developmental transcriptional/epigenetic regulation coordinating cell-cycle decisions.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060669","count":2},{"id":"GO:0048147","count":2},{"id":"GO:0007406","count":2},{"id":"GO:2000134","count":1},{"id":"GO:2001040","count":1}]},{"hash":"1900444435020541122","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0031573","count":2},{"id":"GO:0043111","count":2},{"id":"GO:2000344","count":2},{"id":"GO:0016042","count":2}]},{"hash":"404599353922243556","title":"Plant photosynthesis and light-harvesting","description":"This cluster is centered on photosynthesis and light-responsive processes, including light harvesting in photosystems I and II, responses to different light qualities/intensities (far red, high/low light, UV-A), and nonphotochemical quenching, with additional hints from chlorophyll/phytol biosynthesis. These shared GO terms strongly point to chloroplast photosynthetic machinery and its light-related regulation, justifying a photosynthesis/light-harvesting label.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":4},{"id":"GO:0018298","count":4},{"id":"GO:0009768","count":3},{"id":"GO:1904964","count":3},{"id":"GO:0010218","count":3}]},{"hash":"371426117643655904","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0007584","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0090615","count":4},{"id":"GO:0090617","count":4}]},{"hash":"1826636943605042318","title":"Unknown","description":"The terms span vacuolar transport and secretion (GPI anchor biosynthesis, V-type ATPase assembly, nectar secretion, sucrose/fructose transport) along with unrelated processes (stem cell maintenance, auxin signaling regulation, proteolysis, autophagy regulation, and smooth muscle differentiation). Because there is no single cohesive function linking these proteins, the cluster cannot be assigned a specific biological theme.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":1},{"id":"GO:0070072","count":1},{"id":"GO:0051151","count":1},{"id":"GO:0019827","count":1},{"id":"GO:1902334","count":1}]},{"hash":"1255818408373052209","title":"Chaperone-assisted Translation and Protein Folding","description":"This cluster centers on protein synthesis and maturation, highlighted by GO terms for translation (GO:0006412), positive regulation of mitochondrial translation, and protein folding with chaperone-mediated folding. The presence of iron-sulfur cluster assembly further supports a role in cofactor maturation integral to protein function. While there are some outlier biosynthetic terms (e.g., LPS biosynthesis, arsenic detox), the dominant signal points to a system coordinating translation and proper protein folding with chaperone assistance. ","confidence":"High","size":23,"edges":253,"triangles":1771,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0099132","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0070131","count":2},{"id":"GO:0006457","count":2},{"id":"GO:1990507","count":1}]},{"hash":"1665315060110263954","title":"Gene Expression Regulation","description":"The terms are dominated by transcription-related processes (DNA-templated transcription, transcription termination, transcription antitermination) and translation control (negative regulation of translational initiation) plus tRNA aminoacylation, pointing to regulation of gene expression at both transcription and translation levels; occasional vascular development terms (angiogenesis, vasculogenesis) are present but less central. This supports naming the cluster as Gene Expression Regulation. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0055114","count":2},{"id":"GO:1901006","count":1},{"id":"GO:0070183","count":1},{"id":"GO:0031564","count":1}]},{"hash":"567045837028793408","title":"Unknown","description":"Top GO terms are highly heterogeneous, spanning carotenoid biosynthesis, polyamine catabolic processes, developmental signals (substantia nigra development; megakaryocyte differentiation), chromatin regulation, histone ubiquitination, lipopolysaccharide response, and post-translational modification. The cluster has no edges (Edges: 0, Triangles: 0, Max Degree: 0) and many proteins were re-added by RECIPE, suggesting a composition driven by data processing rather than a single coherent function. Because there is no clear common theme linking these proteins, this cluster is best labeled Unknown, with no confident functional label.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0021762","count":2},{"id":"GO:0046203","count":1},{"id":"GO:0045654","count":1},{"id":"GO:0016117","count":1}]},{"hash":"2219993504765966278","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0010019","count":2},{"id":"GO:0031126","count":1},{"id":"GO:0030420","count":1},{"id":"GO:0090503","count":1}]},{"hash":"273137871886345892","title":"Abiotic stress response and chromatin regulation","description":"The top GO terms point to abiotic stress responses (desiccation, high light, ABA biosynthesis) alongside transcriptional control and chromatin-related processes (RNA Pol II regulation, heterochromatin formation, DNA topology, chromosome condensation), indicating a cluster of proteins coordinating stress response with transcriptional and chromatin remodeling and related developmental/circadian regulation.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009269","count":2},{"id":"GO:0010116","count":2},{"id":"GO:0009644","count":2},{"id":"GO:0000183","count":2},{"id":"GO:0006357","count":1}]},{"hash":"2273628552366570653","title":"Anthocyanin biosynthesis and trichome development","description":"The cluster is dominated by GO terms related to pigment biosynthesis (anthocyanin-containing compounds, anthocyanin biosynthetic process) and epidermal structures (trichome differentiation, trichome patterning, seed coat development), plus jasmonic acid signaling that regulates these processes in plants. While there are a few outlier terms from animal biology, the plant-associated terms strongly suggest a cohesive module for pigment production and epidermal differentiation. ","confidence":"Medium","size":23,"edges":246,"triangles":1637,"max_degree":22,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":11},{"id":"GO:0031542","count":8},{"id":"GO:0045348","count":7},{"id":"GO:0071277","count":7},{"id":"GO:0010026","count":6}]},{"hash":"1809609623754553506","title":"Glutamatergic Synaptic Transmission and Behavioral Modulation","description":"The top GO terms cluster around neural signaling and behavior, especially glutamatergic synaptic transmission, its modulation by GPCR pathways, and related behavioral outputs (memory and ethanol-responsive behavior). While some terms like methanol catabolic process and suckling behavior are peripheral, the core theme ties to synaptic signaling at glutamatergic synapses and how it influences behavior. The lack of interaction edges does not negate this functional theme, as the annotations point to a coherent neural signaling/behavior axis.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006816","count":2},{"id":"GO:0008277","count":2},{"id":"GO:0035249","count":1},{"id":"GO:0001967","count":1},{"id":"GO:0065009","count":1}]},{"hash":"2117456827051934235","title":"RNA splicing and mRNA processing regulation","description":"Based on the top GO terms, the cluster centers on regulation and processing of mRNA, including spliceosome-mediated splicing (regular and alternative), mRNA export, modification, and stabilization, with associated helicase activity. These collectively point to RNA maturation and post-transcriptional control as the core function, while a single term like blastocyst formation appears secondary. ","confidence":"High","size":23,"edges":19,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0051096","count":2},{"id":"GO:0016556","count":2},{"id":"GO:0006406","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0048026","count":2}]},{"hash":"2131183818931820109","title":"Oxidative stress response and signaling","description":"This cluster shows a clear emphasis on cellular redox balance and stress signaling, with terms like hydrogen peroxide biosynthesis, respiratory burst, oxidative stress-induced apoptotic signaling, and cellular stress response to acidic pH. Additional terms such as response to cAMP and negative regulation of protein kinase activity support signaling modulation under stress. A couple of developmental terms (skeletal muscle differentiation, cuticle development) may be collateral rather than core themes.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035914","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0008365","count":2},{"id":"GO:0051591","count":2},{"id":"GO:0050665","count":2}]},{"hash":"2050919343075927720","title":"Nuclear RNA splicing and processing","description":"The top terms cluster around spliceosome-mediated mRNA splicing, snRNP/complex assembly, and other nuclear RNA processing steps (including deadenylation-dependent decapping and tRNA processing) plus import into the nucleus and transcription termination; stress-related terms (ABA and water deprivation) may reflect regulation of gene expression under stress but do not change the core function.","confidence":"High","size":23,"edges":179,"triangles":764,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":3},{"id":"GO:0006369","count":3},{"id":"GO:0009414","count":2},{"id":"GO:0051170","count":2},{"id":"GO:0000290","count":2}]},{"hash":"1349404691828216787","title":"Ubiquitin-Proteasome Degradation Pathways","description":"The cluster is dominated by GO terms related to ubiquitin-dependent protein catabolism, including SCF-dependent proteasomal degradation, autoubiquitination, and ubiquitination processes, with additional links to ERAD and ubiquitin-regulated signaling (e.g., NF-kappaB activation). These collectively point to a coherent function in tagging proteins for degradation via the ubiquitin-proteasome system, plus associated quality-control and signaling roles.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":8},{"id":"GO:0042787","count":8},{"id":"GO:0051865","count":6},{"id":"GO:0030433","count":5},{"id":"GO:0000715","count":5}]},{"hash":"1124308284076073796","title":"RNA Transcription and Ribosome Biogenesis","description":"This cluster is dominated by GO terms for RNA transcription (Pol I/II/III), RNA-templated transcription, ribosome biogenesis, and nucleologenesis, pointing to a shared role in nuclear transcription and ribosome assembly; ancillary terms like nitrogen fixation and iron-sulfur cluster assembly may reflect annotation noise or multifunctional proteins.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":1},{"id":"GO:0001172","count":1},{"id":"GO:0042790","count":1},{"id":"GO:0042797","count":1},{"id":"GO:0042254","count":1}]},{"hash":"2003516002481837879","title":"Adaptive immune signaling and tissue remodeling","description":"This cluster is dominated by GO terms tied to adaptive immunity, including B cell receptor signaling and alpha-beta T cell proliferation, along with negative regulation of cell proliferation. It also includes processes related to tissue remodeling, such as angiogenesis and animal organ regeneration, and signals of cellular proliferation (DNA replication). The presence of PI3K-related terms (even if obsolete) supports PI3K pathway involvement in immune signaling. While a neuronal-related term (dendritic spine morphogenesis) appears, the overall pattern points to adaptive immune signaling intertwined with tissue remodeling.","confidence":"Medium","size":23,"edges":16,"triangles":1,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0008285","count":19},{"id":"GO:0050853","count":18},{"id":"GO:0014068","count":18},{"id":"GO:0006260","count":18},{"id":"GO:0043552","count":18}]},{"hash":"1498658353571208954","title":"Neuronal development and signaling","description":"This cluster is dominated by GO terms related to neural processes, notably dendrite morphogenesis and visual perception, along with potassium ion transport and transcriptional regulation, suggesting a neural development/signaling theme. Some terms (chemotaxis, interleukin-4 response) hint at immune-related roles or mixed cell types, but the neural-related terms are the strongest signal.","confidence":"Medium","size":23,"edges":214,"triangles":1200,"max_degree":22,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":9},{"id":"GO:0006351","count":9},{"id":"GO:0006935","count":8},{"id":"GO:0006813","count":8},{"id":"GO:0048813","count":7}]},{"hash":"1572197698274419809","title":"Ubiquitin-Dependent Protein Degradation","description":"The top GO terms point to ubiquitination and ubiquitin-dependent proteolysis (autoubiquitination, K48- and K6-linked ubiquitination, ubiquitin-dependent protein catabolic process, ERAD-related pathway). Additional terms involve histone turnover and NF-kappaB/TNF signaling regulation, consistent with a cluster of proteins that regulate proteostasis and inflammatory signaling through ubiquitin modification.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":13},{"id":"GO:0030433","count":13},{"id":"GO:0090073","count":12},{"id":"GO:0070936","count":12},{"id":"GO:1903265","count":12}]},{"hash":"1262772446978400850","title":"BMP/TGF-\u03b2 and MAPK signaling regulation","description":"This cluster's terms point to regulation and modulation of signaling pathways\u2014particularly BMP/TGF-\u03b2/SMAD and MAPK\u2014with related developmental roles (e.g., TGF-\u03b2 response, BMP signaling regulation, SMAD complex regulation, and meristem identity maintenance). The inclusion of peptidyl-threonine dephosphorylation and NF-\u03baB-related regulation supports a general theme of signaling control rather than a single enzymatic activity.","confidence":"Medium","size":23,"edges":176,"triangles":756,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0000173","count":23},{"id":"GO:0035970","count":23},{"id":"GO:0061191","count":22},{"id":"GO:0046827","count":22},{"id":"GO:0042347","count":22}]},{"hash":"1255082568610291391","title":"Steroid and retinoid metabolism","description":"This cluster is enriched for glucocorticoid biosynthesis, C21-steroid hormone metabolic process, androgen catabolic process, and retinoic acid biosynthetic process, pointing to metabolism of steroid hormones and retinoids as a core theme. While there are a few outlier terms related to other biosynthetic/catabolic processes, the hormone and retinoid metabolism signals dominate, suggesting a cohesive functional grouping around steroid/retinoid signaling and related development. ","confidence":"Medium","size":23,"edges":39,"triangles":4,"max_degree":8,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":9},{"id":"GO:0042376","count":8},{"id":"GO:0045150","count":8},{"id":"GO:0042761","count":8},{"id":"GO:0030324","count":8}]},{"hash":"1020967677375653595","title":"Kinase Signaling and Proliferation Regulation","description":"This cluster is dominated by GO terms pointing to regulation of kinase activity (serine/threonine) and autophosphorylation, as well as positive regulation of GTPase activity, cell proliferation, and the mitotic cell cycle. These collectively indicate a group of proteins that modulate phosphorylation-driven signaling cascades and cell growth. Some terms like pigmentation are outliers, but the core theme ties to signal transduction and proliferation control.","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:0043547","count":4},{"id":"GO:0008284","count":4},{"id":"GO:0071902","count":4},{"id":"GO:0043473","count":4}]},{"hash":"1852714669462529027","title":"Immune Regulation and Virus Response","description":"The cluster is dominated by GO terms linked to immune functions, including apoptotic cell clearance, positive regulation of T cell proliferation, tolerance induction to self antigen, and cellular response to virus, suggesting a focus on immune regulation and antiviral responses. Some other terms in the list (placental development, ER polarization, protein export from nucleus, meiosis-related processing, parathyroid hormone secretion) appear more peripheral or contextually broad, which lowers the overall cohesion of a single theme. Taken together, the strongest signal is immune-related functions, with some outliers likely reflecting multifunctional proteins or annotation noise.","confidence":"Medium","size":23,"edges":12,"triangles":6,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043277","count":22},{"id":"GO:0046641","count":22},{"id":"GO:0060709","count":22},{"id":"GO:0006611","count":22},{"id":"GO:0061167","count":22}]},{"hash":"546234202418778216","title":"Nutrient and xenobiotic transmembrane transport","description":"This cluster is dominated by GO terms describing transport of nutrients, vitamins, xenobiotics, and antibiotics across membranes, suggesting membrane transporter proteins as a core function. Some co-occurring terms relate to translation and splicing, which may reflect multifunctional proteins rather than the primary cluster feature; overall, membrane transport of nutrients and xenobiotics best explains the set.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0042891","count":5},{"id":"GO:0007584","count":5},{"id":"GO:0006855","count":5},{"id":"GO:0046677","count":5},{"id":"GO:0035461","count":5}]},{"hash":"431940751123174228","title":"Unknown","description":"The top GO terms are highly diverse (immune signaling, development, steroid receptor assembly, sex differentiation, snoRNP and histone-related processes, metabolism, and even plant-specific chlorophyll regulation), with no single coherent function linking the proteins. Edges are absent, suggesting these entries do not form a cohesive functional cluster, so a specific label is not justifiable.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071357","count":6},{"id":"GO:0030850","count":6},{"id":"GO:0006463","count":6},{"id":"GO:0046661","count":6},{"id":"GO:0000492","count":6}]},{"hash":"899370659664056388","title":"Plant development and cuticle biosynthesis regulation","description":"Top GO terms indicate plant-specific developmental processes (multicellular organism development, floral meristem growth, bract and seed development) along with transcriptional regulation (DNA-templated transcription, regulation of DNA-templated transcription), ABA signaling, and cuticle biosynthesis (wax and cutin). This suggests a coordinated role in plant organ/seed development with regulation of cuticle formation and hormone signaling, likely mediated by transcription factors that control these developmental programs. ","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:1904276","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":3},{"id":"GO:1901959","count":3}]},{"hash":"801883587345285637","title":"Unknown","description":"The GO terms span abiotic stress responses (desiccation, high light, ABA biosynthesis), nitrate assimilation, mRNA stability regulation, and ER tubular network formation/maintenance, plus some development terms; no single cohesive function ties them together, and there are no edges, so a cohesive label cannot be assigned.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043488","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0009269","count":1},{"id":"GO:0010116","count":1},{"id":"GO:0009644","count":1}]},{"hash":"1976188582067207232","title":"Plant cell wall biogenesis and fungal detection","description":"This cluster\u2019s top GO terms cluster around plant-specific cell wall biology (xyloglucan metabolism, plant-type cell wall modification, fungal-type wall organization, and cell wall biogenesis) and a immune/recognition signal for fungal origin, suggesting a set of proteins involved in plant cell wall remodeling coupled with pathogen detection. Some terms are obsolete, but the overarching theme is plant cell wall dynamics paired with fungal recognition. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0032491","count":7},{"id":"GO:0009831","count":7},{"id":"GO:0006037","count":7},{"id":"GO:0010411","count":7},{"id":"GO:0042546","count":7}]},{"hash":"1825004210879390231","title":"Organellar RNA Processing and Transcription Regulation","description":"The cluster shows strong representation of transcription-related GO terms (regulation of DNA-templated transcription and DNA-templated transcription) along with multiple organellar RNA processing/editing terms (mitochondrial and chloroplast mRNA processing, cytidine to uridine editing) and chloroplast-nucleus signaling, suggesting a theme of organelle gene expression coordination with nuclear transcription.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0006094","count":2},{"id":"GO:0046686","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1380352898808760523","title":"Oocyte Maturation and Meiotic Spindle Assembly","description":"The top GO terms center on oocyte maturation and spindle assembly in female meiosis I, alongside ubiquitin-proteasome\u2013dependent protein degradation, which together point to regulation of meiosis and protein turnover in oocytes. There are also related developmental terms (neural tube initiation and brain ventricle development) that reflect broader embryogenesis, but the core signal is meiosis-related processes and proteolysis.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":14},{"id":"GO:0001556","count":13},{"id":"GO:0070544","count":13},{"id":"GO:0046785","count":13},{"id":"GO:0042787","count":13}]},{"hash":"1460443693480596257","title":"Mitochondrial Fe-S cluster biogenesis","description":"The cluster is centered on mitochondrial Fe-S cluster assembly and related protein import and maturation processes, as indicated by terms for protein import into the mitochondrial matrix and [2Fe-2S] cluster assembly, with supporting links to iron-responsive regulation and metabolism. This points to a cohesive module dedicated to Fe-S biogenesis in mitochondria rather than a general cell-cycle function.","confidence":"Medium","size":22,"edges":229,"triangles":1501,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0030150","count":2},{"id":"GO:0051220","count":1},{"id":"GO:0044571","count":1}]},{"hash":"2070355005700398591","title":"mRNA Splicing and Processing Regulation","description":"This cluster centers on control of spliceosome-mediated mRNA processing, with terms for positive and negative regulation of splicing, mRNA export and stabilization, but also mRNA modification and ncRNA-mediated silencing. The cohesive theme is regulation of spliceosome activity and subsequent mRNA fate (including alternative splicing), which fits a single functional module, with developmental hints from blastocyst formation.","confidence":"High","size":22,"edges":197,"triangles":982,"max_degree":21,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048025","count":4},{"id":"GO:0016556","count":3},{"id":"GO:0006406","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0048026","count":3}]},{"hash":"637463701112219009","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0015979","count":3},{"id":"GO:0090617","count":3},{"id":"GO:0042793","count":3},{"id":"GO:1905639","count":3}]},{"hash":"880718121709752044","title":"Plant metabolism and photosynthesis","description":"The top GO terms cluster around plant-specific metabolism (glucosinolate, lactose, cellulose catabolism) and light-energy processes (photosynthesis, nonphotochemical quenching), plus signaling pathways (cytokinin-activated signaling, insulin receptor signaling). Translation is a general background process. Together these terms point to a set of proteins involved in plant metabolic activities and light-related energy pathways, justifying the label. ","confidence":"Medium","size":22,"edges":24,"triangles":6,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0046677","count":3},{"id":"GO:0019762","count":3},{"id":"GO:0019512","count":3},{"id":"GO:0009736","count":3}]},{"hash":"277298633924101041","title":"Ribosome Biogenesis and Translation","description":"The dominant GO terms are translation (GO:0006412) and ribosome biogenesis, including large subunit biogenesis/assembly/export, which together point to proteins involved in ribosome production and protein synthesis. The presence of regulation of translation and stress/antibiotic response terms complements this core function, but the primary signal is ribosome assembly and translation machinery.","confidence":"High","size":22,"edges":99,"triangles":185,"max_degree":20,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":15},{"id":"GO:0042254","count":4},{"id":"GO:0046677","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0000055","count":3}]},{"hash":"1805848095177759256","title":"Stress-Response and Neurotransmitter Regulation","description":"The top GO terms point to diverse chemical and immune stress responses (lipopolysaccharide, xenobiotic stimuli, metal ions, ethanol) alongside modulation of neurotransmitter metabolism (dopamine, serotonin) and RNA processing (alternative splicing). This suggests a general stress-response program that also impacts neurotransmitter regulation, rather than a single, tightly linked pathway. The single edge and mixed functions support a broad, multi-function cluster rather than a specific pathway.","confidence":"Medium","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0032496","count":7},{"id":"GO:0009228","count":7},{"id":"GO:0010044","count":7},{"id":"GO:0014063","count":7},{"id":"GO:0042493","count":7}]},{"hash":"332416512311196140","title":"Chromatin assembly and transcriptional regulation in development","description":"The cluster features chromatin-related processes (nucleosome assembly, chromatin assembly during DNA replication, rDNA heterochromatin formation) and transcriptional control (negative regulation of RNA polymerase II), with additional development-related terms such as brain development and gonad/pituitary development. This suggests proteins involved in chromatin remodeling and regulation of gene expression during developmental programs, forming a coherent functional theme.","confidence":"High","size":22,"edges":14,"triangles":4,"max_degree":6,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":7},{"id":"GO:0000183","count":6},{"id":"GO:0055114","count":5},{"id":"GO:0051572","count":5},{"id":"GO:0007420","count":5}]},{"hash":"223395108744581584","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090617","count":5},{"id":"GO:0042793","count":5},{"id":"GO:1905639","count":5},{"id":"GO:1900865","count":5},{"id":"GO:0031426","count":5}]},{"hash":"609469917101531275","title":"Alkaloid and bile acid catabolism","description":"The top GO terms cluster around catabolic and metabolic processing of alkaloids (carbazole, isoquinoline alkaloids, retinoic acid) and bile acids, plus triglyceride metabolism, indicating enzymes dedicated to xenobiotic and lipid breakdown. A few terms about cellular responses to ions are present but appear tangential; the dominant theme is alkaloid/bile acid and related lipid catabolism. ","confidence":"High","size":22,"edges":13,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0046232","count":22},{"id":"GO:0009822","count":21},{"id":"GO:0006641","count":21},{"id":"GO:0071615","count":21},{"id":"GO:0034653","count":21}]},{"hash":"2124196985918282012","title":"Exocyst-Mediated Exocytosis and Golgi-to-PM Transport","description":"The leading GO terms point to vesicle trafficking via the exocytic pathway, with strong emphasis on exocytosis, exocyst assembly/localization, and Golgi-to-plasma membrane transport, indicating a cohesive exocytic/vesicle-trafficking theme; the other terms appear as ancillary processes.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015031","count":3},{"id":"GO:0006887","count":3},{"id":"GO:0006893","count":3},{"id":"GO:0001927","count":3},{"id":"GO:0051601","count":3}]},{"hash":"884988906669852806","title":"Unknown","description":"This cluster shows a mix of GO terms across disparate biology: androgen and testosterone metabolism, retinal and retinol biosynthesis, various biosynthetic pathways (anthocyanin, poly-hydroxybutyrate, secondary alcohol), plus transcription and sporulation. There is only one edge and no clear shared pathway connecting these terms, and several entries are broad or obsolete, so there is no coherent, single function representing the cluster.","confidence":"","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":15},{"id":"GO:0008209","count":8},{"id":"GO:0042574","count":8},{"id":"GO:0006351","count":6},{"id":"GO:0009718","count":6}]},{"hash":"1851813957179569587","title":"Core metabolism and genetic information processing","description":"The terms cluster around ATP metabolism and energy regulation, DNA replication, mRNA export, and viral genome replication, with additional metabolic pathway terms like LPS biosynthesis, indicating a core set of cellular energy and genetic information processing. ","confidence":"Medium","size":22,"edges":16,"triangles":1,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0009103","count":5},{"id":"GO:0045150","count":4},{"id":"GO:0046034","count":4},{"id":"GO:0006406","count":4}]},{"hash":"1822526248791812466","title":"Signaling and chromatin regulation","description":"The cluster highlights two main themes: signal transduction (cytokinin-activated and insulin receptor signaling) and regulation of gene expression via chromatin remodeling, histone methylation, and transcription control. The presence of cell growth and cellular senescence terms suggests functional outcomes of signaling and epigenetic regulation. While a few terms (like cobalamin biosynthesis) are more metabolic or annotation-related, the predominant pattern points to proteins involved in signaling pathways that influence chromatin state and transcription. As such, a concise label would be \u201cSignaling and chromatin regulation.\u201d ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":8},{"id":"GO:0043044","count":6},{"id":"GO:0008286","count":5},{"id":"GO:0016049","count":4},{"id":"GO:0043985","count":4}]},{"hash":"1402690348061870492","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":28,"triangles":7,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006526","count":4},{"id":"GO:0006094","count":3},{"id":"GO:0044205","count":3},{"id":"GO:0006090","count":3},{"id":"GO:0019240","count":3}]},{"hash":"2275238978856842727","title":"RNA Processing and Translation","description":"The top GO terms are dominated by RNA metabolism and gene-expression control, including alternative splicing, polyadenylation, primary miRNA processing, mRNA methylation, and mRNA destabilization, plus cytoplasmic translation. These collectively point to RNA processing and translation regulation as the core function of the cluster, with a few outliers related to growth or development that don\u2019t override the main theme.","confidence":"High","size":22,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000380","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0002181","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0051321","count":1}]},{"hash":"1030062146134321685","title":"Plant development and hormone signaling","description":"The terms are dominated by plant hormone signaling (cytokinin, jasmonic acid) and developmental processes (leaf formation, vegetative growth, flavonol biosynthesis). Nucleosome assembly and rDNA heterochromatin formation hint at chromatin regulation during development, supporting a theme of growth control through hormonal signaling and gene regulation.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009736","count":3},{"id":"GO:0006334","count":3},{"id":"GO:1903770","count":2},{"id":"GO:1900386","count":2},{"id":"GO:0010338","count":2}]},{"hash":"155575684687253270","title":"Cross-Taxa Developmental Regulation","description":"The cluster\u2019s top GO terms point to diverse developmental processes across organisms (pituitary gland development, leaf formation, roof of the mouth development, multicellular organism development) and related transcriptional regulation, plus a plant hormone response, suggesting proteins involved in broad developmental control rather than a single pathway.","confidence":"Medium","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0021983","count":7},{"id":"GO:0055114","count":6},{"id":"GO:0007275","count":6},{"id":"GO:0009737","count":6},{"id":"GO:0000183","count":6}]},{"hash":"122675192731235275","title":"DNA replication and chromatin remodeling","description":"The cluster is dominated by GO terms for DNA replication, its initiation, and prereplicative complex assembly, along with chromatin remodeling and heterochromatin formation, indicating a core theme of genome maintenance and chromatin-state control. While a few terms pertain to oskar mRNA translation, epithelial migration, and apoptotic membrane regulation, these appear ancillary to the central replication/chromatin signal, supporting a label focused on DNA replication and chromatin dynamics.","confidence":"High","size":22,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0006270","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0043044","count":2},{"id":"GO:0030466","count":1}]},{"hash":"1299497335703101429","title":"Ion and Sugar Transporters","description":"This cluster shows a strong enrichment for transmembrane transport of various ions (sodium, potassium, phosphate) and small molecules (galactose, nitrate/nitrite, sialic acid), plus a neuron-specific process of neurotransmitter loading into vesicles. Although an outlier term related to transcription regulation appears, the dominant theme is membrane transport activity across multiple substrates, supporting a cohesive label of ion and sugar transporters.","confidence":"Medium","size":22,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0015707","count":2},{"id":"GO:0042891","count":2},{"id":"GO:0015757","count":2},{"id":"GO:0035725","count":2}]},{"hash":"1586121483655491833","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000147","count":2},{"id":"GO:0015074","count":2},{"id":"GO:0019068","count":2},{"id":"GO:0039651","count":2},{"id":"GO:0039702","count":2}]},{"hash":"1426025907394800614","title":"Ribosome biogenesis and RNA processing","description":"The top GO terms cluster around ribosome assembly and translation (ribosomal small subunit assembly, SSU-rRNA maturation, translation, ribosome biogenesis) as well as RNA processing and splicing (mRNA processing, RNA splicing, spliceosomal tri-snRNP complex assembly). This suggests the proteins predominantly function in ribosome biogenesis and RNA metabolism, with a few terms (mitochondrial ATP transport, insulin response, liver regeneration) likely representing secondary associations or annotation noise. ","confidence":"Medium","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000028","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0000244","count":1}]},{"hash":"428385432781925018","title":"Unknown","description":"The set includes transcription-related GO terms (regulation of transcription, RNA Pol II initiation and snRNA processing) alongside plant-specific seed development and mucilage/pectin metabolism and an outlier placental term, with no clear unifying function across organisms.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0048316","count":2},{"id":"GO:0048358","count":1},{"id":"GO:0042545","count":1},{"id":"GO:0045490","count":1}]},{"hash":"1564778905576399244","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090617","count":6},{"id":"GO:1905639","count":6},{"id":"GO:1900865","count":6},{"id":"GO:0042793","count":6},{"id":"GO:0010019","count":6}]},{"hash":"564390836537165291","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning plant secondary metabolism (sporopollenin, phenylpropanoid, pinoresinol catabolic), bacterial cell-surface biosynthesis (O-antigen, LPS core), transcription, and visual perception, with no single dominant shared function across the cluster. Therefore there isn\u2019t a coherent unifying theme to assign a specific label. ","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0006351","count":1},{"id":"GO:0009699","count":1},{"id":"GO:1902123","count":1}]},{"hash":"798432357213640218","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:1901621","count":2},{"id":"GO:0097428","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0006458","count":2}]},{"hash":"2156480751011608960","title":"RNA Methylation and Related Biosynthetic Modifications","description":"This cluster is dominated by RNA modification processes: several GO terms for RNA guanine-N7 methylation, mRNA 7-methylguanosine capping, tRNA methylation, and rRNA methylation. There are also other biosynthetic terms (sterol, ubiquinone, polyamine) and a protein modification term (peptidyl-arginine hydroxylation), but the strongest, most representative signal is RNA methylation and related RNA processing. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030961","count":2},{"id":"GO:0016126","count":2},{"id":"GO:0043985","count":2},{"id":"GO:0001300","count":2},{"id":"GO:0006744","count":2}]},{"hash":"180871535741140888","title":"Immune Regulation and Tolerance","description":"The prominent GO terms center on immune-related processes, including apoptotic cell clearance, positive regulation of T cell proliferation, and positive regulation of tolerance induction to self antigen, as well as a cellular response to virus. These collectively suggest a theme around immune modulation and self-tolerance, even though other terms point to general cellular processes, which makes the immune signal the strongest, albeit not exclusively cohesive.","confidence":"Medium","size":22,"edges":4,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043277","count":22},{"id":"GO:0046641","count":22},{"id":"GO:0060709","count":22},{"id":"GO:0006611","count":22},{"id":"GO:0061167","count":22}]},{"hash":"600769698866631857","title":"Plant Hormone Signaling and Leaf Formation","description":"The top GO terms cluster around plant hormonal signaling (cytokinin-activated signaling, jasmonic acid response) and development (leaf formation, vegetative growth), with flavonol biosynthesis as a downstream metabolic process, suggesting a module governing growth and developmental responses in plants. A couple of terms (viral process, heterochromatin formation) are less directly connected and may reflect broader cellular regulation, but the dominant signal is hormone-mediated growth and leaf development.","confidence":"Medium","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":7},{"id":"GO:1903770","count":6},{"id":"GO:1900386","count":6},{"id":"GO:0010338","count":6},{"id":"GO:1905615","count":6}]},{"hash":"312507590190164176","title":"Isoprenoid and amino acid biosynthesis","description":"Based on the GO terms, the cluster is enriched for biosynthetic pathways, especially mevalonate/isoprenoid production (isopentenyl diphosphate, farnesyl diphosphate, cholesterol biosynthesis) alongside several amino acid biosynthesis steps (L-threonine, homoserine, methionine). This combination points to a group of proteins involved in general metabolic precursor biosynthesis rather than a single specialized process, hence the label \u201cIsoprenoid and amino acid biosynthesis.\u201d ","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0019287","count":4},{"id":"GO:0009092","count":4},{"id":"GO:0046835","count":4},{"id":"GO:0009088","count":4}]},{"hash":"1051257346372387220","title":"Plant transcriptional regulation and signaling proteins","description":"The cluster is dominated by GO terms for DNA-templated transcription and its regulation, plus plant-specific signaling (cytokinin-activated pathways) and secondary cell wall biogenesis, indicating a group of transcription regulators connected to signaling and cell-wall processes in plants. A few less-coherent terms (e.g., neural patterning) are present but not defining. Confidence: Medium","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0009736","count":3},{"id":"GO:0006935","count":3},{"id":"GO:0030433","count":3}]},{"hash":"1286556601914995857","title":"Detoxification and Lipid Catabolism","description":"The cluster features GO terms for cellular oxidant detoxification and response to toxic substances, plus multiple lipid- and phospholipid-catabolic processes (monoacylglycerol, triglyceride, phosphatidylserine), and lipid signaling (endocannabinoid pathway). Some plant-specific catabolic terms appear but overall the common theme is detox response and lipid turnover.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0098869","count":8},{"id":"GO:0015996","count":7},{"id":"GO:0009636","count":7},{"id":"GO:2000124","count":6},{"id":"GO:0097755","count":6}]},{"hash":"10041476827000816","title":"Transmembrane Transporters and Vesicle Loading","description":"Top GO terms indicate a focus on transmembrane transport of various ions and metabolites (nitrite, sodium, potassium, phosphate, nitrate, galactose, sialic acid) as well as a specific function of neurotransmitter loading into synaptic vesicles, suggesting the cluster comprises membrane transport proteins and vesicular transport components. This combination justifies a concise label that reflects both general transporter activity and vesicle-related loading.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":3},{"id":"GO:0042891","count":3},{"id":"GO:0015757","count":3},{"id":"GO:0035725","count":3},{"id":"GO:0098700","count":3}]},{"hash":"1610430713345689139","title":"Unknown","description":"The top GO terms are diverse (placenta development, translation, cell cycle regulation, neural/glial development and apoptosis, vitamin transport), with no clear single biological process or pathway linking most proteins. This lack of a cohesive theme makes a specific, representative label inappropriate.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001890","count":2},{"id":"GO:0071157","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0035023","count":1},{"id":"GO:0042066","count":1}]},{"hash":"580610736329817772","title":"Ubiquitin-Dependent TNF/NF-\u03baB Signaling","description":"This cluster is enriched for ubiquitin-dependent protein catabolic processes (K48-linked ubiquitination) together with TNF-mediated and NF-kappaB signaling, and it also includes apoptosis regulation, which together point to ubiquitin-driven control of inflammatory and cell-survival pathways.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":10},{"id":"GO:0007250","count":8},{"id":"GO:1901253","count":8},{"id":"GO:0033209","count":8},{"id":"GO:0090073","count":8}]},{"hash":"1912254100744936395","title":"Unknown","description":"The top GO terms show a mix of light-sensing related functions plus a variety of unrelated processes (tRNA modification, nuclear pore localization, ubiquitin-related processes, JNK regulation, growth responses). There isn\u2019t a single coherent theme tying the cluster together, so Unknown with None confidence. ","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050908","count":2},{"id":"GO:0007114","count":1},{"id":"GO:0046329","count":1},{"id":"GO:0002143","count":1},{"id":"GO:0001403","count":1}]},{"hash":"954107769724895500","title":"Development and Protein Homeostasis","description":"The cluster shows developmental signatures (osteoblast differentiation, skeletal system development, forebrain development) alongside proteostasis and trafficking processes (ubiquitin-proteasome degradation, ER-to-Golgi transport, translation initiation complex formation, ER stress\u2013induced apoptosis). This suggests proteins coordinating tissue development with protein quality control and trafficking, justifying the label Development and Protein Homeostasis.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":2},{"id":"GO:0001649","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0070059","count":2},{"id":"GO:0030900","count":2}]},{"hash":"107611485533648094","title":"Lens Fiber Morphogenesis and Light-Stress Response","description":"The top terms are centered on lens fiber cell morphogenesis and responses to light and radiation, plus supportive processes like protein stabilization and regulation of growth. This pattern suggests a functional module tied to lens development with photic/stress signaling, complemented by maintenance of protein homeostasis and transport. The label reflects these dominant themes without overextending to unrelated functions.","confidence":"Medium","size":21,"edges":201,"triangles":1176,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0071480","count":8},{"id":"GO:0032355","count":7},{"id":"GO:0050821","count":7},{"id":"GO:0070309","count":7},{"id":"GO:0007568","count":7}]},{"hash":"1706595492419682506","title":"Transcription Regulators and ER Redox Homeostasis","description":"The cluster is dominated by GO terms for DNA-templated transcription and regulation of transcription by RNA Pol II, plus DNA binding. The presence of ER-related processes (protein folding in the endoplasmic reticulum) and redox/homeostasis terms (deglutathionylation, cellular oxidant detoxification) suggests these proteins participate in transcriptional regulation coordinated with ER redox balance and protein folding. Viral process terms may reflect involvement in host\u2013virus interactions, but the core theme appears to be transcription regulation linked to ER redox/homeostasis.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0000122","count":5},{"id":"GO:0043388","count":4},{"id":"GO:0016032","count":3},{"id":"GO:0045454","count":3}]},{"hash":"2094216922441682925","title":"Vesicle exocytosis regulation in neural development","description":"The top GO terms center on regulation of synaptic vesicle exocytosis, brain development, neural patterning, and signaling via GTPases/Rho, suggesting a cluster of proteins coordinating vesicle release with neuronal differentiation and cytoskeletal dynamics. The presence of insulin secretion and vesicle-related processes further supports a general vesicle exocytosis regulatory theme across cell types. The inclusion of mating projection growth regulation reflects conserved Rho/GTPase signaling rather than a species-specific function, reinforcing a unifying vesicle-trafficking regulatory role in neural contexts.","confidence":"High","size":21,"edges":119,"triangles":228,"max_degree":15,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:2000300","count":6},{"id":"GO:0010796","count":6},{"id":"GO:0007420","count":6},{"id":"GO:0031384","count":6},{"id":"GO:0060304","count":5}]},{"hash":"463418974132500221","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":2},{"id":"GO:0090617","count":2},{"id":"GO:0042793","count":2},{"id":"GO:1905639","count":2},{"id":"GO:1900865","count":2}]},{"hash":"1198587766123269518","title":"Chloroplast RNA Processing and Chloroplast\u2013Nucleus Signaling","description":"This cluster centers on chloroplast/plastid RNA processing, transcription, and RNA editing/modification, with polycistronic mRNA processing, and includes chloroplast\u2013nucleus signaling; mitochondrial mRNA processing/modification terms are also present, indicating coordinated organelle gene expression and cross-talk in plant cells.","confidence":"High","size":21,"edges":3,"triangles":0,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0010019","count":18},{"id":"GO:0031426","count":18},{"id":"GO:0016554","count":18},{"id":"GO:0090615","count":18},{"id":"GO:0031425","count":18}]},{"hash":"236981808509788541","title":"Androgen signaling and prostate development","description":"The top GO terms are dominated by steroid hormone receptor complex assembly, prostate gland development, and male sex differentiation, suggesting a module centered on androgen receptor signaling and male reproductive development. While there are a few seemingly unrelated terms (e.g., photosynthesis, morphine response), the strongest signals align with hormone signaling and prostate/male differentiation processes. Confidence: Medium","confidence":"","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":7},{"id":"GO:0030850","count":6},{"id":"GO:0006463","count":6},{"id":"GO:0046661","count":6},{"id":"GO:0051291","count":5}]},{"hash":"2125738649450285191","title":"Neurodevelopmental transcription regulation","description":"This cluster is dominated by GO terms for DNA-templated transcription and brain development, along with embryonic and multicellular organism development, suggesting a group of proteins involved in regulating gene expression during neurodevelopment and broader developmental processes. While other terms touch on RNA decay and host interactions, the core signal points to transcriptional control in neurodevelopment.","confidence":"High","size":21,"edges":85,"triangles":92,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0007420","count":6},{"id":"GO:0090305","count":6},{"id":"GO:0032508","count":6},{"id":"GO:0000184","count":6}]},{"hash":"253229092702394467","title":"Mitochondrial transport and energy metabolism","description":"The cluster centers on membrane transport of energy-related metabolites (ADP/ATP, thiamine pyrophosphate, glycine, thiosulfate) and mitochondrial transport processes, with supporting GO terms for cellular energy regulation and oxidative stress response. Contexts like cellular response to insulin and liver-related processes (regen, pregnancy) align with metabolic regulation in mitochondria, suggesting a cohesive set of mitochondrial transport/metabolism proteins. ","confidence":"Medium","size":21,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":5},{"id":"GO:0032869","count":5},{"id":"GO:1990544","count":4},{"id":"GO:0097421","count":4},{"id":"GO:0007565","count":4}]},{"hash":"518516165628697309","title":"Vertebrate Development and Gene Regulation","description":"The top GO terms show a strong emphasis on developmental processes (forebrain development, neural tube closure, skeletal system development, multicellular organism development) and transcriptional control (DNA-templated transcription), suggesting proteins involved in vertebrate development regulated at the gene expression level. Some terms indicate stress and immune-related responses (ER-stress\u2013triggered apoptosis, cadmium response, defense against Gram-positive bacteria), which can be linked to developmental contexts or cellular quality control. Overall, the cluster seems to capture vertebrate developmental programs coordinated by transcriptional regulation, with a few peripheral stress-related roles.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0048240","count":9},{"id":"GO:0070059","count":8},{"id":"GO:0030900","count":8},{"id":"GO:0050830","count":8}]},{"hash":"1012579746353231128","title":"Cell-surface receptor signaling and endocytosis","description":"The cluster is dominated by GO terms related to cell-surface receptor signaling (e.g., receptor signaling pathways, receptor internalization) and downstream processes affecting cell behavior (Notch and VEGF signaling, cell motility, junction assembly). While a plant cell-wall term appears, the core theme ties to extracellular signal reception and endocytic regulation shaping signaling outcomes. Confidence: Medium","confidence":"","size":21,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045747","count":4},{"id":"GO:0009834","count":3},{"id":"GO:2000145","count":3},{"id":"GO:0043128","count":3},{"id":"GO:1901223","count":3}]},{"hash":"1063877902258474979","title":"Organelle RNA Processing and Translation","description":"Top terms are dominated by chloroplast and mitochondrial RNA processing and translation-related processes (chloroplast-nucleus signaling, chloroplast RNA processing, mitochondrial mRNA processing, regulation of mitochondrial translation, cytidine to uridine editing, polycistronic mRNA processing). This suggests the cluster centers on organelle gene expression rather than a single external stimulus or cell-cycle function, despite a few outlier terms that may reflect noise.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0042144","count":5},{"id":"GO:0060291","count":4},{"id":"GO:0008284","count":4},{"id":"GO:0000272","count":4},{"id":"GO:0010019","count":4}]},{"hash":"1107102394580111123","title":"Membrane biogenesis and cell wall processes","description":"The top GO terms cluster around membrane-related biogenesis (protein insertion into membrane, outer membrane assembly, cristae formation) and cell wall processes (plant-type cell wall modification, xyloglucan metabolism, chitin/metabolic/biogenesis). This points to a shared theme of building and remodeling membranes and structural barriers, with some immune-related terms appearing peripherally. The connection is present but not perfect across all terms, so a concise umbrella label fits best.","confidence":"Medium","size":21,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051205","count":2},{"id":"GO:0043165","count":2},{"id":"GO:0042407","count":2},{"id":"GO:0033280","count":2},{"id":"GO:0043029","count":2}]},{"hash":"1010531086393161317","title":"Ribosome Biogenesis and Translation Initiation","description":"The top GO terms cluster around ribosome-related processes: formation of the translation preinitiation complex, translation reinitiation, and ribosomal large subunit biogenesis, indicating these proteins collectively participate in assembling and initiating protein synthesis. While there are hints of mRNA processing/export and regulatory silencing, the strongest and most coherent theme is involvement in the ribosome assembly and translation initiation machinery.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0034316","count":2}]},{"hash":"505113602595428587","title":"Cellular stress responses and growth regulation","description":"The cluster exhibits multiple GO terms tied to stress responses (response to heat, response to high light intensity), aging, and regulation of growth, along with protein stabilization and intracellular transport regulation. While there is a lens morphogenesis term, the majority of terms point to stress-related and growth/protein homeostasis processes, suggesting a broader theme rather than a single tissue-specific function.","confidence":"Medium","size":21,"edges":51,"triangles":54,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":3},{"id":"GO:0032355","count":2},{"id":"GO:0050821","count":2},{"id":"GO:0070309","count":2},{"id":"GO:0007568","count":2}]},{"hash":"283749875299789104","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902455","count":1},{"id":"GO:0000389","count":1},{"id":"GO:0000350","count":1},{"id":"GO:0000380","count":1},{"id":"GO:0006415","count":1}]},{"hash":"75391302436597847","title":"Chromatin Remodeling and Transcription Regulation","description":"The cluster centers on transcription by RNA polymerase II and its regulation (GO:0006366, GO:0006351, GO:0006355, GO:0000122) coupled with chromatin-state modifiers (GO:0043044, GO:0000183, GO:0006334), i.e., nucleosome assembly and heterochromatin formation. This points to a coherent theme of transcription control via chromatin remodeling, with the developmental and ABA-response terms likely representing broader regulatory contexts rather than core functions.","confidence":"High","size":21,"edges":174,"triangles":749,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0006355","count":6},{"id":"GO:0000183","count":6},{"id":"GO:0006334","count":5}]},{"hash":"1130800887795822270","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning insect cuticle development, plant and animal hormone signaling, pituitary development, and general stress and signaling processes (response to cAMP, Rho/GTPase regulation, ROS production). There is no single cohesive function or pathway tying these terms together across different contexts, so a specific label isn\u2019t justifiable. ","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008365","count":2},{"id":"GO:0051591","count":2},{"id":"GO:0050665","count":2},{"id":"GO:1990451","count":2},{"id":"GO:0042403","count":2}]},{"hash":"165926713588199484","title":"ncRNA-mediated silencing and splicing regulation","description":"This cluster is enriched for post-transcriptional RNA processing functions: ncRNA-mediated gene silencing, regulation of mRNA splicing via the spliceosome, mRNA export/stability/modification, and general mRNA processing. The dominant GO terms point to coordinated control of RNA fate, with only a couple terms (blastocyst formation, viral translation) as potential noise.","confidence":"High","size":21,"edges":98,"triangles":237,"max_degree":19,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":13},{"id":"GO:0048026","count":13},{"id":"GO:1901407","count":13},{"id":"GO:0010610","count":12},{"id":"GO:0016556","count":11}]},{"hash":"1151216177220256525","title":"Ubiquitin-Dependent Protein Degradation","description":"The cluster is dominated by ubiquitination and proteasome-based protein catabolism terms (ubiquitin-dependent ERAD, SCF-dependent degradation, and general protein ubiquitination), indicating a cohesive role in targeted protein turnover. Occasional terms about peroxisomal protein import and Wnt receptor catabolism point to substrate-specific degradation pathways linked to protein turnover and signaling regulation.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0030433","count":6},{"id":"GO:0042787","count":6},{"id":"GO:0051865","count":5},{"id":"GO:0031146","count":5},{"id":"GO:0016567","count":4}]},{"hash":"902960840736207014","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0090615","count":5},{"id":"GO:0042793","count":5},{"id":"GO:1905639","count":5},{"id":"GO:1900865","count":5},{"id":"GO:0031425","count":5}]},{"hash":"1934560579243485975","title":"TGF-\u03b2/BMP signaling regulators","description":"This cluster is dominated by GO terms related to modulation of TGF-\u03b2/BMP signaling (negative regulation of TGF-\u03b2 receptor signaling and BMP signaling, cellular response to TGF-\u03b2), with supporting references to SMAD-related processes. While a few terms are archaic or tangential, the overarching theme points to proteins that regulate TGF-\u03b2/BMP pathway activity and downstream responses.","confidence":"High","size":21,"edges":9,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0061191","count":5},{"id":"GO:0046827","count":5},{"id":"GO:0042347","count":5},{"id":"GO:0000173","count":5},{"id":"GO:0042006","count":5}]},{"hash":"93404587355523017","title":"Ubiquitin-Dependent Protein Degradation","description":"The cluster is dominated by GO terms for ubiquitin-dependent proteolysis (e.g., ubiquitin-dependent protein catabolic process, SCF-dependent ubiquitin-mediated degradation, K48-linked ubiquitination, autoubiquitination), indicating a shared function in tagging substrates for proteasomal degradation; a few terms like peroxisomal import and Wnt receptor catabolic processes appear but are less central. ","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":12},{"id":"GO:0051865","count":9},{"id":"GO:0030433","count":9},{"id":"GO:0031146","count":8},{"id":"GO:0016558","count":8}]},{"hash":"811902612631541942","title":"Transcription Regulation and Chromatin Remodeling","description":"This cluster is dominated by GO terms related to transcription control (negative regulation of RNA Pol II transcription, DNA-templated transcription, regulation of transcription) and chromatin dynamics (nucleosome assembly, chromatin-related processes), with supporting signals from spindle assembly and ubiquitination that hint at cell-cycle coordination and protein turnover. The overarching theme appears to be transcriptional regulation tightly linked to chromatin structure and cell-cycle/stress signaling.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0051225","count":3},{"id":"GO:0006334","count":3},{"id":"GO:0006469","count":2},{"id":"GO:0071260","count":2}]},{"hash":"2234094112784907319","title":"Ubiquitin-Dependent Immune Regulation","description":"The cluster centers on ubiquitination-related processes (protein ubiquitination, autoubiquitination, ubiquitin-dependent ERAD) and immune system activity (innate and adaptive immunity), with links to signaling pathways such as JNK and TNF. This suggests a cohesive theme of ubiquitin-mediated control of immune signaling and protein turnover.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":5},{"id":"GO:0030433","count":4},{"id":"GO:0042787","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0016567","count":3}]},{"hash":"1265616502366849791","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090617","count":5},{"id":"GO:1905639","count":5},{"id":"GO:1900865","count":5},{"id":"GO:0042793","count":5},{"id":"GO:0031426","count":5}]},{"hash":"113876016867928757","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090617","count":5},{"id":"GO:0042793","count":5},{"id":"GO:1905639","count":5},{"id":"GO:1900865","count":5},{"id":"GO:0010019","count":5}]},{"hash":"1958546637459294249","title":"Plant cytokinin signaling and stress/metabolic responses","description":"The GO terms cluster around cytokinin-activated signaling, unfolded protein response, chlorophyll biosynthesis regulation, and associated metabolic processes, suggesting a plant-specific signaling/stress module. This label captures the hormone-driven signaling together with stress-related and chloroplast metabolic responses.","confidence":"Medium","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0009736","count":5},{"id":"GO:0006986","count":5},{"id":"GO:0043278","count":5},{"id":"GO:0051291","count":4},{"id":"GO:0090526","count":4}]},{"hash":"1669080664365141202","title":"Unknown","description":"The top GO terms are very diverse, spanning plant carbohydrate metabolism (cellulose catabolic, raffinose oligosaccharide biosynthetic), plant development (floral organ morphogenesis), and unrelated animal processes (osteoblast development), plus several obsolete terms; there is no clear shared function or pathway binding these proteins, and the cluster has no edges to suggest a common role. ","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":7},{"id":"GO:0042136","count":7},{"id":"GO:0046340","count":7},{"id":"GO:0019441","count":5},{"id":"GO:0019695","count":5}]},{"hash":"816752397925467484","title":"Ubiquitin-Dependent TNF/NF-kappaB Signaling","description":"Top GO terms point to ubiquitin-dependent protein catabolic processes, autoubiquitination, and K6-linked ubiquitination, along with TNF-mediated signaling, NF-kappaB activation, and JNK cascade regulation. This combination indicates a coherent theme of ubiquitin-mediated regulation of inflammatory signaling pathways, particularly TNF/NF-kappaB, even though the network edges are absent in this cluster.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":14},{"id":"GO:1903265","count":9},{"id":"GO:1903762","count":8},{"id":"GO:0051865","count":8},{"id":"GO:0007250","count":8}]},{"hash":"1633490226995233756","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042793","count":10},{"id":"GO:1905639","count":10},{"id":"GO:1900865","count":10},{"id":"GO:0031425","count":10},{"id":"GO:0016554","count":10}]},{"hash":"939934925258777482","title":"Vesicle trafficking in development","description":"This cluster is dominated by exocytosis and vesicle transport terms (exocytosis, Golgi to plasma membrane transport, vesicle tethering/docking, endosome\u2013Golgi transport), which point to components of the secretory pathway. The presence of development-related terms (petal development, organ boundary specification, retina development, hedgehog-related signaling) suggests these trafficking proteins are involved in tissue patterning and organ formation, across diverse organisms. Thus, a label emphasizing vesicle trafficking in developmental contexts captures the shared theme.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010199","count":2},{"id":"GO:0048441","count":2},{"id":"GO:0034498","count":1},{"id":"GO:0006887","count":1},{"id":"GO:0006893","count":1}]},{"hash":"2224072734771049195","title":"Multivesicular body trafficking and degradation","description":"Most of the top GO terms point to endosomal sorting and degradation via the multivesicular body pathway: intracellular transport, MVB sorting, ubiquitin-dependent and independent catabolic processes, and MVB-lysosome fusion. A couple of terms describe tissue-specific roles (lens maintenance, follicle cell in egg chamber), but the core signal is MVB-mediated trafficking and degradation.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006886","count":2},{"id":"GO:0071985","count":1},{"id":"GO:0030713","count":1},{"id":"GO:0090611","count":1},{"id":"GO:0036438","count":1}]},{"hash":"1276802274488221532","title":"Unknown","description":"The GO terms are highly diverse and several are obsolete, with no clear shared function or pathway connecting the proteins. There is no network connectivity (edges/triangles zero), so a cohesive, specific label can't be inferred.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0051567","count":2},{"id":"GO:0006349","count":2},{"id":"GO:0051344","count":2}]},{"hash":"2050933640518045966","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":163,"triangles":757,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0015979","count":1},{"id":"GO:0090615","count":1},{"id":"GO:0090617","count":1},{"id":"GO:0042793","count":1}]},{"hash":"1923129736292488190","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":110,"triangles":446,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0006096","count":5},{"id":"GO:0008615","count":5},{"id":"GO:0006006","count":5},{"id":"GO:0051402","count":4}]},{"hash":"1976064624556755971","title":"Transcription and Translation Machinery","description":"This cluster centers on gene expression processes, with multiple GO terms for cytoplasmic and mitochondrial translation and DNA-templated transcription, plus transcription antitermination and miRNA catabolic processes, indicating a focus on protein synthesis and RNA regulation; a few outlier terms such as responses to antibiotics and developmental signals do not negate the core theme.","confidence":"Medium","size":20,"edges":140,"triangles":500,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0002181","count":2},{"id":"GO:0032543","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0006777","count":2}]},{"hash":"1213901304048512530","title":"PSII Assembly and Light Response","description":"The terms point to photosystem II\u2013related processes (oxygen-evolving complex assembly, light harvesting in PSII) and light-responsive regulation (response to high/low far red light), suggesting a cluster centered on PSII assembly and chloroplast light-adaptive photosynthesis. Some translation/chloroplast-related terms support a chloroplast context but don\u2019t override the main PSII/light theme.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010270","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0055114","count":2},{"id":"GO:1904964","count":1},{"id":"GO:0010218","count":1}]},{"hash":"361787780305542468","title":"Amino acid metabolism and Fe-S cluster biosynthesis","description":"This cluster is dominated by amino acid metabolism terms (serine, alanine, glycine, cysteine, tryptophan catabolic and quinolinate biosynthesis) and explicit Fe-S cluster biogenesis terms ([2Fe-2S] cluster assembly and iron incorporation into metallo-sulfur clusters), suggesting a cohesive module coordinating amino acid turnover with iron-sulfur cluster assembly. Some signaling-related terms like response to cAMP and glucocorticoid may reflect regulatory cross-talk or annotation noise.","confidence":"Medium","size":20,"edges":133,"triangles":582,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0006564","count":10},{"id":"GO:0042853","count":9},{"id":"GO:0019805","count":9},{"id":"GO:0006546","count":8},{"id":"GO:0051591","count":8}]},{"hash":"248132195070625365","title":"ER Protein Folding and Redox Homeostasis","description":"The cluster is dominated by GO terms for endoplasmic reticulum\u2013related protein folding (GO:0034975) and redox/homeostasis processes (GO:0045454, GO:0098869, GO:0055114, GO:0080058), suggesting a functional module focused on protein maturation under oxidative conditions and redox balance. The inclusion of peptidyl-proline hydroxylation hints at post-translational modifications relevant to ER-secreted or collagen-related proteins, while detoxification and deglutathionylation further support a redox-regulated quality-control role. Some transcription- or virus-related terms may reflect broader regulatory connections or incidental annotations, but the core pattern aligns with ER-associated folding and redox regulation.","confidence":"High","size":20,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045454","count":6},{"id":"GO:0034975","count":5},{"id":"GO:0098869","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0006351","count":4}]},{"hash":"2000950677687950990","title":"Arabinogalactan protein glycosylation and epidermal development","description":"This cluster is dominated by terms related to arabinogalactan proteins (AGPs) and their Hyp-O glycosylation, plus processes like root hair development and seed coat mucilage formation. Together these point to plant cell-wall\u2013associated glycoproteins (AGPs) and their roles in epidermal differentiation and mucilage/seed coat biology.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018258","count":4},{"id":"GO:0075015","count":4},{"id":"GO:0010405","count":4},{"id":"GO:0048354","count":4},{"id":"GO:0001744","count":4}]},{"hash":"1992457897865287931","title":"Ribosome biogenesis and translation","description":"This cluster is dominated by GO terms related to protein synthesis machinery and ribosome assembly: translation, ribosome biogenesis, ribosomal subunit biogenesis, large subunit export from nucleus, translational termination, and tRNA modification. Some terms like apoptotic process and cell division-related processes appear secondary, but the core theme remains ribosome function and translation.","confidence":"High","size":20,"edges":116,"triangles":422,"max_degree":17,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":13},{"id":"GO:0042254","count":7},{"id":"GO:0046677","count":5},{"id":"GO:0042274","count":4},{"id":"GO:0000055","count":4}]},{"hash":"852813255818464243","title":"Photosynthesis and Light-Response","description":"The GO terms cluster around photosynthesis (PSI/PSII light harvesting), responses to different light qualities and intensities (far-red, UV-A, high/low light), and nonphotochemical quenching, with an additional hint from a chlorophyll/chromophore linkage term. Together these point to proteins involved in chloroplast light harvesting and photoprotective/light-sensing processes, justifying the label.","confidence":"High","size":20,"edges":2,"triangles":0,"max_degree":1,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":3},{"id":"GO:0009768","count":2},{"id":"GO:1904964","count":2},{"id":"GO:0010218","count":2},{"id":"GO:0071486","count":2}]},{"hash":"1866857111955932449","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":127,"triangles":418,"max_degree":19,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0031047","count":5},{"id":"GO:0048026","count":5},{"id":"GO:1901621","count":4},{"id":"GO:1905259","count":4}]},{"hash":"463605080019560553","title":"Developmental gene expression programs","description":"The cluster appears to center on transcriptional control linked to development and tissue differentiation. GO terms emphasize gene expression programs driving lineage specification, including myoblast fate determination and skeletal muscle fiber development, GABAergic neuron differentiation, and endocrine pancreas development, as well as transcription by RNA polymerase II. Additional terms touch on regulatory processes such as circadian clock entrainment and modulation of glucocorticoid signaling, suggesting broad regulatory roles in developmental contexts across tissues. Taken together, the proteins likely participate in coordinating gene expression programs that guide cell fate decisions during organogenesis.","confidence":"Medium","size":20,"edges":190,"triangles":1140,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":15},{"id":"GO:2000323","count":14},{"id":"GO:0007518","count":14},{"id":"GO:0048658","count":14},{"id":"GO:0009649","count":14}]},{"hash":"1093760218328667954","title":"Unknown","description":"The terms are a mix of various metabolic and signaling processes (alkaloid and bile acid metabolism, triglyceride and retinoic acid catabolism, etc.) along with unrelated or broad categories (uterus development, ion responses, inflammatory regulation). There isn\u2019t a single cohesive function or pathway that ties the majority of these terms together into a clear, specific cluster identity, so a precise label cannot be assigned beyond Unknown.","confidence":"","size":20,"edges":66,"triangles":88,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0060065","count":5},{"id":"GO:0009822","count":4},{"id":"GO:0006641","count":4},{"id":"GO:0071615","count":4},{"id":"GO:0034653","count":4}]},{"hash":"563145257221077542","title":"Organelle gene expression and tRNA charging","description":"This cluster combines GO terms for transcription (DNA-templated transcription) and translation, with several mitochondrial tRNA aminoacylation processes, plus a photosynthesis term, pointing to gene expression and protein synthesis in chloroplasts/mitochondria. The presence of translational fidelity regulation and tRNA charging suggests a cohesive theme of organelle-encoded gene expression machinery, despite some less common terms like selenocysteine biosynthesis. Overall, the label reflects the shared function of organelle gene expression.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0070150","count":1},{"id":"GO:0070159","count":1},{"id":"GO:0006450","count":1}]},{"hash":"820472496336366039","title":"Chloroplast and Mitochondrial Protein Import Metabolism","description":"GO terms strongly point to import and assembly in chloroplasts and mitochondria (protein import into chloroplast stroma; protein import into mitochondrial matrix; protein insertion into mitochondrial inner membrane), indicating a cluster of proteins involved in organelle targeting and inner membrane biogenesis. Some metabolism-related terms (phylloquinone catabolic process; poly-hydroxybutyrate biosynthetic process) reflect plastid-associated pathways, while stress/food-response terms may relate to energy/nutrient status in plants. Overall, the unifying theme is chloroplast/mitochondrial protein targeting and plastid metabolism.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0042619","count":3},{"id":"GO:0045037","count":2},{"id":"GO:0045039","count":2}]},{"hash":"632657724053267811","title":"Ribosome Biogenesis and Translation","description":"This cluster is driven by GO terms for translation and ribosome biogenesis (cytoplasmic translation, ribosomal subunit biogenesis/export, tRNA modification), indicating proteins involved in ribosome assembly and protein synthesis. While a few terms like cell septum assembly and antibiotic response are present, the dominant signal reflects ribosome function.","confidence":"High","size":20,"edges":69,"triangles":109,"max_degree":19,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":15},{"id":"GO:0042254","count":7},{"id":"GO:0046677","count":6},{"id":"GO:0000055","count":5},{"id":"GO:0006400","count":5}]},{"hash":"1914309714656508738","title":"RNA modification and ribosome biogenesis","description":"The proteins are enriched for translation, ribosome biogenesis, and RNA pseudouridine synthesis (snRNA, tRNA, and mRNA), suggesting a core role in RNA maturation and protein synthesis; a few outlier terms (chromatin organization, collagen catabolic process) likely reflect broader annotations rather than the cluster\u2019s main function.","confidence":"High","size":20,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0035551","count":2},{"id":"GO:0034396","count":2},{"id":"GO:0034724","count":2},{"id":"GO:0030574","count":2}]},{"hash":"811116375308853012","title":"RNA Splicing and mRNA Processing Regulators","description":"The top GO terms cluster around spliceosome-mediated mRNA splicing, mRNA processing and export, regulation of splicing, and translation initiation steps. This suggests a functional group of proteins involved in RNA maturation and gene expression control at both splicing and initiation stages, rather than a single catalytic function.","confidence":"High","size":20,"edges":39,"triangles":13,"max_degree":11,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":11},{"id":"GO:0048026","count":11},{"id":"GO:1901407","count":10},{"id":"GO:0001731","count":9},{"id":"GO:0002188","count":9}]},{"hash":"1298392007126757406","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":20,"triangles":9,"max_degree":7,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0090615","count":12},{"id":"GO:0090617","count":12},{"id":"GO:1905639","count":12},{"id":"GO:1900865","count":12},{"id":"GO:0042793","count":12}]},{"hash":"652240584659826477","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0010019","count":15},{"id":"GO:0031426","count":15},{"id":"GO:0016554","count":15},{"id":"GO:0090615","count":15},{"id":"GO:0070129","count":15}]},{"hash":"954136204438169155","title":"Developmental Regulation and Organogenesis","description":"The cluster is enriched for broad developmental processes and regulatory transcription across multiple organs and stages, from early gastrulation (primitive streak formation) to organogenesis (pituitary, inner ear, forebrain neurons, pancreas, pharyngeal system, gonads, uterus, ureteric bud), indicating a module of genes involved in developmental gene regulation rather than a single tissue-specific path.","confidence":"Medium","size":20,"edges":129,"triangles":395,"max_degree":19,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":7},{"id":"GO:0021983","count":5},{"id":"GO:0042472","count":5},{"id":"GO:0021902","count":5},{"id":"GO:0003309","count":5}]},{"hash":"2095158312938362620","title":"Chromatin Modification and Nucleosome Assembly","description":"This cluster is dominated by GO terms related to histone modification (peptidyl-lysine N6-acetylation, H3-K4 trimethylation), nucleosome assembly, and subtelomeric heterochromatin formation, pointing to chromatin organization and epigenetic regulation. While a few metabolic terms (polyamine and sugar metabolism) appear, the strongest signals tie to chromatin maintenance and remodeling.","confidence":"High","size":20,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0018003","count":6},{"id":"GO:0006348","count":6},{"id":"GO:0080182","count":5},{"id":"GO:0006334","count":5},{"id":"GO:0045150","count":5}]},{"hash":"556159890900735961","title":"Endocannabinoid signaling and lipid catabolism","description":"The top GO terms cluster around regulation of endocannabinoid signaling and several lipid catabolic processes (monoacylglycerol, diacylglycerol, triglyceride, phosphatidylserine), suggesting a shared theme of lipid metabolism linked to endocannabinoid signaling. A few other terms (menaquinone, biotin biosynthesis, cellulose catabolic) are present but less coherent with this core theme. ","confidence":"High","size":20,"edges":12,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:2000124","count":6},{"id":"GO:0052651","count":6},{"id":"GO:0019433","count":6},{"id":"GO:0006660","count":6},{"id":"GO:0030245","count":5}]},{"hash":"1201090872159528647","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031426","count":4},{"id":"GO:0090615","count":3},{"id":"GO:0090617","count":3},{"id":"GO:0042793","count":3},{"id":"GO:1905639","count":3}]},{"hash":"175198011198268113","title":"Plant Growth, Development, and Metabolism","description":"Most terms point to plant-specific biology, including chloroplast stroma protein import, flavonoid biosynthesis, lateral root formation, and regulation of developmental timing from vegetative to reproductive phases. The karrikin response and sucrose catabolic process further support a plant signaling and metabolism theme, while translation appears more general. Overall, the cluster seems to reflect a broad plant growth and metabolic program rather than a single molecular function.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0045037","count":2},{"id":"GO:0009813","count":1},{"id":"GO:0080167","count":1},{"id":"GO:0060296","count":1}]},{"hash":"980031651157484871","title":"Fungal cell wall biosynthesis and glycosylation","description":"This cluster is dominated by GO terms for fungal-type cell wall biogenesis and related glycosylation pathways, including galactomannan/galactoglucomannan/mannan biosynthesis, mannoprotein biosynthesis, and N-linked glycosylation, along with cell division processes like septum assembly and budding. Collectively, these indicate proteins involved in constructing and remodeling the fungal cell wall and associated glycosylation rather than cytosolic metabolism, justifying a fungal cell wall/glycosylation theme.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010192","count":6},{"id":"GO:0000917","count":3},{"id":"GO:0007114","count":3},{"id":"GO:0000032","count":3},{"id":"GO:0009272","count":3}]},{"hash":"1791586671754215375","title":"DNA repair and telomere maintenance","description":"The top GO terms indicate a clear theme around genome integrity: double-strand break repair via classical nonhomologous end joining and telomere maintenance/regulation, with a cellular response to DNA damage (X-ray). A few terms related to brain development and neuronal guidance may reflect multifunctionality or broader annotations, but the core signal is DNA repair and telomere biology.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":1},{"id":"GO:0071481","count":1},{"id":"GO:0008045","count":1},{"id":"GO:0007535","count":1},{"id":"GO:1904430","count":1}]},{"hash":"285850948813436674","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning plant cytokinin signaling and diverse animal developmental and cellular processes (centrosome maintenance, mitotic regulation, germarium cystoblast division, atrial septum and ureter development) with little shared function. With no coherent theme linking the proteins and only minimal network connectivity, a single representative label cannot be confidently assigned.","confidence":"","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009736","count":2},{"id":"GO:0043086","count":2},{"id":"GO:0051291","count":1},{"id":"GO:0051661","count":1},{"id":"GO:0048142","count":1}]},{"hash":"607311483014375907","title":"Nucleocytoplasmic transport and translation regulation","description":"The cluster\u2019s top GO terms center on nuclear pore complex assembly and export of the ribosomal small subunit from the nucleus, as well as translation and its regulation, pointing to a core function in nucleocytoplasmic transport and ribosome biogenesis/translation control. Additional terms like P granule assembly and septin ring processes suggest related RNA processing and cell-cycle-associated structures, but the dominant connection is RNA export and translation regulation.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051754","count":2},{"id":"GO:0051292","count":2},{"id":"GO:0000056","count":2},{"id":"GO:0042176","count":2},{"id":"GO:0045727","count":2}]},{"hash":"1585520653884111941","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090617","count":4},{"id":"GO:1905639","count":4},{"id":"GO:1900865","count":4},{"id":"GO:0042793","count":4},{"id":"GO:0031426","count":4}]},{"hash":"542450428934078251","title":"Neural development and synaptic signaling","description":"Based on the top GO terms, cerebellum development and excitatory postsynaptic potential are the dominant signals, pointing to neural development and synaptic function. Other terms reflect broader developmental and cellular processes, suggesting a mixed, development-centric cluster with a weaker, non-specific immune and cellular stress component. This makes neural development and synaptic signaling the best overall label given the strongest terms, while acknowledging other included functions.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0021549","count":17},{"id":"GO:0006349","count":17},{"id":"GO:0060079","count":17},{"id":"GO:0043277","count":16},{"id":"GO:0046641","count":16}]},{"hash":"1652622382837061576","title":"Cardiac development and electrophysiology","description":"The presence of GO terms for regulation of atrial cardiac muscle cell action potential, regulation of SA node cell action potential, and outflow tract morphogenesis strongly points to a heart-specific module governing development and electrical activity. Additional terms about cardiac hypertrophy in stress support a myocardial functional context. Other terms like phosphorylation and transport are more general, so the core signal is cardiac development and electrophysiology.","confidence":"High","size":20,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0016310","count":2},{"id":"GO:0008360","count":2},{"id":"GO:0015031","count":2},{"id":"GO:0098910","count":2}]},{"hash":"1896865680591733195","title":"TGF-beta/BMP Signaling Regulation","description":"Based on the top GO terms, the proteins cluster around modulation of TGF-beta signaling and downstream SMAD/BMP pathways, including negative regulation of TGF-beta receptor signaling, BMP signaling, and SMAD complex assembly, as well as cellular responses to TGF-beta stimulus. Additional terms point to dephosphorylation and nuclear export processes that can modulate signaling and transcriptional outputs. A non-core term about photosystem stoichiometry likely represents annotation noise rather than a central function. ","confidence":"High","size":20,"edges":95,"triangles":179,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046827","count":10},{"id":"GO:0071560","count":7},{"id":"GO:0000173","count":7},{"id":"GO:0030514","count":7},{"id":"GO:0030512","count":7}]},{"hash":"313652716004727930","title":"Immune regulation and developmental signals","description":"The cluster shows strong enrichment for immune-related processes (apoptotic cell clearance, T cell proliferation, tolerance induction to self antigen, response to virus) alongside development-related terms (placental differentiation, organ regeneration, meiosis-related processing, ER polarization). The shared theme is regulatory signaling that modulates immune function and developmental processes, so this label captures the core functionality represented. ","confidence":"Medium","size":20,"edges":182,"triangles":1008,"max_degree":19,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043277","count":20},{"id":"GO:0046641","count":20},{"id":"GO:0060709","count":20},{"id":"GO:0006611","count":20},{"id":"GO:0061167","count":20}]},{"hash":"1477160178509927219","title":"Cell division and ubiquitin-mediated proteolysis","description":"The top GO terms cluster around mitotic cell cycle, cell division, and chromatin organization, with strong signals for ubiquitin-dependent proteasomal degradation (SCF-dependent, protein polyubiquitination). This points to coordinated regulation of cell-cycle progression and degradation of regulatory proteins, common in mitosis control. There are additional signals of signaling modification (dephosphorylation) and Golgi-related retention that may reflect handling of regulatory proteins, but the dominant theme is cell division coupled with targeted proteolysis. High","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0000920","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0045053","count":3}]},{"hash":"314835875645949657","title":"Adaptive immune response and neutrophil regulation","description":"GO terms center on adaptive immune response and neutrophil-related processes (neutrophil clearance, neutrophil apoptotic regulation) with additional signals related to T-helper 2 differentiation and transcriptional activity (DNA-templated transcription). This pattern suggests a cluster enriched for immune system regulation and gene expression control, rather than a single metabolic pathway.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032088","count":3},{"id":"GO:0031532","count":3},{"id":"GO:0097350","count":3},{"id":"GO:0030216","count":3},{"id":"GO:0002250","count":3}]},{"hash":"1484420297777093937","title":"Proteoglycan and glycosaminoglycan biosynthesis","description":"The Top Terms strongly converge on proteoglycan and glycosaminoglycan biosynthesis, including chondroitin sulfate, heparan sulfate, and heparin proteoglycan biosynthetic processes, as well as related glycosylation terms. This suggests the cluster is functionally linked to the production of proteoglycans/GAGs. A few other terms (e.g., antibiotic response, mitochondrial processes) appear sparsely and likely reflect noise rather than a cohesive alternate function.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0006044","count":2},{"id":"GO:0006486","count":2},{"id":"GO:0050650","count":2},{"id":"GO:0015012","count":2}]},{"hash":"624764977030850312","title":"TNF-NF-\u03baB signaling with ubiquitination","description":"The proteins in this cluster are dominated by GO terms tied to TNF-mediated signaling, NF-\u03baB activation (including I-\u03baB phosphorylation and NF-\u03baB-inducing kinase activity), JNK pathway regulation, and ubiquitin-dependent regulation (including autoubiquitination and K6-linked ubiquitination), pointing to a cohesive theme of inflammatory signaling controlled by ubiquitination. A deprecated term about voltage-gated potassium channels appears incidental and does not define the cluster\u2019s main function. ","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:1903762","count":8},{"id":"GO:0042787","count":8},{"id":"GO:0051865","count":8},{"id":"GO:0007250","count":8},{"id":"GO:1901253","count":8}]},{"hash":"1780476429617934108","title":"Ubiquitin-Dependent Regulation of Transcription and Cell Cycle","description":"The top terms center on ubiquitin-mediated protein degradation (ubiquitin-dependent protein catabolic process, protein polyubiquitination, K6-linked ubiquitination) and extend to regulation of transcription, cell cycle, apoptosis/necroptosis, and signaling pathways (TLR). This suggests a cohesive cluster of proteins coordinating ubiquitin-driven proteostasis with cell cycle control and cell fate signaling.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:0000209","count":6},{"id":"GO:0000122","count":4},{"id":"GO:0071157","count":4},{"id":"GO:0085020","count":4}]},{"hash":"28671799137124523","title":"Neuroimmune signaling and development","description":"The top GO terms point to both neural development/function (corpus callosum development, positive regulation of synapse assembly, behavioral response to pain) and immune signaling (innate immune response, T cell receptor signaling). The cluster seems to reflect a neuroimmune intersection rather than a single coherent process, with additional terms like bone/mammary development and cadmium response likely representing background or secondary associations.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":5},{"id":"GO:0051965","count":4},{"id":"GO:0061368","count":4},{"id":"GO:0022038","count":4},{"id":"GO:0014068","count":4}]},{"hash":"1360822500377956720","title":"Chloroplast and mitochondrial RNA processing and transcription","description":"The top GO terms point to organelle gene expression and RNA processing, especially chloroplast/plastid transcription and RNA processing/modification, plus mitochondrial mRNA processing and RNA editing, with evidence of chloroplast-nucleus signaling. This suggests a cohesive theme of coordinated gene expression and RNA metabolism within chloroplasts/plastids and mitochondria.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0010019","count":6},{"id":"GO:0031426","count":6},{"id":"GO:0016554","count":6},{"id":"GO:0090615","count":6}]},{"hash":"1154047664207101697","title":"Ion Transport and Membrane Homeostasis","description":"The cluster is dominated by GO terms for transporting ions across membranes (potassium and sodium, proton) and maintaining ionic/osmotic balance (cell volume homeostasis, salt stress response). This points to a cohesive theme of membrane ion transport and ionic homeostasis, with a secondary link to cardiac conduction and signaling, but overall the core signal is transport of ions across the plasma membrane. Confidence is High.","confidence":"","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030007","count":5},{"id":"GO:0098719","count":5},{"id":"GO:0097623","count":5},{"id":"GO:0086092","count":4},{"id":"GO:0009651","count":4}]},{"hash":"1354639903987600233","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning metabolism (TCA cycle, acetyl-CoA, succinyl-CoA, PHB biosynthesis) and distinct processes like apoptosis, sporulation, and development, with no single shared function linking all members. Because there is no cohesive theme, I cannot assign a meaningful specific label.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006915","count":2},{"id":"GO:0030324","count":2},{"id":"GO:0030435","count":2},{"id":"GO:0046677","count":2}]},{"hash":"180584073193749805","title":"Plant Development and Hormone-Defense Signaling","description":"The proteins show enrichment for plant development (floral meristem growth, multicellular organism development) and transcription regulation, along with ABA-activated signaling and defense-related responses (response to chitin). While some RNA processing terms are also present, the overall theme centers on plant developmental processes linked to hormone signaling and defense, rather than a single specific pathway.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000184","count":1},{"id":"GO:1903259","count":1},{"id":"GO:0007275","count":1},{"id":"GO:1904276","count":1},{"id":"GO:0006351","count":1}]},{"hash":"1201287105256609757","title":"Diverse regulators of signaling and metabolism","description":"GO terms mainly reflect regulation of Rho/GTPase signaling, calcium response, insulin secretion, and lipid transport, suggesting the proteins function as regulators of cellular signaling and metabolic processes; a few outlier terms (neural axis, aging, mismatch repair) are present but do not change the overall theme.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0043087","count":3},{"id":"GO:1904468","count":2},{"id":"GO:0021997","count":2},{"id":"GO:0035773","count":2}]},{"hash":"618935262416850164","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0090615","count":20},{"id":"GO:0090617","count":20},{"id":"GO:0042793","count":20},{"id":"GO:1905639","count":20},{"id":"GO:1900865","count":20}]},{"hash":"2242071230111722966","title":"Teichoic acid and cell wall biosynthesis","description":"The cluster is enriched for terms tied to teichoic and lipid biosynthesis, lipoteichoic acid biosynthesis, cell wall organization, and related envelope components, indicating a cohesive role in Gram-positive cell wall assembly and modification. Additional terms like fatty acid biosynthesis and antibiotic biosynthetic process support a broader envelope biosynthesis context.","confidence":"High","size":19,"edges":171,"triangles":969,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0009245","count":3},{"id":"GO:0070395","count":3},{"id":"GO:0009258","count":3},{"id":"GO:0043041","count":3},{"id":"GO:0017000","count":3}]},{"hash":"54938072154882281","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":94,"triangles":263,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":9},{"id":"GO:0048701","count":8},{"id":"GO:0000393","count":5},{"id":"GO:0071035","count":5},{"id":"GO:0001113","count":5}]},{"hash":"1983310419928004098","title":"Carbohydrate and energy metabolism","description":"The GO terms cluster around energy metabolism and carbohydrate processing (glycolysis, sucrose response, tagatose catabolism, and mitochondrial NADH-to-ubiquinone electron transport). A few development-related terms appear, but the dominant theme is metabolic energy production and carbohydrate utilization, suggesting the proteins collectively participate in broad metabolic energy pathways rather than a single, tightly defined process. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032094","count":3},{"id":"GO:0021762","count":2},{"id":"GO:0045471","count":2},{"id":"GO:0001701","count":2},{"id":"GO:0000105","count":2}]},{"hash":"1103284319864175882","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":12,"triangles":6,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":7},{"id":"GO:0031047","count":6},{"id":"GO:0045292","count":6},{"id":"GO:0006378","count":6},{"id":"GO:0071035","count":5}]},{"hash":"616774617380768483","title":"RNA processing and stability regulation","description":"The top GO terms cluster around RNA metabolism: regulation of mRNA stability in stress, mRNA polyadenylation (including mitochondrial), RNA exonuclease activity, splicing, and miRNA turnover. These signals point to a core theme of RNA maturation, processing, and degradation, with a few unrelated terms that do not overshadow this primary function. ","confidence":"High","size":19,"edges":171,"triangles":969,"max_degree":18,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":17},{"id":"GO:0006378","count":10},{"id":"GO:0090503","count":10},{"id":"GO:0010323","count":10},{"id":"GO:2000627","count":10}]},{"hash":"2046469526081694303","title":"Metabolic and stress-response pathways","description":"The top GO terms cluster around lipid- and energy-related metabolism (fatty acid biosynthesis; retinoic acid metabolism; ethanol/pyruvate fermentation) and environmental stress responses (response to copper ion, lipopolysaccharide). This suggests a theme of metabolic activity coupled to stress signaling, though some terms are obsolete or noisy, reducing confidence somewhat.","confidence":"Medium","size":19,"edges":23,"triangles":7,"max_degree":9,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0006633","count":5},{"id":"GO:0019878","count":5},{"id":"GO:0019518","count":4},{"id":"GO:0042573","count":3}]},{"hash":"2142421880791731225","title":"Hormone biosynthesis and metabolic regulation","description":"Enriched terms point to hormone biosynthesis and endocrine development (pituitary gland development, positive regulation of hormone biosynthetic process), along with metabolic cofactors (NAD+ biosynthetic process, lipoate metabolic process) and related processes. A secondary signal appears in stress-related responses and apoptosis, but the core theme is hormone metabolism and metabolic regulation.","confidence":"Medium","size":19,"edges":25,"triangles":2,"max_degree":9,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0021983","count":7},{"id":"GO:0009435","count":6},{"id":"GO:0009635","count":6},{"id":"GO:0046886","count":6}]},{"hash":"12445179505438018","title":"Developmental growth and transcriptional regulation","description":"This cluster centers on developmental processes across tissues (gonad, brain, bone), including multicellular growth and osteoblast differentiation, with accompanying transcriptional/epigenetic regulation signals (negative regulation of RNAP II, histone H3 acetylation) and related responses (vitamin D). Some outliers (isoquinoline alkaloid metabolism, Gram-positive defense) may reflect annotation noise or multifunctional proteins, but the core pattern supports developmental regulation and differentiation. ","confidence":"Medium","size":19,"edges":6,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0008584","count":4},{"id":"GO:0000122","count":4},{"id":"GO:0033076","count":3},{"id":"GO:0033280","count":3},{"id":"GO:0007420","count":3}]},{"hash":"2099945017685261509","title":"Neural signaling, RNA processing, and cell cycle regulation","description":"The top GO terms indicate distinct but related regulatory roles across neural signaling (e.g., negative regulation of excitatory postsynaptic potential; neuron apoptotic process), RNA processing (regulatory ncRNA-mediated gene silencing; splicing via spliceosome), and core cell cycle events (mitotic cell cycle, cell division). This points to a cluster of proteins involved in broad regulatory machinery that links neural function with gene expression control and proliferation, rather than a single focused pathway.","confidence":"Medium","size":19,"edges":59,"triangles":145,"max_degree":11,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0090394","count":10},{"id":"GO:0031047","count":10},{"id":"GO:0048026","count":10},{"id":"GO:0043525","count":6},{"id":"GO:0000278","count":6}]},{"hash":"1645470207977938716","title":"Ribosome Biogenesis and Translation Regulation","description":"This cluster is dominated by terms related to ribosome assembly and rRNA maturation (maturation of LSU- and SSU-rRNA, ribosome biogenesis) and to translation, including formation of the translation preinitiation complex and positive regulation of translation. Additional terms link to mRNA export and turnover (poly(A) tail shortening), consistent with a coordinated ribosome production\u2013translation regulation module. The convergence of these GO terms suggests a cohesive ribosome biogenesis/translation functional cluster, with a strong representative signal. ","confidence":"High","size":19,"edges":66,"triangles":67,"max_degree":14,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000463","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0006412","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0000466","count":3}]},{"hash":"443074422113794534","title":"Gene expression and RNA processing","description":"This cluster shows GO terms spanning transcription (DNA- and RNA-templated), RNA splicing, translation initiation and reinitiation, and general translation, indicating involvement in core gene expression and RNA processing. A few terms like DNA replication or ERAD are present but do not dominate, so the primary theme is the gene expression machinery.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0031564","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0002188","count":2}]},{"hash":"221458659218285479","title":"DNA replication, repair, and telomere maintenance","description":"This cluster is dominated by nuclear DNA metabolism terms: DNA replication, DNA-templated transcription, DNA repair, and regulation of telomere maintenance via telomerase, suggesting a coherent role in genome stability and DNA processing. While other terms like apoptotic process, viral process, and Rho signaling appear, they likely reflect broader stress responses or signaling contexts linked to genome maintenance rather than defining the core function. Therefore, the label highlights the central theme of DNA replication/repair and telomere maintenance in this cluster.","confidence":"High","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0006281","count":3},{"id":"GO:0009636","count":3},{"id":"GO:0016032","count":3}]},{"hash":"2011814811424761421","title":"Unknown","description":"The Top Terms include plant cytokinin signaling, cell division, phosphorylation, prostate gland development, male sex differentiation, interferon response, gluconeogenesis, protein heterooligomerization, and APC-dependent catabolic process. Such a mix spans plant-specific signaling and animal development and general cellular processes, with no clear shared function tying all proteins together. Because there is no cohesive GO term theme or common pathway, the cluster is best described as Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0009736","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0016310","count":4},{"id":"GO:0030850","count":4},{"id":"GO:0006463","count":4}]},{"hash":"1348362408920287318","title":"Unknown","description":"The top GO terms span distinct, unrelated biological themes (nuclear transcription regulation, mitochondrial and plastid processes, rRNA maturation and translation, RNA splicing, and cellulose catabolic processes) and there are no interactions among proteins (Edges: 0, Triangles: 0). This eclectic mix provides no single cohesive function for the cluster, so 'Unknown' is appropriate.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0034553","count":1},{"id":"GO:0006120","count":1},{"id":"GO:0032544","count":1},{"id":"GO:0043486","count":1}]},{"hash":"2135110413907848114","title":"Gene Expression Machinery and Morphogenesis Signaling","description":"The top GO terms point to core gene expression processes (cytoplasmic translation; tRNA transcription; DNA-templated transcription; mRNA transport) and nuclear import, coupled with signaling regulation (GTPase activity, protein kinase activity) and morphogenesis-related processes (angiogenesis, branching in blood vessel morphogenesis, dendritic spine morphogenesis). This suggests a cluster of proteins involved in transcription/translation machinery and its regulation, with connections to morphogenesis through signaling pathways.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0002181","count":3},{"id":"GO:0006607","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0001569","count":2}]},{"hash":"606496115167731707","title":"Transcriptional Regulation and RNA Processing","description":"The top GO terms cluster around mRNA processing (export, splicing, polyadenylation), transcriptional control (DNA-templated transcription, SAGA complex localization to regulatory regions), and chromatin modification (histone deubiquitination), plus proteasome assembly. This points to a cohesive module coordinating transcription initiation/elongation with RNA processing and chromatin remodeling. Developmental terms like filamentous growth and vulval development likely reflect organism-specific regulatory contexts but do not negate the core theme of transcriptional regulation and RNA processing.","confidence":"Medium","size":19,"edges":20,"triangles":4,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0043248","count":1},{"id":"GO:0006351","count":1}]},{"hash":"1566697043515357592","title":"Plant Development and Transcription Regulation","description":"The cluster is enriched for plant-specific developmental processes (seed/bract development, cutin biosynthesis, ethylene signaling) and transcriptional control (DNA-templated transcription, regulation of transcription, miRNA processing), suggesting a cohesive group of proteins involved in regulating plant development at the transcriptional/post-transcriptional level.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0097421","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0035196","count":2},{"id":"GO:0007275","count":2}]},{"hash":"301845575575713199","title":"Ubiquitin-Proteasome Regulation and TNF Signaling","description":"The cluster is enriched for ubiquitin-dependent protein catabolic processes (ubiquitination, SCF-dependent proteasomal ubiquitin-dependent proteolysis) and signaling pathways tied to TNF and NF-\u03baB, along with apoptosis regulation. This suggests a cohesive module centered on protein turnover and inflammatory signaling, with apoptotic control, rather than unrelated processes.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:0031146","count":6},{"id":"GO:0007250","count":5},{"id":"GO:1901253","count":5},{"id":"GO:0033209","count":5}]},{"hash":"139874722357659384","title":"Metabolic Cofactor and Substrate Transporters","description":"The top GO terms point to transmembrane transport of energy and cofactors (mitochondrial ATP/ADP, NAD, thiamine pyrophosphate) and various metabolites (glycine, thiosulfate), indicating a cluster of transporter proteins\u2014likely mitochondrial carriers and related solute transporters. Some organism-level terms appear, but the core signal is membrane transport activity for energy/metabolite cofactors. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1990544","count":6},{"id":"GO:0097421","count":6},{"id":"GO:0032869","count":6},{"id":"GO:0007565","count":6},{"id":"GO:0030974","count":6}]},{"hash":"2166289913357613938","title":"Developmental Signaling and Regulation","description":"The cluster combines development-related GO terms (spermatid development, heart development, chorio-allantoic fusion) with signaling pathways (intracellular signal transduction, GPCR-associated signaling, calcium transport) and regulatory processes (kinase activity, ubiquitination, mRNA decay), suggesting proteins that coordinate developmental signaling with post-translational and post-transcriptional regulation. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007286","count":2},{"id":"GO:0035556","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0070588","count":2},{"id":"GO:0007507","count":2}]},{"hash":"1982307655771786052","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0090615","count":3},{"id":"GO:0090617","count":3},{"id":"GO:1905639","count":3},{"id":"GO:1900865","count":3}]},{"hash":"1983760196855915555","title":"Plant immune signaling and cuticle biosynthesis","description":"The cluster is enriched for transcriptional regulation (DNA-templated transcription and its regulation) alongside plant defense and immune signaling (innate immune response-activating pathway, defense response to bacterium, hypersensitive response) and stress-related ABA signaling, plus wax and cutin biosynthesis. This suggests a coordinated module where transcriptional control drives defense signaling and cuticle remodeling in response to stress.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0010204","count":2},{"id":"GO:0034051","count":2},{"id":"GO:0009816","count":2}]},{"hash":"1342796987248373103","title":"Immune Activation and Tolerance","description":"Based on the top GO terms, the cluster is dominated by immune-related processes: apoptotic cell clearance (phagocytosis of dying cells), positive regulation of alpha-beta T cell proliferation, cellular response to virus, and positive regulation of tolerance induction to self antigen. These suggest a functional theme centered on immune activation and regulation of self-tolerance. Some development and cell-biology terms (placental glycogen differentiation, ER polarization, protein export from nucleus) may reflect broader cellular roles or pleiotropy, but do not outweigh the predominant immune signals.","confidence":"High","size":19,"edges":141,"triangles":576,"max_degree":18,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043277","count":19},{"id":"GO:0046641","count":19},{"id":"GO:0060709","count":19},{"id":"GO:0006611","count":19},{"id":"GO:0061167","count":19}]},{"hash":"58483288173525960","title":"Neuronal signaling and memory","description":"The top terms point to neural activity: excitatory postsynaptic potential, long-term memory, calcium ion transport, and responses to neurotransmitter-related stimuli (e.g., amphetamine). Together they suggest proteins involved in synaptic transmission and plasticity, which underlie memory formation. The presence of an abiotic/plant pathway term (abscisic acid-activated signaling) seems less compatible with the neural theme and may reflect annotation noise or cross-kingdom term usage, but the neuronal terms dominate, supporting the proposed label.","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009738","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0008284","count":3},{"id":"GO:0006469","count":3},{"id":"GO:0007616","count":3}]},{"hash":"1276247767223705683","title":"Metal ion homeostasis and detoxification","description":"These proteins cluster around metal handling: copper, zinc, cadmium, and mercury transport and detoxification, including copper ion export and intracellular copper homeostasis, along with mercury ion response. The translation term is present but secondary, while the core theme is metal ion transport/homeostasis and detoxification.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0000055","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0060003","count":2},{"id":"GO:0050787","count":2}]},{"hash":"1785977403056332570","title":"Endocannabinoid Lipid Metabolism","description":"This cluster is enriched for lipid catabolic processes (monoacylglycerol, triglyceride, diacylglycerol, phosphatidylserine) and includes regulation of endocannabinoid signaling, pointing to a module of enzymes involved in lipid breakdown and modulation of endocannabinoid pathways.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000124","count":5},{"id":"GO:0052651","count":5},{"id":"GO:0019433","count":5},{"id":"GO:0006660","count":5},{"id":"GO:0055114","count":4}]},{"hash":"966680698590131161","title":"Broad developmental differentiation","description":"These proteins aggregate around GO terms tied to development and cell-fate specification across diverse tissues (skeletal muscle, neural, endocrine, etc.), including myoblast fate, muscle fiber development, astrocyte and GABAergic neuron differentiation, and pancreas development. The common thread is broad differentiation programs rather than a single signaling pathway, suggesting a general role in lineage specification and tissue morphogenesis.","confidence":"Medium","size":19,"edges":171,"triangles":969,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:2001016","count":13},{"id":"GO:2000323","count":10},{"id":"GO:0007518","count":10},{"id":"GO:0048658","count":10},{"id":"GO:0009649","count":10}]},{"hash":"2143947340771008787","title":"Unknown","description":"The terms span chromatin organization, ubiquitin-proteasome pathways, TGF-\u03b2 and glucose signaling, spinal cord development, actin filament capping, DNA repair, and protein complex formation, with no clear common function or interaction pattern and no edges connecting the proteins. This lack of a cohesive theme makes a specific, representative label inappropriate.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070262","count":1},{"id":"GO:0031497","count":1},{"id":"GO:0000209","count":1},{"id":"GO:0071560","count":1},{"id":"GO:0031146","count":1}]},{"hash":"1255344900590758667","title":"Ciliary and Photoreceptor Development","description":"Reason: This cluster features GO terms tied to cilium assembly and localization, opsin transport, photoreceptor outer segment organization, and cochlear development, all hallmark processes of ciliary sensory cells in the retina and inner ear. The inclusion of Wnt/planar polarity regulation reinforces a ciliary signaling context. Despite one outlier (cardiac muscle differentiation), the dominant theme is cilia-based sensory development.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060271","count":1},{"id":"GO:0061512","count":1},{"id":"GO:0036372","count":1},{"id":"GO:0055007","count":1},{"id":"GO:0060828","count":1}]},{"hash":"2268318061312672619","title":"Ubiquitin-mediated protein degradation and receptor turnover","description":"The cluster is dominated by ubiquitination and proteasomal degradation terms (ubiquitin-dependent degradation, SCF-dependent ubiquitination, K48-linked ubiquitination, protein ubiquitination), pointing to a core function in tagging and destroying proteins. Wnt receptor catabolic process and related growth-regulation terms further support a theme of regulated protein turnover affecting signaling and growth. Some peroxisomal import and dosage-compensation terms may be related peripherally through broader ubiquitin signaling, but the central pattern is ubiquitin-dependent proteolysis.","confidence":"High","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0042787","count":8},{"id":"GO:0016558","count":7},{"id":"GO:0031146","count":7},{"id":"GO:0016567","count":6},{"id":"GO:0051865","count":6}]},{"hash":"2244603092491583811","title":"Neural-immune stress signaling","description":"This cluster centers on neural functions like regulation of synaptic vesicle exocytosis and brain development, but also includes immune signaling (Th1 response, IL-23 regulation) and stress/survival pathways (JNK regulation, mitochondrial outer membrane permeabilization, autophagosome regulation), suggesting a theme of neural signaling intertwined with immune and cellular stress responses rather than a single, isolated function.","confidence":"Medium","size":19,"edges":150,"triangles":656,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:2000300","count":4},{"id":"GO:0010796","count":4},{"id":"GO:0042088","count":4},{"id":"GO:0046330","count":4},{"id":"GO:0032707","count":4}]},{"hash":"1674641969845765643","title":"Unknown","description":"The cluster's proteins map to a highly diverse set of GO terms, including glycerophospholipid catabolic process, phosphate ion transport, organ boundary specification, petal development, pinocytosis, neural differentiation, spindle assembly, pain perception, multicellular organismal process, and NOD2 signaling. With no edges or coherent shared function evident, there is no single interpretable theme to name beyond Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046475","count":2},{"id":"GO:0035435","count":2},{"id":"GO:0010199","count":2},{"id":"GO:0048441","count":2},{"id":"GO:0048549","count":1}]},{"hash":"262594115654715841","title":"Antiviral Interferon-Responsive Proteins","description":"This cluster is dominated by terms related to antiviral innate immunity, including cellular response to type I interferon, defense response to virus, and cellular response to exogenous dsRNA, suggesting an antiviral/interferon signaling theme. Some other terms (cell division, histone modification) appear less central and may reflect broader annotations, but the antiviral/interferon signals are the strongest common thread.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0071357","count":4},{"id":"GO:0090526","count":4},{"id":"GO:0031145","count":4},{"id":"GO:0016570","count":4}]},{"hash":"326057758015310516","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048358","count":2},{"id":"GO:0042545","count":2},{"id":"GO:0045490","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0090617","count":2}]},{"hash":"1867865169384284841","title":"Vertebrate Development and Notch Signaling","description":"The top terms point to broad vertebrate development (forebrain and neural tube closure, skeletal system development, multicellular organism development) and signaling via Notch, along with DNA-templated transcription\u2014suggesting regulatory networks active during embryonic development. Some stress-related terms appear, but the cohesive theme centers on developmental processes with Notch involvement.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0070059","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0071276","count":2}]},{"hash":"912366933023465831","title":"Neural development and NF-\u03baB\u2013mediated inflammation","description":"GO terms cluster around neural development (brain development, neural tube closure) and inflammatory signaling (inflammatory response, NF-\u03baB pathways), with transcriptional regulation and NO biosynthesis involvement. This points to a neurodevelopmental context coupled with NF-\u03baB\u2013driven inflammatory regulation.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007584","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0045429","count":2},{"id":"GO:0001843","count":2},{"id":"GO:0090073","count":2}]},{"hash":"922842892440558522","title":"Ubiquitin-Dependent Proteolysis Cluster","description":"The proteins are dominated by GO terms for ubiquitin-dependent degradation (ubiquitin-dependent protein catabolic process; SCF-proteasomal pathway; ERAD; protein autoubiquitination; polyubiquitination). Additional terms touch on circadian rhythm regulation and innate immune defense, which can relate to proteostasis and signaling in immune and circadian pathways. Overall, the core theme is ubiquitin-mediated protein turnover.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":13},{"id":"GO:0030433","count":8},{"id":"GO:0031146","count":8},{"id":"GO:0042752","count":7},{"id":"GO:0000083","count":6}]},{"hash":"1984428039372108494","title":"Neuronal vesicle trafficking and synaptic transport","description":"The cluster\u2019s top GO terms center on intracellular vesicle transport, especially ER-to-Golgi and synaptic vesicle priming, plus microtubule-based movement, which together indicate a cohesive role in vesicle trafficking and neuronal/synaptic function. Brain and spinal cord development terms further support a neural context, making this a specific cluster about neuronal vesicle transport, despite a few outlier terms like acrosome reaction. ","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0007420","count":4},{"id":"GO:0006886","count":4},{"id":"GO:0021510","count":3},{"id":"GO:0007018","count":3}]},{"hash":"202490206544857337","title":"Unknown","description":"The top GO terms span immunological regulation, development, cellular trafficking, and hormone signaling with no single shared function. The terms include apoptotic cell clearance, T cell proliferation, tolerance induction, placental and organ development, protein export from nucleus, ER polarization, viral response, organ regeneration, meiotic DSB processing, and parathyroid hormone secretion, suggesting a heterogeneous mix rather than a cohesive functional theme. There are no edges connecting the proteins, further supporting the lack of a unified pathway or process to label this cluster precisely.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043277","count":19},{"id":"GO:0046641","count":19},{"id":"GO:0060709","count":19},{"id":"GO:0006611","count":19},{"id":"GO:0061167","count":19}]},{"hash":"18822150357668339","title":"Neuro-immune signaling and synapse morphogenesis","description":"The top GO terms mix neural development (nerve branching, axonal fasciculation, synapse assembly) with innate immune signaling (TLR pathways, LPS detection, I-kappaB/NF-kB phosphorylation) and TH1 responses, pointing to a cluster of proteins coordinating neuro-immune communication and morphogenesis rather than a single pathway.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:2000172","count":13},{"id":"GO:0002730","count":13},{"id":"GO:0007413","count":13},{"id":"GO:0034142","count":13},{"id":"GO:0051965","count":13}]},{"hash":"2048720127509047606","title":"Plant development and gene expression","description":"The top GO terms include core gene expression processes (DNA-templated transcription, formation of translation preinitiation complex, ribosomal biogenesis) alongside plant-specific developmental processes (root hair growth, radial patterning, bundle sheath fate, seed germination regulation, seed dormancy, secondary shoot formation). This mix suggests a cluster of proteins involved both in general transcription/translation machinery and in plant development, reflecting a theme of plant growth regulation at the intersection of gene expression and developmental pathways.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0001731","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0048768","count":2},{"id":"GO:0009956","count":2}]},{"hash":"572680192681094368","title":"Peptide maturation and lysosomal proteolysis","description":"The top GO terms point to peptide maturation (insulin processing, peptide pheromone maturation, nerve growth factor production) and a vacuolar protein catabolic process, suggesting a theme of peptide processing and lysosomal turnover within secretory/vacuolar pathways. Other terms like oxidant detoxification and ion transport may reflect broader cellular stress responses but are not as tightly linked. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010447","count":2},{"id":"GO:0006813","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0007039","count":1},{"id":"GO:0030070","count":1}]},{"hash":"1451044064169213018","title":"Vitamin and antibiotic biosynthesis with xenobiotic response","description":"This cluster\u2019s top GO terms are dominated by biosynthetic processes for vitamins and antibiotics (biotin and cobalamin biosynthesis, antibiotic biosynthetic process), along with cellular responses to xenobiotics and toxic substances. This points to a core theme of small-molecule biosynthesis coupled with chemical stress/foreign compound response, making the label Vitamin and antibiotic biosynthesis with xenobiotic response a concise, representative name.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042220","count":4},{"id":"GO:0009102","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0009636","count":3},{"id":"GO:0055114","count":3}]},{"hash":"22057013544068449","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":3},{"id":"GO:0090617","count":3},{"id":"GO:0042793","count":3},{"id":"GO:1905639","count":3},{"id":"GO:1900865","count":3}]},{"hash":"1601088195491851492","title":"Plant cell wall biosynthesis and abiotic stress response","description":"The terms clearly center on plant cell wall component biosynthesis (xylan, xyloglucan, plant-type secondary cell wall biogenesis) and related metabolic processes, with additional signals of abiotic stress responses (response to freezing) and detox-related phytochelatin biosynthesis. While there are some generic terms like proteolysis, the dominant theme ties to cell wall construction and stress adaptation in plants.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":5},{"id":"GO:1904715","count":5},{"id":"GO:0043085","count":5},{"id":"GO:0046938","count":5},{"id":"GO:0009834","count":3}]},{"hash":"810246863916650599","title":"Ubiquitin-Proteasome Regulation in Meiosis and Development","description":"The enriched terms point to ubiquitin-dependent proteolysis (SCF-dependent pathways) as the dominant theme, suggesting a core role in regulated protein degradation. Coupled with meiosis-related processes (oocyte maturation, spindle assembly in female meiosis I) and developmental events (neural tube and ventricle development) as well as microtubule dynamics, the cluster likely reflects proteostasis mechanisms coordinating meiosis and embryonic development. ","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":13},{"id":"GO:0031146","count":11},{"id":"GO:0042752","count":10},{"id":"GO:0001556","count":10},{"id":"GO:0070544","count":10}]},{"hash":"2271762387920136516","title":"Organelle inheritance and membrane trafficking","description":"GO terms cluster around inheritance of mitochondria, peroxisomes, and Golgi, along with vesicle transport, membrane repair, and spindle organization, suggesting a theme of intracellular membrane maintenance and organelle partitioning. The presence of development-related terms may reflect tissue-specific expression, but the dominant signal appears to be organelle inheritance and membrane dynamics.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001778","count":3},{"id":"GO:0000001","count":2},{"id":"GO:1904970","count":2},{"id":"GO:0007051","count":2},{"id":"GO:0021592","count":2}]},{"hash":"274359229159627460","title":"Chromatin Remodeling and Transcription Regulation","description":"The top GO terms are concentrated on chromatin dynamics (chromatin remodeling; nucleosome assembly) and transcription control (regulation of DNA-templated transcription), each appearing multiple times, indicating the proteins collectively participate in chromatin organization and gene expression regulation. Some peripheral terms (e.g., vitamin D receptor signaling, mitochondrial-related processes) exist but do not override the core chromatin/transcription theme.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":2},{"id":"GO:0070562","count":2},{"id":"GO:0006334","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0010867","count":1}]},{"hash":"301792305980529307","title":"Growth and Secretion Trafficking","description":"This cluster centers on growth-related processes such as pseudohyphal and invasive growth, alongside a set of trafficking and secretion functions (ER exit, cell surface localization, lysosomal enzyme secretion). Although there are some outlier terms (pain perception, nitric oxide/inflammatory terms), the dominant pattern links growth responses with protein trafficking and secretion. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007124","count":3},{"id":"GO:0001403","count":3},{"id":"GO:0007275","count":2},{"id":"GO:0019233","count":2},{"id":"GO:0006813","count":2}]},{"hash":"1819677086305249478","title":"Bacterial SOS Response and LPS Biosynthesis","description":"The top GO terms cluster around DNA damage response (DNA-templated transcription, DNA repair, SOS response) and lipopolysaccharide biosynthesis (O antigen, LPS core, the heptose precursor), suggesting a theme of bacterial stress response linked to envelope biosynthesis; a few terms appear as outliers (liver development, phenylpropanoid metabolism).","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006281","count":2},{"id":"GO:0009432","count":2},{"id":"GO:0001889","count":2},{"id":"GO:0009699","count":1}]},{"hash":"957985953248700275","title":"Autophagy and programmed cell death with RNA/DNA processing","description":"The top terms are dominated by macroautophagy and programmed cell death, with supporting annotations in RNA/DNA processing (mRNA processing, tRNA modification) and DNA repair, plus mitochondrial involvement in necrotic death. This points to a cohesive theme of cellular maintenance and stress responses leading to controlled cell fate, rather than a specific tissue function like bone formation, hence a label centered on autophagy/death and nucleic acid maintenance. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045668","count":1},{"id":"GO:0016236","count":1},{"id":"GO:0030500","count":1},{"id":"GO:0035552","count":1},{"id":"GO:0012501","count":1}]},{"hash":"1786451495792525692","title":"Bacterial cell wall remodeling and sporulation","description":"The terms cluster around peptidoglycan biosynthesis and catabolism, cell wall organization, and regulation of cell shape, with sporulation signaling forming a cohesive theme of cell envelope remodeling coupled to spore formation. Some chitin-related terms may reflect environmental sensing linked to cell-wall\u2013associated processes, but the dominant signal is bacterial cell wall turnover and sporulation.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016998","count":1},{"id":"GO:0009252","count":1},{"id":"GO:1902083","count":1},{"id":"GO:0008360","count":1},{"id":"GO:0071555","count":1}]},{"hash":"2238688004001488954","title":"Mitochondrial Translation and Energy Metabolism","description":"The terms cluster around mitochondrial gene expression (mitochondrial translation, mitochondrial mRNA processing, ribosomal subunit assembly, translation) and energy generation (proton motive force-driven ATP synthesis), with redox balance (cell redox homeostasis) and related metabolic signals, suggesting a cohesive mitochondrial translation\u2013energy production program.","confidence":"High","size":18,"edges":138,"triangles":628,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0032543","count":2},{"id":"GO:0016126","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0017148","count":1}]},{"hash":"209424393158669013","title":"Transcription Regulation and Chemical Stress Response","description":"This cluster is dominated by GO terms for transcription control (DNA-templated transcription, transcription antitermination, DNA recombination) alongside chemical/oxidative stress responses (xenobiotic/toxic substances, hydrogen peroxide, osmotic stress), suggesting a core role in gene expression regulation under chemical/oxidative stress. Some developmental and digestive terms appear but are less prominent, likely secondary associations.","confidence":"Medium","size":18,"edges":81,"triangles":141,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0042493","count":4},{"id":"GO:0006310","count":3},{"id":"GO:0009636","count":3},{"id":"GO:0070301","count":2}]},{"hash":"354689541441500853","title":"Ribosome biogenesis and translation","description":"The cluster is dominated by GO terms related to ribosome production and protein synthesis (translation, ribosome biogenesis, snoRNP assembly) and reinforced by growth-regulation signals (TORC1 signaling, mRNA transport) and cell-cycle processes, suggesting a cohesive module centered on ribosome assembly and translation coupled to proliferation.","confidence":"High","size":18,"edges":14,"triangles":1,"max_degree":6,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0042254","count":4},{"id":"GO:0000492","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0007338","count":3}]},{"hash":"260285361722193905","title":"Prostaglandin and lipid metabolism","description":"The strongest signals cluster around lipid-derived signaling and metabolism: prostaglandin biosynthesis, triglyceride and bile acid metabolism, and retinoic acid catabolism. Although there are some outliers (e.g., uterus development, ion responses), the dominant GO terms point to lipid signaling and metabolic pathways that tie these proteins together.","confidence":"Medium","size":18,"edges":40,"triangles":36,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":13},{"id":"GO:0060065","count":12},{"id":"GO:0009822","count":10},{"id":"GO:0006641","count":10},{"id":"GO:0071615","count":10}]},{"hash":"451378940944811837","title":"Ribosome Biogenesis and Translation","description":"The cluster centers on translation and ribosome-related processes, including translation itself and ribosome biogenesis for small and large subunits, plus tRNA modification, all pointing to protein synthesis machinery. The presence of terms related to responses to translation inhibitors (antibiotics and cycloheximide) supports a connection to ribosome function and its stress responses. A few outlier terms like cell septum assembly and conjugation appear but do not define the core theme. Overall, the cluster represents components of the ribosome assembly pathway and translation machinery.","confidence":"High","size":18,"edges":20,"triangles":8,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0006400","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0042273","count":2},{"id":"GO:0046898","count":2}]},{"hash":"638354388838242905","title":"Plant Redox Homeostasis and Defense Signaling","description":"This cluster is enriched for oxidative stress and redox-related terms (oxidation-reduction, cellular oxidant detoxification, redox homeostasis) and defense/hormone-related responses (response to chitin, antifungal innate immune response, gibberellin and ethylene precursor ACC responses) as well as cell wall-related differentiation (sclerenchyma). While an animal-like term (male gonad development) appears, the dominant pattern points to a plant-specific stress-response and defense signaling module centered on redox balance and hormone-driven defense. ","confidence":"High","size":18,"edges":96,"triangles":262,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0098869","count":4},{"id":"GO:0045454","count":4},{"id":"GO:0008584","count":3},{"id":"GO:0030416","count":3}]},{"hash":"2122600521465365401","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1901621","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0097428","count":4},{"id":"GO:0045454","count":4},{"id":"GO:0006458","count":4}]},{"hash":"2066692324768522174","title":"Cell Polarity and Organelle Inheritance","description":"Top GO terms cluster around establishing or maintaining cell polarity and regulating cell shape, mitochondrial inheritance, mitotic spindle assembly, and vesicular trafficking (endosome to lysosome transport). The mix of polarity, division, inheritance, and trafficking processes suggests a functional cluster of proteins coordinating cell polarity with chromosome segregation and organelle distribution, as well as growth signals. While some terms touch development and mating projection growth, the core theme ties to how cells organize polarity during division and manage organelle trafficking.","confidence":"Medium","size":18,"edges":66,"triangles":106,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071963","count":11},{"id":"GO:0000001","count":11},{"id":"GO:0090307","count":11},{"id":"GO:0010628","count":11},{"id":"GO:0021762","count":11}]},{"hash":"89565474381965386","title":"Growth and Morphogenesis Signaling","description":"The cluster centers on signaling networks that regulate cell growth, shape changes, migration, and tissue remodeling\u2014evidenced by terms for DNA replication, cell morphogenesis, angiogenesis, cell migration, PI3K and Wnt signaling, and apoptotic regulation. A peripheral immune term is present but does not overshadow the core theme of growth and morphogenesis signaling.","confidence":"Medium","size":18,"edges":21,"triangles":5,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":14},{"id":"GO:0000902","count":13},{"id":"GO:0014068","count":13},{"id":"GO:0071333","count":13},{"id":"GO:0045766","count":13}]},{"hash":"531668731109887596","title":"Developmental Transcription Regulators","description":"Terms cluster around embryonic organogenesis (pancreas, kidney, liver) and neural crest migration, with a recurring theme of transcriptional regulation (negative regulation of transcription by RNA polymerase II). This suggests proteins that regulate gene expression during development, makingDevelopmental Transcription Regulators a fitting label.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":6},{"id":"GO:0009736","count":6},{"id":"GO:0031018","count":5},{"id":"GO:0090190","count":5},{"id":"GO:0001755","count":5}]},{"hash":"1576673386213592352","title":"Immune response and tolerance","description":"The top GO terms cluster around immune functions: apoptotic cell clearance, positive regulation of T cell proliferation, tolerance induction to self antigens, and cellular responses to virus. While a few terms touch on development or basic cellular processes, the strongest cohesive signal is immune activation and tolerance mechanisms.","confidence":"Medium","size":18,"edges":112,"triangles":325,"max_degree":16,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043277","count":15},{"id":"GO:0046641","count":15},{"id":"GO:0060709","count":15},{"id":"GO:0006611","count":15},{"id":"GO:0061167","count":15}]},{"hash":"417745978038209168","title":"Steroid/Bile Acid Biosynthesis and Vitamin Metabolism","description":"The cluster prominently features biosynthetic processes for steroids (C21-steroid hormone biosynthesis), bile acids, and vitamins (ascorbic acid and retinoic acid). Additional terms point to detox-related metabolism (glucuronate), tissue homeostasis, and signaling pathways (PI3K/AKT), suggesting a cohesive theme around lipid/hormone biosynthesis and related homeostatic regulation. Confidence: Medium","confidence":"","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0009414","count":18},{"id":"GO:0006699","count":18},{"id":"GO:0042840","count":18},{"id":"GO:1900053","count":18},{"id":"GO:0019853","count":18}]},{"hash":"555721583249600699","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042793","count":3},{"id":"GO:0019853","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0070485","count":2},{"id":"GO:0009636","count":2}]},{"hash":"1213433784691497504","title":"Translation initiation machinery","description":"Dominant GO terms are about translation initiation and initiation complex formation (translation, formation of cytoplasmic translation initiation complex, formation of translation preinitiation complex, cytoplasmic translational initiation, eIF4F complex assembly). A couple terms mention neural glial development (oligodendrocyte and astrocyte development), which may reflect broader roles of translation-related proteins in neural cells. Overall, the core theme is translation initiation machinery, with high confidence.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0001732","count":2},{"id":"GO:0014003","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0002176","count":2}]},{"hash":"705131996740765608","title":"Carbohydrate and Metabolite Transport","description":"TheTop terms show a clear emphasis on transport of sugars and related metabolites (glucose/fructose/trehalose) across membranes, and responses to glucose starvation, suggesting a transport/metabolic function for this cluster. While a few terms are unrelated outliers (regulatory ncRNA silencing, senescence regulation, obsolete quorum sensing/antibiotic transport), the dominant signal is membrane transport of sugars and small metabolites.","confidence":"Medium","size":18,"edges":10,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":2},{"id":"GO:0042149","count":2},{"id":"GO:1990539","count":2},{"id":"GO:0043252","count":2},{"id":"GO:0015771","count":2}]},{"hash":"2142213688134105218","title":"Nutrient Sensing and Growth Regulation","description":"The top GO terms point to metabolic and nutrient-status signaling (positive regulation of insulin secretion, response to glucose, nitrogen starvation response) and growth-related processes (positive regulation of epithelial cell proliferation). While some terms are broad or obsolete, the common theme ties nutrient sensing to regulation of growth and cellular interactions, suggesting this cluster centers on metabolic signaling coupled to growth. Confidence: Medium","confidence":"","size":18,"edges":19,"triangles":2,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0032024","count":4},{"id":"GO:0090295","count":3},{"id":"GO:0010756","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0050679","count":3}]},{"hash":"1562269240920618780","title":"RNA processing and translation regulation","description":"These proteins cluster around RNA-centric processes: mRNA processing, translation, and splicing regulation, plus protein export from the nucleus, suggesting a core theme of RNA processing and translational control. A subset of terms points to signaling (JNK cascade) and some metabolism or development processes that may be peripheral. Overall, the dominant connection is regulation of gene expression at the RNA/translation level, with related signaling context. ","confidence":"Medium","size":18,"edges":59,"triangles":58,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046330","count":4},{"id":"GO:0006397","count":4},{"id":"GO:0045727","count":4},{"id":"GO:0008542","count":4},{"id":"GO:0006695","count":4}]},{"hash":"1610749291856097524","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":3},{"id":"GO:0090617","count":3},{"id":"GO:0042793","count":3},{"id":"GO:1905639","count":3},{"id":"GO:1900865","count":3}]},{"hash":"1405066254285489285","title":"Oocyte meiosis and chromosome cohesion","description":"The top terms cluster around meiotic control in oocytes, including sister chromatid cohesion at centromeres, regulation of meiotic cell cycle and female meiotic nuclear division, as well as regulation of DNA replication. Supporting terms on nuclear import, mitotic membrane reassembly, desumoylation, and TORC1 signaling fit a broader view of meiotic regulation and nuclear dynamics in oocytes. This combination supports a coherent label focused on meiosis-specific cell cycle control and chromosomal dynamics.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051754","count":5},{"id":"GO:0070262","count":4},{"id":"GO:0006275","count":4},{"id":"GO:0006610","count":4},{"id":"GO:1903538","count":4}]},{"hash":"2084299272369479816","title":"Actin Cytoskeleton Remodeling and Motility","description":"This cluster is labeled Actin Cytoskeleton Remodeling and Motility because several top terms point to actin- and GTPase-regulated processes that govern cell shape changes and movement, including mitotic actomyosin contractile ring assembly, ruffle assembly, and epithelial cell migration. While a few terms are more peripheral (e.g., vacuolar acidification, GPCR signaling), the dominant theme is cytoskeleton remodeling driving motility.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903475","count":2},{"id":"GO:0030845","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0007035","count":2},{"id":"GO:0032220","count":1}]},{"hash":"699021062772515531","title":"RNA processing and ER stress\u2013responsive translation","description":"The proteins show enrichment for RNA metabolism functions (mRNA export, splicing, regulatory ncRNA\u2013mediated silencing) and translation initiation regulation in response to ER stress, with some cell-cycle terms suggesting proliferation context. Although one term (hair follicle maturation) seems unrelated and there is an obsolete annotation, the dominant theme is RNA biogenesis/metabolism coupled with stress-driven translation control.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098789","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006986","count":2},{"id":"GO:0036494","count":2}]},{"hash":"1408802936829674321","title":"Amino acid and neurotransmitter membrane transport","description":"The cluster is dominated by transmembrane transport terms for amino acids and related neurotransmitters (D-serine, lysine, arginine, GABA, carnitine), indicating a shared function in membrane transport of small molecules. Additional terms touch on osmotic/volume responses and signaling (nitric oxide production, regulation of macrophage activation), but the strongest common theme remains amino acid/neurotransmitter transport across membranes.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006884","count":2},{"id":"GO:0042942","count":2},{"id":"GO:0071477","count":2},{"id":"GO:1902274","count":2},{"id":"GO:0097639","count":2}]},{"hash":"877450157214177934","title":"Golgi\u2013endosome\u2013lysosome trafficking","description":"This cluster is dominated by GO terms describing vesicle transport within the secretory and endomembrane systems, including Golgi to vacuole transport, ER-to-Golgi transport, retrograde endosome-to-Golgi trafficking, endocytic recycling, and lysosomal transport, plus regulation of dense core granule transport and lipid homeostasis. These collectively point to intracellular vesicle trafficking and secretory pathway processes as the shared theme, with some terms (e.g., seed mucilage biosynthesis) reflecting plant-specific secretory activity that relies on these pathways.","confidence":"High","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006896","count":3},{"id":"GO:0006888","count":2},{"id":"GO:0048354","count":2},{"id":"GO:0042147","count":2},{"id":"GO:0032456","count":2}]},{"hash":"834004191211852118","title":"Cell Cycle Regulation and DNA Replication","description":"Most of the top GO terms point to core cell cycle processes (meiotic cell cycle, DNA replication, G1/S transition, kinetochore localization, apoptosis, and regulation of cell proliferation). While there are some neural or signaling-related terms (Schwann cell development, excitatory postsynaptic potential, response to cocaine, peptide hormone stimulus), these appear less central to the cluster. The dominant theme appears to be proteins involved in cell cycle control and DNA replication, with some cross-talk to signaling pathways. ","confidence":"Medium","size":18,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051321","count":7},{"id":"GO:0014044","count":7},{"id":"GO:0006260","count":7},{"id":"GO:0042220","count":7},{"id":"GO:0034501","count":7}]},{"hash":"1181338095402420611","title":"Osmotic Stress Response and Translational Control","description":"The top GO terms cluster around osmotic stress response, water homeostasis, and ion transport, pointing to osmotic/ionic stress management. The presence of translation-related terms (translation, regulation of translational fidelity) and ribosomal RNA maturation/splicing suggests coordinated RNA processing and protein synthesis control during stress, complemented by transcription regulation and proteasomal degradation. Together, these indicate a coherent program linking environmental stress sensing to adjustments in gene expression at the transcriptional, translational, and RNA-processing levels.","confidence":"Medium","size":18,"edges":104,"triangles":322,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0071470","count":4},{"id":"GO:0009992","count":4},{"id":"GO:0034220","count":4},{"id":"GO:0000122","count":3},{"id":"GO:0032436","count":3}]},{"hash":"1463013451358005530","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045493","count":2},{"id":"GO:2000344","count":2},{"id":"GO:2000884","count":2},{"id":"GO:0007283","count":2},{"id":"GO:0016042","count":2}]},{"hash":"2021850416158103051","title":"Plant carbohydrate biosynthesis (starch, trehalose, mucilage)","description":"The cluster shows multiple GO terms tied to carbohydrate production and storage, including trehalose biosynthesis, starch and amylopectin biosynthesis, glycogen biosynthesis, and mucilage biosynthesis, pointing to a shared role in plant polysaccharide biosynthesis. Other terms like transcription by RNA polymerase II, mRNA tail shortening, and N-linked glycosylation are present but less central, suggesting they reflect general cellular functions of the proteins rather than a cohesive secondary pathway. The sparse network (degree 1, no triangles) supports a set of related enzymes rather than a single protein complex. ","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0005992","count":3},{"id":"GO:0005978","count":3},{"id":"GO:0006366","count":2},{"id":"GO:0000289","count":2},{"id":"GO:0006487","count":2}]},{"hash":"1710264814203894298","title":"Placental and embryonic development","description":"The top GO terms are dominated by placenta-related processes (maternal placenta development; glycogen cell differentiation in embryonic placenta development; labyrinthine layer blood vessel development) and other embryogenesis activities (spinal cord development, hyaluronan metabolism). While there are also broad cell processes (insulin signaling, microtubule movement, JNK regulation), the strongest signal centers on placental and embryonic tissue development, justifying this label.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001893","count":2},{"id":"GO:0060709","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0008286","count":2},{"id":"GO:0060716","count":2}]},{"hash":"126700460509465724","title":"Gene Expression and Chromatin Regulation","description":"Terms point to control of gene expression at multiple levels: transcription (DNA-templated transcription; RNA Pol II regulation) and chromatin state (histone H3-K27/K4 methylation). Additional terms touch on translation fidelity and cell-cycle-related processes like spindle assembly, suggesting a broader regulatory program that coordinates expression with division and development (anther morphogenesis). Overall, the cluster appears to represent regulators of gene expression and chromatin dynamics with ancillary cell-cycle/development roles.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990145","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0061087","count":2},{"id":"GO:2001040","count":2},{"id":"GO:1901097","count":2}]},{"hash":"564873294758661704","title":"ABA-driven plant cell wall remodeling","description":"The cluster centers on plant-specific processes of cell wall modification, pectin catabolism, and mucilage pectin biosynthesis, all linked to abscisic acid-activated signaling, suggesting ABA-regulated cell wall remodeling during stress or development. Additional terms touching on cell cycle and apoptosis may reflect growth-stress responses under ABA, while a few terms seem less connected (e.g., Schwann cell development, muscle activity), but the dominant theme is ABA-associated remodeling of the plant cell wall.","confidence":"Medium","size":18,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042545","count":3},{"id":"GO:0045490","count":3},{"id":"GO:0048358","count":2},{"id":"GO:0009738","count":2},{"id":"GO:0014850","count":2}]},{"hash":"946200857375759545","title":"Renin-angiotensin signaling and kidney development","description":"Most terms center on the renin-angiotensin axis and kidney development (renin-angiotensin regulation of aldosterone production; angiotensin maturation; mesonephros development) and related drinking behavior. Additional terms point to general peptide/protein processing and immune antigen handling (proteolysis; protein catabolic process; protein autoprocessing; MHC II antigen presentation; APP processing), suggesting a broader theme of peptide maturation and turnover with renal and neuro-immune links. The clearest coherent label is renin-angiotensin signaling and kidney development.","confidence":"Medium","size":18,"edges":22,"triangles":3,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0002018","count":2},{"id":"GO:0002003","count":2},{"id":"GO:0042756","count":2},{"id":"GO:0019886","count":2},{"id":"GO:0006508","count":2}]},{"hash":"822162643434925074","title":"Flavonoid glycoside biosynthesis and phenylpropanoid metabolism","description":"The cluster is dominated by GO terms for flavonoid glycoside biosynthesis (kaempferol/quercetin/cyanidin O-glucosides) and lignin/phenylpropanoid metabolism, indicating a cohesive theme around flavonoid glycoside production and related phenylpropanoid pathways. Some terms like estrogen catabolic and antibiotic metabolism appear ancillary, but the strongest signal centers on flavonoid glycoside biosynthesis and lignin-related metabolism.","confidence":"High","size":18,"edges":29,"triangles":8,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006711","count":16},{"id":"GO:0030259","count":16},{"id":"GO:0052696","count":16},{"id":"GO:0070980","count":16},{"id":"GO:0033330","count":16}]},{"hash":"2151366084563910422","title":"Plant metabolism and plasmodesmata transport","description":"Top GO terms show a mix of diverse metabolic processes (oxalate, purine/ureide/allantoin, ethanol catabolism) and a few biosynthetic processes, with a plant-specific signal from plasmodesmata-mediated intercellular transport. This suggests a cluster centered on broad plant metabolism coupled with intercellular metabolite movement, rather than a single precise pathway. Confidence in this label is Medium.","confidence":"Medium","size":18,"edges":8,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0017000","count":4},{"id":"GO:0033609","count":4},{"id":"GO:0010497","count":4},{"id":"GO:0042572","count":4}]},{"hash":"148274465493739648","title":"LDL Receptor\u2013Mediated Lipoprotein Catabolism","description":"The dominant GO terms point to LDL particle receptor\u2013related catabolic processes, including LDL particle receptor catabolic process and its regulation (positive and negative). This suggests the cluster\u2019s proteins are involved in receptor-mediated lipoprotein processing and clearance. A few terms (stomatal morphogenesis, renin secretion, iron homeostasis) appear unrelated or are likely background annotations, so they don\u2019t redefine the cluster\u2019s core theme. Overall, the form and directionality of the LDL receptor\u2013associated pathways best capture the shared function.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0010103","count":4},{"id":"GO:0007039","count":3},{"id":"GO:0010989","count":3},{"id":"GO:0006879","count":3},{"id":"GO:1905596","count":3}]},{"hash":"1383156389461346696","title":"Amino acid and porphyrin biosynthesis","description":"This cluster\u2019s top GO terms are dominated by biosynthetic processes, especially amino acid biosynthesis (arginine/ornithine, beta-alanine, lysine, alanine) and porphyrin (protoporphyrinogen IX) biosynthesis, with additional related pathways like ectoine and antibiotic biosynthesis. A flooding-response term appears peripheral and not central to the core function. Overall, the common thread is metabolic biosynthesis of amino acids and related compounds, with porphyrin synthesis as a related backbone. Confidence: Medium","confidence":"","size":18,"edges":22,"triangles":5,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0010121","count":2},{"id":"GO:0006782","count":2},{"id":"GO:0006593","count":2},{"id":"GO:0019481","count":2},{"id":"GO:0017000","count":2}]},{"hash":"280245865415902014","title":"TLR-Mediated Innate Immune Signaling","description":"The top GO terms cluster around toll-like receptor signaling (TLR4, TLR8, TLR10), downstream cytokine and chemokine production, dendritic cell cytokine regulation, and defense against viruses, indicating a coherent module of innate immune sensing and response driven by TLR pathways.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006963","count":12},{"id":"GO:0002756","count":12},{"id":"GO:0034158","count":12},{"id":"GO:0002730","count":12},{"id":"GO:0034142","count":12}]},{"hash":"405597597185502163","title":"Unknown","description":"The top GO terms span apoptotic clearance, immune activation, placental development, nuclear export, ER polarization, virus response, organ regeneration, meiotic DNA processing, immune tolerance, and hormone secretion, with no single dominant process. This lack of a cohesive shared function makes a concise, specific label unreliable, so the cluster is best described as Unknown.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043277","count":18},{"id":"GO:0046641","count":18},{"id":"GO:0060709","count":18},{"id":"GO:0006611","count":18},{"id":"GO:0061167","count":18}]},{"hash":"378160582515114130","title":"Golgi-Centric vesicle trafficking","description":"Most top GO terms point to Golgi localization and vesicle transport, including endosome-to-Golgi retrograde transport, Golgi-to-ER retrograde transport, Golgi-to-vacuole transport, and both anterograde and synaptic vesicle processes. This pattern indicates a cluster of proteins involved in Golgi-centered cargo sorting and vesicle trafficking across the secretory pathway. Pigmentation and locomotory behavior terms are present but less central to the core trafficking theme, possibly reflecting species-specific connections to pigment transport or behavior linked to vesicle trafficking.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051645","count":2},{"id":"GO:0042147","count":2},{"id":"GO:0043473","count":2},{"id":"GO:0009615","count":2},{"id":"GO:0016185","count":2}]},{"hash":"2037053834277369546","title":"Transcription Regulation and Chemical Response","description":"The most represented terms are DNA-templated transcription and its regulation, suggesting the proteins cluster around transcriptional control. There is also strong indication of chemical responsiveness (response to cocaine, xenobiotic stimulus). Additional terms imply broader cell-cycle or developmental roles, indicating some functional diversity. Thus the name highlights the core transcriptional regulatory role with a chemical-stress component, while acknowledging outlier terms.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0042220","count":5},{"id":"GO:0006935","count":5},{"id":"GO:0045793","count":5},{"id":"GO:0006355","count":5}]},{"hash":"2196405346635297959","title":"Retroviral integration and latency","description":"The GO terms strongly point to a retroviral life cycle: entry into the host cell, nuclear penetration, reverse transcription (RNA-templated DNA biosynthesis), DNA integration, recombination, and establishment of integrated proviral latency. Additional terms about DNA replication/removal of RNA primer and microtubule association fit into the broader context of viral genome replication and host cell trafficking. Overall, the cluster is best described by retroviral genome integration and proviral latency.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046718","count":1},{"id":"GO:0015074","count":1},{"id":"GO:0039651","count":1},{"id":"GO:0006278","count":1},{"id":"GO:0006310","count":1}]},{"hash":"634438577822830834","title":"Developmental signaling and ECM biosynthesis","description":"Dominant terms include BMP signaling and various embryonic development processes (fin morphogenesis, skeletal joint, olfactory bulb development). Also enrichment for proteoglycan biosynthesis (heparan sulfate) and endomembrane system organization, suggesting a coordinated role in developmental signaling and extracellular matrix assembly. Some plant cell-wall terms appear, but the core pattern points to vertebrate developmental signaling and ECM modulation.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008101","count":6},{"id":"GO:0035118","count":6},{"id":"GO:0035884","count":6},{"id":"GO:0021772","count":6},{"id":"GO:0072498","count":6}]},{"hash":"32553708084735419","title":"Unknown","description":"The GO terms span a mix of immune-related processes (apoptotic cell clearance, T cell proliferation, response to virus, tolerance induction) and diverse development/nuclear/secretory functions (placental differentiation, organ regeneration, protein export from nucleus, ER polarization, meiosis, hormone secretion). There isn\u2019t a single cohesive biological theme tying all terms together, so a concise, meaningful label cannot be confidently assigned.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043277","count":18},{"id":"GO:0046641","count":18},{"id":"GO:0060709","count":18},{"id":"GO:0006611","count":18},{"id":"GO:0061167","count":18}]},{"hash":"2207933238707721557","title":"Plant cell wall biosynthesis and fungal detection","description":"The top GO terms are dominated by plant-specific processes (xyloglucan metabolism, cell wall biogenesis, fungal-type wall organization, stamen filaments) and by detection of molecules of fungal origin, pointing to a plant cell wall remodeling/immune signaling theme. Some terms (keratinocyte differentiation) appear as noise, but overall the cluster centers on plant cell wall production and plant immune sensing.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030216","count":2},{"id":"GO:0032491","count":1},{"id":"GO:0009831","count":1},{"id":"GO:0006037","count":1},{"id":"GO:0080086","count":1}]},{"hash":"385416595869557549","title":"Melanosome Biogenesis and Pigment Transport","description":"The prominent GO terms point to pigmentation and melanosome assembly, complemented by multiple vesicle trafficking processes in the secretory pathway (ER\u2013Golgi and Golgi-to-plasma membrane transport, COPII vesicle coating). This pattern suggests a cohesive role in pigment granule formation and delivery to the plasma membrane. Some terms (autophagy, cuticle development, snRNA pseudouridine synthesis) are peripheral, but the core signal centers on melanosome-related pigment production and trafficking.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043473","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0006893","count":2},{"id":"GO:0048208","count":1},{"id":"GO:1903232","count":1}]},{"hash":"2162460338633379341","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090617","count":14},{"id":"GO:0042793","count":14},{"id":"GO:1905639","count":14},{"id":"GO:1900865","count":14},{"id":"GO:0031426","count":14}]},{"hash":"2130453029533459703","title":"Ribosome Biogenesis and RNA Processing","description":"The top GO terms cluster around RNA-processing activities and ribosome production: ribosomal large subunit biogenesis, maturation of 5.8S and SSU rRNA, and mRNA splicing via spliceosome, suggesting a core function in RNA processing and ribosome assembly. Additional vesicle trafficking and cell-division terms (COPII, ER\u2013Golgi transport, mitotic chromosome condensation) appear but are less central to the core theme; overall, RNA processing and ribosome biogenesis best explain the cluster.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042273","count":3},{"id":"GO:0090114","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0007076","count":2}]},{"hash":"1578752716109534123","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0090615","count":4},{"id":"GO:0090617","count":4},{"id":"GO:0042793","count":4},{"id":"GO:1905639","count":4},{"id":"GO:1900865","count":4}]},{"hash":"1772199687096111401","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090617","count":3},{"id":"GO:0042793","count":3},{"id":"GO:1905639","count":3},{"id":"GO:1900865","count":3},{"id":"GO:0031426","count":3}]},{"hash":"2251248684780024595","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":8},{"id":"GO:0090617","count":8},{"id":"GO:0042793","count":8},{"id":"GO:1905639","count":8},{"id":"GO:1900865","count":8}]},{"hash":"1564577545792709695","title":"Developmental tissue remodeling","description":"The terms cluster around remodeling and morphogenesis across development: bone remodeling (bone resorption, intramembranous ossification), basement membrane disassembly, lung branching morphogenesis, decidualization, and related catabolic/hormonal processes. This points to a broad theme of developmental tissue remodeling rather than a single coherent pathway, despite the diversity of the specific GO terms.","confidence":"Medium","size":17,"edges":44,"triangles":68,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0097067","count":2},{"id":"GO:0051603","count":2},{"id":"GO:0010815","count":2},{"id":"GO:0060448","count":2},{"id":"GO:0001957","count":2}]},{"hash":"1277692735856256221","title":"Oxidative Stress Response and Metabolism","description":"The strongest signals are oxidative stress and redox-related terms (oxidation-reduction process, cellular oxidant detoxification, cellular response to oxidative stress), suggesting these proteins help manage oxidative damage. There are also several metabolic terms (alkaloid metabolism, nitrogen utilization, uracil catabolic process, ubiquinone biosynthesis) indicating involvement in diverse metabolic pathways; the presence of transcription and phosphorylation terms hints regulatory roles. Taken together, the cluster seems centered on redox homeostasis with supporting metabolic functions.","confidence":"Medium","size":17,"edges":34,"triangles":13,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0098869","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0034599","count":2},{"id":"GO:0016310","count":2}]},{"hash":"1260946889995172737","title":"Ion and Fluid Transport","description":"These proteins cluster around transport and movement of ions and fluids across membranes and into organelles: bicarbonate, chloride, and borate transmembrane transport, general fluid transport, and chloroplast stroma protein import. A few terms about neuronal development appear, but the dominant theme is membrane transport and ion/homeostasis, justifying a transport-focused label.","confidence":"Medium","size":17,"edges":12,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0045037","count":2},{"id":"GO:0051453","count":1},{"id":"GO:0033326","count":1},{"id":"GO:0015701","count":1},{"id":"GO:0021860","count":1}]},{"hash":"1090207453743359465","title":"Antiviral response and cell-cycle control","description":"Based on the top GO terms, the cluster contains antiviral-related processes (defense response to virus, cellular response to type I interferon) alongside cell-cycle\u2013related processes (cell division, anaphase-promoting complex\u2013dependent catabolic process, asymmetric neuroblast division). This suggests a dual theme rather than a single, cohesive function. Some terms are obsolete or low-frequency, indicating partial signals, but the antiviral and cell-cycle signals are the strongest cohesive threads.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051607","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0071357","count":1},{"id":"GO:0055059","count":1},{"id":"GO:0090526","count":1}]},{"hash":"1454074908605752274","title":"Xenobiotic and lipid metabolism","description":"These terms cluster around broad metabolism of small molecules, including alkaloids, bile acids, triglycerides, and vitamins/retinoids (vitamin D, retinoic acid). No single pathway dominates, so a broad \u201cxenobiotic and lipid metabolism\u201d label fits best.","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0033280","count":13},{"id":"GO:0046232","count":13},{"id":"GO:0009822","count":12},{"id":"GO:0006641","count":12},{"id":"GO:0071615","count":12}]},{"hash":"2269998731799160120","title":"Membrane Targeting and ER Stress Response","description":"Most terms describe targeting of nascent proteins to membranes (SRP-dependent and post-translational translocation), responses to unfolded proteins and ER stress, and regulation of apoptosis under stress. This suggests a cluster centered on membrane protein biogenesis and ER quality control, with a few auxiliary associations to iron-sulfur cluster assembly and DNA replication as minor links.","confidence":"Medium","size":17,"edges":9,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0071353","count":2},{"id":"GO:0016226","count":2},{"id":"GO:0006616","count":2},{"id":"GO:0034620","count":2},{"id":"GO:1903382","count":2}]},{"hash":"392239223713359658","title":"Lipid and small-molecule metabolism","description":"The top GO terms are dominated by lipid-related biosynthetic and catabolic processes: prostaglandin biosynthesis, bile acid biosynthesis, triglyceride metabolism, retinoic acid catabolic process, and alkaloid metabolism. This pattern suggests a cohesive focus on metabolism of lipids and other small molecules (including vitamins and xenobiotic-like compounds), with some inflammatory regulation linked to lipid signaling. A concise label that captures this core theme is \"Lipid and small-molecule metabolism.\" ","confidence":"Medium","size":17,"edges":20,"triangles":1,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":16},{"id":"GO:0009822","count":14},{"id":"GO:0006641","count":14},{"id":"GO:0071615","count":14},{"id":"GO:0034653","count":14}]},{"hash":"2267036317295611052","title":"Nuclear import and intracellular trafficking","description":"This cluster centers on GO terms tied to nuclear localization and transport (protein localization to the nuclear pore, protein import into the nucleus, DNA-templated transcription initiation) and vesicle trafficking between the Golgi and ER, suggesting a shared role in intracellular movement and nuclear import processes. Some outlier terms (light absorption, daunorubicin biosynthesis) are likely noise. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008202","count":1},{"id":"GO:0090204","count":1},{"id":"GO:0071806","count":1},{"id":"GO:0000060","count":1},{"id":"GO:0016037","count":1}]},{"hash":"676637394728473312","title":"Regulated mRNA Splicing and Processing","description":"The GO terms cluster around spliceosome-mediated splicing, regulation of splicing, mRNA modification and export, and stress-related mRNA stability, indicating a cohesive set of proteins involved in post-transcriptional processing and control of gene expression. While a few terms are more peripheral (ncRNA-mediated silencing, viral translation), the dominant signal points to mRNA maturation and regulatory processes.","confidence":"High","size":17,"edges":116,"triangles":483,"max_degree":16,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":9},{"id":"GO:0048026","count":8},{"id":"GO:0031047","count":7},{"id":"GO:1901407","count":7},{"id":"GO:0000398","count":7}]},{"hash":"1181954631273704868","title":"Plant Hormone Signaling and Epidermal Differentiation","description":"The top terms cluster around plant hormone responses (gibberellin, salicylic acid, ACC/ethylene) and epidermal/vascular differentiation (atrichoblast, sclerenchyma), with supporting notes on chitin defense and antifungal immunity, pointing to a cohesive theme of growth-regulating signaling linked to epidermal development and defense in plants. The lone animal term (pituitary gland development) appears as an outlier rather than a core driver of the cluster\u2019s function.","confidence":"Medium","size":17,"edges":9,"triangles":0,"max_degree":6,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0021983","count":7},{"id":"GO:0009739","count":7},{"id":"GO:0009751","count":7},{"id":"GO:0006355","count":7},{"id":"GO:0009961","count":5}]},{"hash":"1814303844484358508","title":"ER Stress and DNA Replication/Cell Cycle","description":"The top GO terms split between ER unfolded protein response and protein quality control (ER-Golgi transport, chaperone-dependent refolding) and core nuclear processes (DNA replication, transcription, G1/S transition). This dual theme suggests a cluster linking secretory-pathway quality control with DNA maintenance/cell-cycle activities. Cytokinin biosynthesis and ATP metabolism appear peripheral. Therefore, this label captures the dominant themes without overfitting to one subset.","confidence":"Medium","size":17,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0006515","count":3},{"id":"GO:0070389","count":3},{"id":"GO:0030968","count":3}]},{"hash":"2077189877942876017","title":"Unknown","description":"The top GO terms in this cluster cover a broad mix of metabolic (oxidation-reduction, propylene and uracil catabolic processes), stress/chemical responses (fungicide, ethanol), development (neuron maturation, pituitary gland development), transcriptional regulation, and RNA processing, with several terms flagged as obsolete. There is no clear, cohesive function tying the proteins together, nor any network connectivity (edges/triangles are zero), so a single representative label cannot be confidently assigned.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0042208","count":3},{"id":"GO:0060992","count":3},{"id":"GO:0042551","count":3},{"id":"GO:0006212","count":3}]},{"hash":"1436542972467682277","title":"Energy metabolism and redox balance","description":"This cluster centers on metabolic and redox-related processes: redox homeostasis, oxidation-reduction activity, glycolysis, mitochondrial electron transport, and 2-oxoglutarate metabolism, indicating proteins involved in cellular energy production and redox regulation. Some terms appear outdated or less informative, but the dominant theme ties to energy generation and redox control.","confidence":"High","size":17,"edges":2,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0045454","count":7},{"id":"GO:0021983","count":7},{"id":"GO:0042493","count":7},{"id":"GO:0051573","count":7}]},{"hash":"212668665020180521","title":"Ribosome Biogenesis and rRNA Processing","description":"The cluster is dominated by GO terms tied to ribosome biogenesis and rRNA maturation, including maturation of LSU- and SSU-rRNA and ITS1 cleavage, as well as RNA guanine-N7 methylation. These collectively point to roles in ribosomal subunit assembly and precursor rRNA processing, which appear to be the core theme linking these proteins. Some development-related terms are present but appear ancillary to the main ribosome-focused signal.","confidence":"High","size":17,"edges":99,"triangles":312,"max_degree":16,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":7},{"id":"GO:0008283","count":5},{"id":"GO:0000463","count":5},{"id":"GO:0000462","count":4},{"id":"GO:0000447","count":4}]},{"hash":"1110373211652323108","title":"Rab-dependent vesicle transport and geranylgeranylation","description":"This cluster centers on Rab GTPase signaling, Rab-mediated protein transport, and the role of protein geranylgeranylation in membrane targeting, as reflected by GO terms on GTPase activation, Rab signal transduction, geranylgeranylation, and protein transport; some terms hint at species-specific development, but the core theme is Rab-driven trafficking and lipid modification.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090630","count":1},{"id":"GO:0048798","count":1},{"id":"GO:0018344","count":1},{"id":"GO:0050771","count":1},{"id":"GO:0032482","count":1}]},{"hash":"452778232192264909","title":"Chloroplast gene expression and RNA editing","description":"The top GO terms cluster around chloroplast/plastid processes\u2014chloroplast-nucleus signaling, chloroplast RNA processing, plastid transcription, chloroplast RNA modification, and mRNA processing/editing\u2014with additional mitochondrial mRNA modification terms. This suggests a cohesive theme of organelle gene expression and cross-compartment signaling, despite a peripheral seed dormancy term. Overall, the cluster appears to reflect chloroplast/plastid RNA processing and transcriptional regulation, with related mitochondrial RNA regulation.","confidence":"High","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010019","count":14},{"id":"GO:0031426","count":14},{"id":"GO:0016554","count":14},{"id":"GO:0031425","count":14},{"id":"GO:0042793","count":14}]},{"hash":"1162049588263263181","title":"Retroviral replication and latency with host interaction","description":"The top GO terms point to viral lifecycle steps\u2014RNA-templated DNA biosynthesis (reverse transcription), host-mediated activation of viral replication, and proviral latency\u2014and include host entry and leukocyte migration, implying virus\u2013host interaction and immune involvement. A couple terms seem unrelated (e.g., sepal formation) and may be noise, but the overall pattern supports a retroviral replication/latency theme.","confidence":"Medium","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":"protein folding","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0044829","count":5},{"id":"GO:0006278","count":5},{"id":"GO:0050714","count":5},{"id":"GO:2000276","count":5}]},{"hash":"590826622507725117","title":"Osmotic Stress Response and Carbohydrate/Lipid Biosynthesis","description":"The top GO terms cluster around osmotic stress responses (water deprivation, flooding, mannitol, sucrose) alongside metabolic/biosynthetic processes for carbohydrates and lipids (glucose, starch, glycolipid, phospholipid) and bacillithiol biosynthesis, suggesting a cohesive theme of osmotic adaptation coupled with carbohydrate and lipid metabolism.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009414","count":2},{"id":"GO:0008654","count":2},{"id":"GO:0009413","count":2},{"id":"GO:0009744","count":2},{"id":"GO:0097502","count":2}]},{"hash":"36822303235479613","title":"Cytoskeleton-Driven Vesicle Trafficking","description":"The top GO terms cluster around actin cytoskeleton dynamics (Arp2/3-mediated nucleation, cortical patch assembly), calcium-regulated exocytosis, and intracellular transport involving endosomes/lysosomes and small GTPases, suggesting a theme of cytoskeleton-associated vesicle movement; some outliers exist (root morphogenesis, intron splicing, mitochondrial inheritance), but the core connections are vesicle trafficking linked to the cytoskeleton.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045956","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0010102","count":1},{"id":"GO:0000373","count":1},{"id":"GO:0000001","count":1}]},{"hash":"478733617613698774","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0032543","count":1},{"id":"GO:0000028","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0042254","count":1}]},{"hash":"2086907475821232252","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0090615","count":17},{"id":"GO:0090617","count":17},{"id":"GO:0042793","count":17},{"id":"GO:1905639","count":17},{"id":"GO:1900865","count":17}]},{"hash":"494392438309841402","title":"Plant Hormone Biosynthesis and Fruit Ripening","description":"This cluster is dominated by GO terms for plant hormone metabolism and fruit development, including auxin catabolic, ethylene and gibberellin biosynthesis/catabolism, and the fruit ripening process, plus related signals like salicylic acid catabolism and hydrogen peroxide\u2013mediated programmed cell death. The consistency of hormone biosynthesis and ripening terms suggests a cohesive group centered on hormone-regulated fruit maturation and associated stress responses.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0009852","count":5},{"id":"GO:0009835","count":5},{"id":"GO:1902835","count":5},{"id":"GO:0009693","count":5}]},{"hash":"618666092813442181","title":"Membrane Transport and Osmotic Stress Response","description":"This cluster is dominated by GO terms related to transmembrane transport and osmotic regulation, including D-serine transport, L-lysine import, L-arginine catabolism, and cellular/osmotic stress responses. A couple of outlier terms (mRNA splicing and macrophage activation) are less aligned with this theme, suggesting the cluster is somewhat heterogeneous. Overall, the label captures the most prominent functions, with moderate confidence.","confidence":"Medium","size":17,"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:0006884","count":1},{"id":"GO:0042942","count":1},{"id":"GO:0071477","count":1}]},{"hash":"403671125498006392","title":"RNA Processing and Translation Machinery","description":"The cluster is dominated by GO terms related to RNA metabolism and gene expression: translation initiation and reinitiation, mRNA export, splicing, and mRNA modification, as well as transcription. This points to a core gene-expression machinery cluster that coordinates transcription, RNA processing/export, and translation. Some terms (DNA repair, immune defense, development) appear as less central or context-dependent annotations, but do not override the main theme. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001731","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0006406","count":3},{"id":"GO:0001825","count":3},{"id":"GO:0045292","count":3}]},{"hash":"2232445218030700095","title":"Plant reproduction and cell wall dynamics","description":"The top GO terms center on plant-specific processes such as pollen tube guidance and plant-type cell wall loosening, coupled with sexual reproduction and defense against fungi. While there are glycosylation-related terms too, the strongest signal is plant reproductive growth and cell-wall remodeling, so the cluster is best labeled as Plant reproduction and cell wall dynamics. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":1},{"id":"GO:0010183","count":1},{"id":"GO:0006488","count":1},{"id":"GO:0006949","count":1},{"id":"GO:0009828","count":1}]},{"hash":"1380848602463341079","title":"Neuroimmune development and inflammatory signaling","description":"This cluster combines neural development terms (corpus callosum development, synapse assembly, bud growth) with innate immune and inflammatory responses (LPS signaling, dsRNA response, interferon-beta production, defense against bacteria, pain behavior), suggesting a neuroimmune/inflammatory theme that links development and sensory/inflammatory signaling.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002091","count":3},{"id":"GO:0007118","count":3},{"id":"GO:0051965","count":3},{"id":"GO:0045359","count":3},{"id":"GO:0061368","count":3}]},{"hash":"444605311797920374","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0000027","count":2},{"id":"GO:0042254","count":2}]},{"hash":"766777113871832862","title":"Nuclear transport and ribosome biogenesis","description":"The cluster is driven by GO terms tied to nucleocytoplasmic transport (mRNA export, ribosomal subunit export, ribosomal protein import) and nuclear pore complex assembly, pointing to a shared role in moving ribonucleoproteins in and out of the nucleus and assembling ribosomal components. Additional terms about splicing factor import and transcriptional regulation hint at related RNA processing and regulatory coordination within the nucleus, supporting a cohesive theme around nuclear transport and ribosome biogenesis.","confidence":"High","size":17,"edges":23,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":4},{"id":"GO:0000056","count":4},{"id":"GO:0051292","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0006610","count":3}]},{"hash":"1907909966669405448","title":"IRES-dependent viral translation initiation","description":"The proteins show a strong enrichment of translation initiation terms, including formation of the preinitiation complex, translation reinitiation, and IRES-dependent viral initiation, with regulation of translational initiation also represented. While a few mRNA processing terms appear, the dominant theme is initiation of translation, especially viral IRES-driven mechanisms, justifying this label.","confidence":"High","size":17,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":3},{"id":"GO:0075525","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0006446","count":3}]},{"hash":"2133082949345928150","title":"Photomorphogenesis-linked transcription regulation","description":"Top GO terms point to light-responsive gene regulation (positive regulation of photomorphogenesis; regulation/negative regulation of RNA Pol II transcription) along with related cellular processes (cell wall organization, metabolic regulation). This suggests a cluster of proteins involved in light-regulated transcriptional control and associated metabolism in plants, despite some obsolete terms. Therefore, the label emphasizes the core theme of photomorphogenesis-associated transcription regulation.","confidence":"Medium","size":17,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0005978","count":3},{"id":"GO:0009405","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0045898","count":2},{"id":"GO:1900446","count":2}]},{"hash":"1789892961444161694","title":"Auxin Transport and Root Development","description":"The dominant GO terms are about auxin movement (transmembrane transport, polar transport, ER-to-cytosol transport, auxin export) and auxin-activated signaling, with a clear link to adventitious root development. Although redox-related terms appear, the core theme centers on auxin distribution and its role in root formation, justifying this concise label.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055085","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0010315","count":1},{"id":"GO:0010252","count":1}]},{"hash":"1471750752824242259","title":"Ubiquitin-Dependent Protein Regulation","description":"Based on the Top Terms, the cluster is dominated by ubiquitin-related processes: protein ubiquitination, ubiquitin-dependent protein catabolic pathways via multivesicular body sorting, and positive regulation of ubiquitin-dependent endocytosis, with additional terms for regulation of ubiquitination and membrane-associated processes. Some Drosophila-specific developmental terms may reflect roles of ubiquitin signaling in gametogenesis, but the overarching theme is ubiquitin-mediated regulation and trafficking, justifying this label as representative for the cluster.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0045087","count":2},{"id":"GO:0043162","count":1},{"id":"GO:2000397","count":1},{"id":"GO:0007293","count":1}]},{"hash":"1197732386370615310","title":"Proliferating T cells, immune signaling, and ECM remodeling","description":"The cluster centers on DNA replication and mitotic cell cycle, indicating proliferating cells, with strong T cell\u2013related signals (T cell receptor signaling, T cell proliferation, tolerance induction). ECM remodeling terms (focal adhesion regulation, extracellular matrix disassembly) suggest migration and tissue remodeling typical of immune responses. Apoptotic cell clearance also fits immune regulation. While other terms are less central, the dominant theme ties immune activation/proliferation to matrix dynamics.","confidence":"High","size":17,"edges":100,"triangles":284,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006260","count":16},{"id":"GO:0000278","count":16},{"id":"GO:0043277","count":15},{"id":"GO:0046641","count":15},{"id":"GO:0002651","count":15}]},{"hash":"1862001310613068226","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031145","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0090617","count":2},{"id":"GO:1905639","count":2}]},{"hash":"237349854743330834","title":"Neuronal vesicle trafficking and brain development","description":"Top GO terms show a coherent theme of synaptic vesicle exocytosis regulation and brain development (including substantia nigra), with supporting endosomal-lysosomal transport and protein localization terms that fit neuronal trafficking and polarity. This suggests a cluster of proteins involved in synaptic vesicle handling and neuronal maturation.","confidence":"High","size":17,"edges":10,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000300","count":5},{"id":"GO:0010796","count":5},{"id":"GO:0007420","count":5},{"id":"GO:0031384","count":5},{"id":"GO:0008283","count":4}]},{"hash":"12401698487734424","title":"Secondary Metabolism and Lipid Biosynthesis","description":"This cluster is driven by multiple biosynthetic and lipid-related processes: antibiotic biosynthetic process, acetoin catabolic process, mycolic acid biosynthetic process, fatty acid elongation, and melanin biosynthesis, which together suggest a theme of secondary metabolism and lipid/outer-murface biosynthesis. Some terms (lung development, hormone metabolism, transcription regulation) are less aligned, but the predominant pattern is metabolic biosynthesis, giving a reasonable, though not perfect, cohesion.","confidence":"Medium","size":17,"edges":7,"triangles":1,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":10},{"id":"GO:0017000","count":10},{"id":"GO:0045150","count":9},{"id":"GO:0030324","count":9},{"id":"GO:0006355","count":9}]},{"hash":"665599314334664538","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090617","count":5},{"id":"GO:0042793","count":5},{"id":"GO:1905639","count":5},{"id":"GO:1900865","count":5},{"id":"GO:0010019","count":5}]},{"hash":"1057106787854159624","title":"Ion Transport and Membrane Potential Regulation","description":"The top GO terms are centered on membrane hyperpolarization and potassium/sodium ion transport across membranes, indicating a core function in regulating membrane potential via ion flux. Other terms like transcription and development are present but less consistent with the primary theme, which is driven by ion transport signals.","confidence":"Medium","size":17,"edges":10,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060081","count":4},{"id":"GO:0071805","count":4},{"id":"GO:0098719","count":4},{"id":"GO:0097623","count":4},{"id":"GO:0046827","count":3}]},{"hash":"2247347934069752548","title":"DNA repair and genome maintenance","description":"The top GO terms are dominated by DNA repair and recombination processes (DNA recombination, base-excision repair, DNA catabolic process), indicating the cluster proteins are largely involved in maintaining genome integrity. While a few terms touch on RNA stability and cellular signaling (e.g., regulation of mRNA stability, cellular response to cAMP), these are supplementary and do not overshadow the DNA repair theme. Overall, the cluster appears to represent proteins engaged in DNA repair and genome maintenance functions.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":3},{"id":"GO:0006284","count":3},{"id":"GO:0090502","count":3},{"id":"GO:0006308","count":2},{"id":"GO:0007568","count":2}]},{"hash":"1337236704406014267","title":"Tissue Development and Signaling","description":"The cluster\u2019s top GO terms cluster around tissue development (nervous system development, skeletal muscle development, osteoclast differentiation) and signaling processes (prostaglandin biosynthesis, B cell receptor signaling). While there are additional terms related to metal ion homeostasis and ethylene response, the dominant pattern points to developmental processes coupled with cellular signaling across tissues. This justifies a concise label focusing on development and signaling themes.","confidence":"Medium","size":17,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":2},{"id":"GO:0007519","count":2},{"id":"GO:0050853","count":2},{"id":"GO:0071421","count":1},{"id":"GO:0006880","count":1}]},{"hash":"1648845716453183701","title":"Transmembrane Transporters and Metabolic Processes","description":"Top GO terms show multiple transmembrane transport activities (sodium, nitrate, nitrite, phosphate, galactose) along with metabolic/detoxification processes and a vesicular neurotransmitter loading term, suggesting proteins primarily involved in moving metabolites across membranes and handling metabolic tasks. This shared theme of membrane transport coupled to metabolism best defines the cluster, despite some functional diversity.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006004","count":1},{"id":"GO:0098700","count":1},{"id":"GO:0015757","count":1}]},{"hash":"742286716768435558","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0051092","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0035372","count":2},{"id":"GO:0048733","count":1}]},{"hash":"188169474016716782","title":"Mitochondrial Metabolite Transporters","description":"The cluster's top GO terms are dominated by transmembrane transport of energy-related metabolites and cofactors (ADP, NAD, thiamine pyrophosphate) across membranes, especially mitochondria, plus imports such as glycine and thiosulfate. This consistent transport-focused pattern suggests the proteins function as metabolite transporters, often tied to mitochondrial energy metabolism. Some broad terms like liver regeneration and female pregnancy appear noise relative to this strong transporter signal.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990544","count":16},{"id":"GO:0097421","count":16},{"id":"GO:0032869","count":16},{"id":"GO:0007565","count":16},{"id":"GO:0030974","count":16}]},{"hash":"1587896116060767134","title":"Stress-Responsive Transcription and Oxylipin Biosynthesis","description":"The cluster shows enrichment for stress-related GO terms ( ozone response, immobilization stress, xenobiotic response) together with oxylipin biosynthesis and transcriptional regulation (DNA-templated transcription, negative regulation of RNA Pol II) and methylation, suggesting a link between lipid signaling, epigenetic or transcriptional control, and environmental stress response.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032259","count":4},{"id":"GO:0010193","count":3},{"id":"GO:0035902","count":3},{"id":"GO:0031408","count":3},{"id":"GO:0006351","count":3}]},{"hash":"2045342761085395857","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0090615","count":3},{"id":"GO:0090617","count":3},{"id":"GO:1905639","count":3}]},{"hash":"226335343239977415","title":"RNA transcription and processing proteins","description":"This cluster centers on transcription-related processes (DNA-templated transcription, RNA polymerase import) and RNA processing pathways (miRNA, lsiRNA processing) along with RNAi antiviral responses, suggesting a cohesive group of factors regulating RNA production and processing. Some cohesion-related and germline terms are present but appear incidental to the dominant RNA-focused theme.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044376","count":1},{"id":"GO:0007064","count":1},{"id":"GO:0034087","count":1},{"id":"GO:1990022","count":1},{"id":"GO:0060145","count":1}]},{"hash":"234659232335117970","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":1},{"id":"GO:0006397","count":1},{"id":"GO:0034477","count":1},{"id":"GO:0030223","count":1},{"id":"GO:0008380","count":1}]},{"hash":"124944065048604397","title":"Ubiquitin-Driven Chromatin and RNA Regulation","description":"Top GO terms indicate protein ubiquitination/autoubiquitination, chromatin organization, and mRNA transport, with additional signals from cell cycle and stress pathways (hypoxia, TGF-\u03b2). This points to a nuclear regulatory module where ubiquitin signaling modulates chromatin state and RNA processing/export, integrating growth and stress responses. The diverse terms suggest a broad regulatory cluster rather than a single pathway.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000209","count":3},{"id":"GO:0051028","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0071456","count":3},{"id":"GO:1901253","count":2}]},{"hash":"1575147868760296082","title":"Ubiquitin-Proteasome\u2013Mediated Protein Degradation","description":"The top GO terms cluster around ubiquitin-dependent protein catabolic processes, protein polyubiquitination, and SCF-dependent proteasomal degradation, indicating a proteostasis-focused group of proteins. Other terms reflect stress responses and cell-cycle/checkpoint signaling, but the dominant theme is ubiquitin-proteasome\u2013driven protein turnover.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":13},{"id":"GO:0000209","count":11},{"id":"GO:0031146","count":9},{"id":"GO:1903378","count":7},{"id":"GO:0000083","count":7}]},{"hash":"739626182875215007","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":3},{"id":"GO:0090617","count":3},{"id":"GO:0042793","count":3},{"id":"GO:1905639","count":3},{"id":"GO:1900865","count":3}]},{"hash":"1796341089530015690","title":"Unknown","description":"The top GO terms span both plant and animal processes (pollen tube growth; neuroblast proliferation; pigmentation) and include several unrelated or obsolete terms, with no clear shared function, pathway, or molecular activity. The cluster also shows no edges or connectivity, making a cohesive biological theme unlikely. Therefore, a specific functional label cannot be confidently assigned.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009860","count":1},{"id":"GO:0080092","count":1},{"id":"GO:0009405","count":1},{"id":"GO:0021847","count":1},{"id":"GO:0043473","count":1}]},{"hash":"854702538418665227","title":"Plant Hormone Signaling and Growth","description":"This cluster is mainly tied to plant biology: responses to gibberellin and jasmonic acid indicate hormone signaling; leaf formation and vegetative growth regulation point to development; flavonol biosynthesis reflects secondary metabolism linked to growth and defense. An outlier term about glutamatergic synaptic transmission appears, but the dominant themes support a plant hormone\u2013driven growth/development focus.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009739","count":3},{"id":"GO:0035249","count":2},{"id":"GO:1903770","count":2},{"id":"GO:1900386","count":2},{"id":"GO:0010338","count":2}]},{"hash":"1364453750854632503","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":17},{"id":"GO:0090617","count":17},{"id":"GO:0042793","count":17},{"id":"GO:1905639","count":17},{"id":"GO:1900865","count":17}]},{"hash":"998621104920696435","title":"Plant immune signaling and chromatin remodeling","description":"Top terms emphasize plant defense (defense response to virus, innate immune response) and hormone signaling (salicylic acid, gibberellin), with nucleosome assembly and epigenetic regulation suggesting chromatin remodeling accompanying defense activation. A few terms may reflect broad annotations outside this theme, but the core appears to be immunity linked to chromatin dynamics.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0002091","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0006334","count":2}]},{"hash":"1280960458609674416","title":"Unknown","description":"The GO terms include response to estradiol, lens fiber morphogenesis, aging, growth and transport regulation, ROS modulation, and muscle contraction, with no clear shared biological process across all proteins. As such, there isn't a robust, specific theme to name the cluster confidently.","confidence":"","size":16,"edges":25,"triangles":9,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0032355","count":3},{"id":"GO:0050821","count":3},{"id":"GO:0070309","count":3},{"id":"GO:0007568","count":3},{"id":"GO:0030308","count":3}]},{"hash":"120443413182006166","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009113","count":1},{"id":"GO:0070329","count":1},{"id":"GO:0006541","count":1},{"id":"GO:0006189","count":1},{"id":"GO:0046892","count":1}]},{"hash":"1095197387321374721","title":"Lysine and tryptophan metabolism","description":"The top GO terms center on lysine pathways (biosynthesis via aminoadipic acid and catabolic to acetyl-CoA) and tryptophan catabolism to kynurenine, including kynurenic acid biosynthesis. This points to amino acid metabolism as the core function of the cluster, with additional metabolism-related terms reflecting broader metabolic connectivity. Therefore, labeling as Lysine and tryptophan metabolism captures the dominant theme.","confidence":"Medium","size":16,"edges":119,"triangles":546,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019878","count":8},{"id":"GO:0019441","count":4},{"id":"GO:0032869","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0006107","count":4}]},{"hash":"1450175904259117127","title":"Plant metabolism, lignin biosynthesis, and defense","description":"The set of top GO terms includes diverse metabolic processes (L-alanine catabolism, fructose and propylene catabolism, retinol metabolism, lignin biosynthesis) and immune/hormonal regulation (response to lipopolysaccharide, positive regulation of hormone biosynthetic process). This pattern suggests a cluster focused on metabolic pathways that interface with defense signaling and hormone production, a common theme in plant metabolic networks where lignin formation and hormone biosynthesis are coordinated during defense.","confidence":"Medium","size":16,"edges":61,"triangles":109,"max_degree":11,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0042853","count":4},{"id":"GO:0051573","count":4},{"id":"GO:0034720","count":4},{"id":"GO:0032496","count":4}]},{"hash":"2152866730732004972","title":"Lens Stress Response and Growth Regulation","description":"This cluster is enriched for heat and high light stress responses and a lens-specific term (lens fiber cell morphogenesis), along with protein stabilization and negative regulation of growth and intracellular transport, pointing to a group of proteins that help cells cope with stress while modulating growth and protein interactions\u2014particularly in lens-related contexts. A minor spread to muscle contraction terms may reflect shared cytoskeletal/regulatory roles rather than a single tissue type.","confidence":"Medium","size":16,"edges":11,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":4},{"id":"GO:0032355","count":3},{"id":"GO:0050821","count":3},{"id":"GO:0070309","count":3},{"id":"GO:0007568","count":3}]},{"hash":"996762042505765783","title":"Regulation of cell differentiation across tissues","description":"The top GO terms center on regulation (both negative and positive) of differentiation across multiple lineages (bone, muscle, astrocytes, neurons, and even plant anther development) and include signaling pathway regulation (androgen receptor, glucocorticoid receptor) as well as circadian clock entrainment. This suggests a common theme of controlling cell fate and tissue development rather than a single specific pathway or tissue, justifying a broad label around differentiation regulation across diverse tissues.","confidence":"Medium","size":16,"edges":119,"triangles":546,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045668","count":13},{"id":"GO:0060766","count":13},{"id":"GO:2000323","count":7},{"id":"GO:0007518","count":7},{"id":"GO:0048658","count":7}]},{"hash":"196424898125150739","title":"RNA Splicing and Processing Regulation","description":"These proteins cluster around RNA maturation and regulation of mRNA processing (splicing via the spliceosome, mRNA stability, export, and modification), plus ncRNA-mediated gene silencing; the dominant GO terms point to spliceosome-dependent regulation of splicing and mRNA fate.","confidence":"High","size":16,"edges":23,"triangles":9,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":7},{"id":"GO:0048026","count":7},{"id":"GO:0010610","count":7},{"id":"GO:0045292","count":7},{"id":"GO:0006378","count":7}]},{"hash":"1620792440925562451","title":"Plant energy metabolism and flavonoid biosynthesis","description":"The cluster is dominated by core metabolic processes: TCA cycle, glycolysis, gluconeogenesis, and fatty acid biosynthesis, indicating central energy and lipid metabolism. In addition, there are plant-specific secondary metabolism terms such as chalcone and flavonoid biosynthetic processes, suggesting involvement in plant metabolite production. A few terms (DIF-1 biosynthetic process, cell wall layer assembly) are less central but do not override the main metabolic theme. Overall, the group seems focused on energy metabolism with plant secondary metabolism, justifying this label.","confidence":"Medium","size":16,"edges":60,"triangles":92,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":6},{"id":"GO:0006094","count":5},{"id":"GO:0006096","count":5},{"id":"GO:0006633","count":5},{"id":"GO:0033512","count":4}]},{"hash":"6123269637042080","title":"DNA replication and genome maintenance","description":"The cluster\u2019s frequent GO terms center on DNA replication, cell cycle regulation, and DNA repair/maintenance (e.g., DNA replication, RNA primer removal in mitosis, resolution of recombination intermediates, maintenance of trinucleotide repeats, base-excision repair, and cell cycle regulation). A few terms like photosynthesis and myeloid progenitor differentiation appear unrelated and may reflect annotation noise, but the dominant theme supports genome maintenance during replication.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002318","count":2},{"id":"GO:2000495","count":2},{"id":"GO:0007050","count":2},{"id":"GO:0015979","count":1},{"id":"GO:0006286","count":1}]},{"hash":"1130432667194873977","title":"DNA repair and mitotic regulation","description":"Dominant terms point to genome maintenance and cell-cycle control (mismatch repair, regulation of mitotic recombination, sister chromatid segregation, and transcription regulation). Protein folding appears as a broader cellular process, while several terms (hypoxia/visible light detection, plant ethylene signaling, immune regulation) seem peripheral, making the core theme plausible but not exclusive. ","confidence":"Medium","size":16,"edges":27,"triangles":2,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006457","count":2},{"id":"GO:0006298","count":1},{"id":"GO:0045870","count":1},{"id":"GO:0000019","count":1},{"id":"GO:0070483","count":1}]},{"hash":"513177429064083071","title":"Unknown","description":"The terms mix transcription-related processes (DNA-templated transcription, regulation of DNA binding, negative regulation of transcription by RNA polymerase II) with cell wall biosynthesis topics (cell wall organization, lipid A biosynthetic process, cell wall mannoprotein biosynthetic process), and several terms are obsolete. There is no single cohesive function tying these proteins together, so a clear cluster label cannot be inferred.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043388","count":6},{"id":"GO:0008360","count":5},{"id":"GO:0071555","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0000122","count":5}]},{"hash":"1179268115154741168","title":"Glutamatergic synaptic plasticity and ribosome biogenesis","description":"This cluster combines strong signals for glutamatergic synaptic transmission and long-term potentiation (synaptic plasticity) with genes involved in ribosome biogenesis and regulation of ribosomal protein gene transcription, suggesting coordinated control of synaptic function and protein synthesis. While some terms hint at broader cellular processes (apoptosis regulation, sphingolipid biosynthesis, myoblast fusion), the dominant theme centers on neuronal synaptic activity and ribosome-related gene expression.","confidence":"Medium","size":16,"edges":83,"triangles":217,"max_degree":13,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":7},{"id":"GO:0032147","count":6},{"id":"GO:0035249","count":4},{"id":"GO:0001324","count":4},{"id":"GO:0043065","count":4}]},{"hash":"1148988775074789126","title":"Nuclear DNA Replication and Transcription with ER Protein Folding","description":"The cluster centers on DNA replication and DNA-templated transcription, with accompanying RNA surveillance (nonsense-mediated decay) and signals of ER-associated protein folding and membrane targeting, suggesting a link between nuclear gene expression and ER quality control. Some terms are obsolete, but the core pattern reflects genome expression alongside protein maturation processes.","confidence":"Medium","size":16,"edges":32,"triangles":20,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0000184","count":6},{"id":"GO:0070389","count":5},{"id":"GO:0090305","count":5},{"id":"GO:0032508","count":5}]},{"hash":"891861932669162501","title":"Ribosome rRNA maturation and biogenesis","description":"These proteins are enriched for GO terms that center on maturation of SSU- and LSU-rRNA (including 5.8S) and ribosomal large subunit biogenesis, pointing to a shared role in ribosome assembly and RNA processing. A minor signal for spliceosome-mediated mRNA splicing appears, but the dominant pattern supports ribosome biogenesis. ","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0042273","count":2}]},{"hash":"1926703805334753097","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":32,"triangles":20,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1901621","count":8},{"id":"GO:0006260","count":8},{"id":"GO:0097428","count":8},{"id":"GO:0045454","count":8},{"id":"GO:0006458","count":8}]},{"hash":"1771774068018770642","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":4},{"id":"GO:0043981","count":3},{"id":"GO:0031146","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0001731","count":3}]},{"hash":"1221323879706218708","title":"Cell Cycle and Stress Response","description":"The cluster is enriched for mitotic processes (mitotic cell cycle, cell division, anaphase-promoting complex\u2013dependent catabolic process), suggesting a core association with cell cycle regulation. The presence of immune/defense terms (defense response to virus, innate immune response) and stress-related processes (ERAD, cadmium ion response, metal ion transport, histone methylation regulation) hints at roles in broader cellular stress responses or protein quality control that may influence division. The mix indicates proteins that participate in mitosis while also linking to stress- or defense-related pathways, rather than a single highly cohesive function.","confidence":"Medium","size":16,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051607","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0045087","count":2},{"id":"GO:2001162","count":2},{"id":"GO:0061087","count":2}]},{"hash":"260259387280898387","title":"Plant Defense Signaling and Development","description":"Top terms suggest plant-focused biology: innate immune signaling and jasmonic acid response, plus leaf formation and vegetative growth, with flavonol biosynthesis and even viral process. This points to a broad theme of defense signaling intertwined with development in plants, though the sparse connectivity means the label is an approximate overview rather than a precise module.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072422","count":1},{"id":"GO:0009870","count":1},{"id":"GO:1903770","count":1},{"id":"GO:0010338","count":1},{"id":"GO:1900386","count":1}]},{"hash":"1566818969861719784","title":"Ribosome biogenesis and translation","description":"The top GO terms cluster around ribosome assembly, SSU rRNA maturation, and translation initiation, indicating a core function in ribosome biogenesis and protein synthesis. The meiotic checkpoint and DNA damage terms appear less central, possibly reflecting secondary roles or co-regulation under stress.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006413","count":1},{"id":"GO:0042273","count":1},{"id":"GO:0000028","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0006412","count":1}]},{"hash":"1882190276475237602","title":"Endocytosis and endosomal sorting","description":"This cluster is dominated by terms describing membrane trafficking, especially endocytosis and multivesicular body (MVB) sorting, plus related endosomal transport and clathrin-dependent processes. The presence of GO terms for EGFR/PDGFR signaling regulation also fits with receptor internalization mechanisms. While a few terms are less connected (e.g., iron transport, pregnancy), the core theme clearly centers on endocytic trafficking and vesicle sorting.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098711","count":1},{"id":"GO:2000588","count":1},{"id":"GO:0071985","count":1},{"id":"GO:0007565","count":1},{"id":"GO:0045742","count":1}]},{"hash":"1279059642382356688","title":"Broad Signaling and Stress Response","description":"This cluster shows enrichment for multiple signaling-related GO terms (ABA signaling, cAMP response, calcium signaling, opsin signaling regulation) and stress-related processes (multicellular stress response, hydrogen peroxide biosynthesis), plus related transport and phosphorylation regulation. The terms point to a general theme of signaling and stress response rather than a single precise pathway, so a broad label fits best.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009738","count":2},{"id":"GO:0033555","count":1},{"id":"GO:0051591","count":1},{"id":"GO:0050665","count":1},{"id":"GO:0019749","count":1}]},{"hash":"1212281177209433848","title":"Unknown","description":"The terms cover signaling, RNA processing, immune response, metabolism, cell cycle, and plant-specific processes with no clear shared function, so a single label cannot represent the cluster.","confidence":"","size":16,"edges":5,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008277","count":7},{"id":"GO:0000492","count":6},{"id":"GO:0071357","count":5},{"id":"GO:0090526","count":5},{"id":"GO:0031145","count":5}]},{"hash":"712472066152327156","title":"ERAD and Autophagy Regulators","description":"The cluster is enriched for terms tied to endoplasmic reticulum\u2013associated degradation (ERAD) and autophagic processes (aggrephagy, autophagosome maturation), as well as regulators of membrane trafficking (endocytosis, GPCR internalization) and related signaling/gating (store-operated calcium channels, TLR3 signaling). This points to a functional module coordinating protein quality control in the ER with trafficking and turnover at the plasma membrane, rather than a single canonical pathway.","confidence":"Medium","size":16,"edges":81,"triangles":215,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":5},{"id":"GO:1904378","count":5},{"id":"GO:1901097","count":4},{"id":"GO:0035973","count":4},{"id":"GO:1903071","count":4}]},{"hash":"2174642038580335615","title":"Endomembrane trafficking and cytoskeleton","description":"The cluster is dominated by GO terms for vesicle transport within the secretory pathway (ER-Golgi, endosome-to-Golgi, endosome-to-late endosome, plasma membrane localization) and exocytosis, paired with tubulin/cytoskeletal assembly terms (tubulin complex, mitotic spindle). This points to a cohesive function in cytoskeleton-guided intracellular transport and membrane trafficking. Unknown terms like the Cvt pathway and sporulation assembly appear as peripheral context but do not override the trafficking theme.","confidence":"High","size":16,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007021","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0045022","count":2},{"id":"GO:0045956","count":2},{"id":"GO:1903078","count":2}]},{"hash":"1454031075101426782","title":"Cross-Tissue Development and Differentiation","description":"The top GO terms span transcription by RNA polymerase II and a broad array of tissue-specific differentiation processes (muscle, neural, pancreas, astrocyte, plant reproductive tissue, circadian entrainment). This suggests the cluster reflects general developmental and differentiation programs across multiple tissues rather than a single pathway, justifying a high-level umbrella label.","confidence":"Medium","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":16},{"id":"GO:2000323","count":14},{"id":"GO:0007518","count":14},{"id":"GO:0048658","count":14},{"id":"GO:0009649","count":14}]},{"hash":"2225537928983297837","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010019","count":4},{"id":"GO:0031426","count":4},{"id":"GO:0016554","count":4},{"id":"GO:0090615","count":4},{"id":"GO:0070129","count":4}]},{"hash":"2092175584554521071","title":"RNA splicing and mRNA processing regulation","description":"This cluster is dominated by GO terms tied to post-transcriptional RNA processing: splicing (cis and alternative) via the spliceosome, mRNA export, modification, and regulation of mRNA stability, including stress responses and ncRNA-mediated gene silencing. The strong emphasis on spliceosome-driven regulation and various aspects of mRNA maturation points to a cohesive function in RNA processing and splicing control, with a possible link to development (blastocyst formation). Overall, the terms cohere around RNA splicing and mRNA metabolism regulation.","confidence":"High","size":16,"edges":100,"triangles":387,"max_degree":15,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":10},{"id":"GO:1901407","count":10},{"id":"GO:0006378","count":10},{"id":"GO:0031047","count":9},{"id":"GO:0048026","count":9}]},{"hash":"1022934179098642766","title":"Craniofacial development and cell cycle regulation","description":"This cluster centers on embryonic cranial skeleton morphogenesis, cell migration, and regulation of signaling and proliferation. The presence of negative regulation of Wnt signaling, positive regulation of GTPase activity, apoptosis, and DNA replication/mitotic cycle terms suggests coordinated tissue remodeling and proliferative growth during craniofacial development, with migration and signaling control guiding morphogenesis. Visual perception terms appear incidental to the main developmental pattern. ","confidence":"High","size":16,"edges":30,"triangles":22,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0016477","count":7},{"id":"GO:0043547","count":6},{"id":"GO:0008285","count":6},{"id":"GO:0090090","count":6},{"id":"GO:0043065","count":6}]},{"hash":"189712972382069104","title":"Spliceosome-mediated mRNA processing and export","description":"The cluster is dominated by GO terms tied to mRNA splicing via the spliceosome, mRNA modification, and mRNA export, plus regulatory splicing control and ncRNA-mediated gene silencing, indicating a cohesive set of proteins focused on RNA maturation and transport. While a couple terms (blastocyst formation, viral translation termination-reinitiation) are less related, they do not override the main mRNA-processing theme.","confidence":"High","size":16,"edges":14,"triangles":10,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":6},{"id":"GO:0045292","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0016556","count":3},{"id":"GO:0006406","count":3}]},{"hash":"1391703921251111280","title":"DNA damage and oxidative stress response","description":"The top GO terms center on DNA metabolism (DNA catabolic process, DNA recombination) and oxidative/stress responses (cell redox homeostasis, cellular response to hydrogen peroxide), suggesting a core function in DNA processing linked to redox/oxidative stress signaling; other terms are more general or obsolete, but the DNA/oxidative stress theme remains dominant.","confidence":"Medium","size":16,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006308","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0071320","count":2},{"id":"GO:0045454","count":2},{"id":"GO:1903507","count":2}]},{"hash":"1162382224432785553","title":"ABA-regulated plant development and cuticle biosynthesis","description":"Based on the GO terms, the cluster centers on plant developmental processes (floral meristem growth, bract and seed development, multicellular development) and cuticle formation (wax and cutin biosynthesis), with an ABA-activated signaling pathway indicating hormonal regulation of these programs. A defense-related term (response to chitin) is present but peripheral to the main theme. ","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":5},{"id":"GO:0009738","count":4},{"id":"GO:0007275","count":3},{"id":"GO:1904276","count":3},{"id":"GO:0006351","count":3}]},{"hash":"363849627222673687","title":"Plant Hormone Signaling and Flavonoid Biosynthesis","description":"The top GO terms point to cytokinin-activated signaling and jasmonic acid response, alongside leaf formation, vegetative growth, and flavonol biosynthesis, indicating a cohesive theme of hormone-regulated plant development and secondary metabolism. Some chromatin-related and viral-process terms may be noise, but the dominant signal ties growth regulation to hormone signaling and flavonoid production.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":8},{"id":"GO:0000183","count":7},{"id":"GO:1903770","count":6},{"id":"GO:1900386","count":6},{"id":"GO:0010338","count":6}]},{"hash":"121748318045581216","title":"Plant Development and Cuticle Biosynthesis Regulation","description":"Top GO terms point to plant developmental processes (multicellular development, floral meristem growth, bract and seed development) alongside cuticle biosynthesis regulation (wax/cutin) and signaling (ABA) with defense (response to chitin) and transcriptional regulation. This suggests a regulatory module coordinating development with cuticle formation and hormone signaling, rather than a single cohesive pathway. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:1904276","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:1901959","count":2}]},{"hash":"1897942544292138593","title":"Osmotic stress response and lipid and carbohydrate biosynthesis","description":"Top terms indicate osmotic stress responses (water deprivation, flooding, mannitol, sucrose) alongside lipid and carbohydrate biosynthesis (phospholipids, glycolipids, starch, glucose), with bacillithiol biosynthesis hinting at a Bacillus-type defense. This suggests a cohesive theme of osmotic adaptation linked to membrane and sugar metabolism.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009414","count":2},{"id":"GO:0008654","count":2},{"id":"GO:0009413","count":2},{"id":"GO:0009744","count":2},{"id":"GO:0097502","count":2}]},{"hash":"1205810794723401288","title":"Unknown","description":"The GO terms span very different processes (nucleotide metabolism, fatty acid and lipid biosynthesis, cell wall processes in bacteria, translation and RNA turnover, plus chloroplast-related nonphotochemical quenching and thylakoid organization), with no clear, single functional theme tying the proteins together. Edges are zero, suggesting lack of interactions to define a cohesive pathway. Therefore no unambiguous label; Unknown with None.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090305","count":1},{"id":"GO:0046079","count":1},{"id":"GO:0006633","count":1},{"id":"GO:0009245","count":1},{"id":"GO:0009254","count":1}]},{"hash":"1993234230408385891","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0045214","count":3},{"id":"GO:0090617","count":2},{"id":"GO:0042793","count":2},{"id":"GO:1905639","count":2}]},{"hash":"221062369659009925","title":"Chloroplast and mitochondrial RNA editing","description":"The top GO terms cluster around chloroplast/plastid RNA processing, plastid transcription, chloroplast RNA modification, and mitochondrial mRNA modification, including cytidine to uridine editing. This points to RNA editing and post-transcriptional processing in plant organelles as the core function of the cluster, with related plant developmental and stress-related terms as secondary signals. ","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901001","count":2},{"id":"GO:0051245","count":2},{"id":"GO:0016554","count":2},{"id":"GO:0031425","count":2},{"id":"GO:0042793","count":2}]},{"hash":"400312020060458665","title":"Ubiquitin-Proteasome Degradation","description":"This cluster is defined by GO terms related to ubiquitin-dependent protein catabolic processes and proteasomal degradation (K48-linked, SCF-dependent, autoubiquitination, ERAD). The peroxisomal import term is present but less central; overall, the proteins appear to be components of the ubiquitin-proteasome system and protein quality control.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":9},{"id":"GO:0031146","count":6},{"id":"GO:0070936","count":6},{"id":"GO:0051865","count":6},{"id":"GO:0016558","count":6}]},{"hash":"755340710269943698","title":"Unknown","description":"These proteins are annotated with a highly diverse set of GO terms spanning immune regulation (apoptotic cell clearance, T cell proliferation, tolerance to self antigen), viral response, and placental/developmental processes, along with intracellular trafficking (protein export from nucleus, ER polarization) and even endocrine signaling (parathyroid hormone secretion). There is no clear, cohesive biological function or pathway dominating the cluster, making a single interpretable label inappropriate. Therefore, Unknown with no confident representative function.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043277","count":16},{"id":"GO:0046641","count":16},{"id":"GO:0060709","count":16},{"id":"GO:0006611","count":16},{"id":"GO:0061167","count":16}]},{"hash":"1364494693257961639","title":"Unknown","description":"This cluster shows three disparate GO terms: DNA methylation-dependent heterochromatin formation, regulation of translational fidelity, and mitochondrial alanyl-tRNA aminoacylation. With no edges connecting the proteins and these terms representing distinct cellular processes, there isn\u2019t a cohesive theme to label the cluster beyond Unknown.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006346","count":1},{"id":"GO:0006450","count":1},{"id":"GO:0070143","count":1}]},{"hash":"1321597093013239076","title":"Spliceosome-driven mRNA processing","description":"The proteins are enriched in spliceosome-mediated mRNA splicing and related processing steps, including splicing regulation, mRNA export, modification, and stabilization, as well as ncRNA-mediated silencing. This indicates a cohesive theme around mRNA maturation and regulation via the spliceosome.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":4},{"id":"GO:0031047","count":3},{"id":"GO:0045292","count":3},{"id":"GO:0016556","count":2},{"id":"GO:0006406","count":2}]},{"hash":"388660215435205636","title":"Meiosis and Chromosome Condensation","description":"The top terms are dominated by meiotic processes (meiotic cell cycle, meiotic DSB formation, meiotic chromosome condensation) and chromosome condensation/cohesion, suggesting a cluster of proteins involved in meiotic chromosome dynamics and DNA replication/maintenance during division. Some outliers (SOS response, tRNA gene clustering) exist but do not override the overall theme.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051321","count":1},{"id":"GO:0060821","count":1},{"id":"GO:0009432","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0032876","count":1}]},{"hash":"1020527286611770882","title":"Unknown","description":"The proteins show a highly diverse set of GO terms (lipid transport, gluconeogenesis, defense against fungus, stress response, growth regulation, etc.) with no clear shared pathway or function, and there are no interactions among them. This lack of a cohesive theme makes a precise, representative label unreliable.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":2},{"id":"GO:0010951","count":1},{"id":"GO:0006869","count":1},{"id":"GO:0050832","count":1},{"id":"GO:0006094","count":1}]},{"hash":"1356342777240081887","title":"Unknown","description":"The GO terms span diverse processes (immune clearance, T cell regulation, viral response, placental development, hormone secretion, organ regeneration, meiosis, and intracellular transport) with no single cohesive function linking them. The lack of a common theme and zero interactions suggests no clear, representative label other than Unknown.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043277","count":16},{"id":"GO:0046641","count":16},{"id":"GO:0060709","count":16},{"id":"GO:0006611","count":16},{"id":"GO:0061167","count":16}]},{"hash":"1573800348753492133","title":"Unknown","description":"The top GO terms span diverse processes (vesicular transport, apoptosis regulation, Rho signaling, pinocytosis, neuronal differentiation, autophagy, spindle assembly, pain sensing, multicellular processes, and NOD2 signaling) with no clear shared function and no network connectivity (Edges 0, Triangles 0, Max Degree 0), so there isn't a coherent theme to name besides Unknown.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":1},{"id":"GO:2000269","count":1},{"id":"GO:0035023","count":1},{"id":"GO:0048549","count":1},{"id":"GO:0021707","count":1}]},{"hash":"1909159042840206195","title":"Plant Development and Cell Wall Biogenesis","description":"GO terms cluster around plant growth and development, including root meristem growth, flower development, somatic embryogenesis, and fruit dehiscence, with strong emphasis on plant-type secondary cell wall biogenesis; additional terms reflect transcriptional regulation and proteolysis that support these processes.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":2},{"id":"GO:1901348","count":2},{"id":"GO:0010082","count":2},{"id":"GO:0009908","count":2},{"id":"GO:0010262","count":2}]},{"hash":"76342623444072069","title":"Meiosis and Germline Development","description":"Although the cluster shows a mix of terms, the strongest signal centers on germline and meiotic biology, with GO terms for G2/MI transition of the meiotic cell cycle, spermatocyte division, and male germ-line cyst formation. The other terms (spliceosomal assembly, translation initiation factor complex assembly, hair follicle maturation, energy homeostasis) appear more peripheral, suggesting the core theme is meiotic/germline processes with broader regulatory context.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008315","count":1},{"id":"GO:0000387","count":1},{"id":"GO:2000507","count":1},{"id":"GO:0010801","count":1},{"id":"GO:0048136","count":1}]},{"hash":"1331024177127363666","title":"ER Stress Proteostasis and Membrane Targeting","description":"The cluster is enriched for unfolded protein response, ER stress regulation, and SRP- and post-translational membrane targeting, pointing to a shared role in proteostasis and membrane protein biogenesis under stress. While DNA replication appears, the strongest signals are in ER stress response and membrane targeting, including regulatory aspects of stress-induced apoptosis, supporting a proteostasis/membrane-targeting theme.","confidence":"High","size":15,"edges":38,"triangles":62,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0016226","count":7},{"id":"GO:0006616","count":7},{"id":"GO:0034620","count":7},{"id":"GO:1903382","count":7}]},{"hash":"53495573037143753","title":"Bacterial Metabolism and DNA Processing","description":"This cluster features GO terms tied to core cellular metabolism (ATP metabolism, lipid A biosynthesis, molybdopterin cofactor biosynthesis) and genetic information processing (DNA-templated transcription, DNA replication, mRNA export). The few other terms (viral genome replication, N-linked glycosylation) appear as outliers, suggesting a mixed set rather than a single pathway. Nevertheless, the dominant themes point to basic bacterial biosynthesis and DNA-related activities, supporting a label centered on metabolism and DNA processing.","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0009245","count":2},{"id":"GO:0006777","count":2},{"id":"GO:0046034","count":1},{"id":"GO:0006351","count":1}]},{"hash":"1227950887497591410","title":"Unknown","description":"The Top Terms are highly heterogeneous, spanning translation, unfolded protein response, several insect developmental processes (spermatid differentiation, wing cell fate, cone cell fate), EGFR ligand maturation, ER-to-cytosol proteolysis, NK cell regulation, and mitochondrial electron transport. There is no dominant shared function or clear connectivity across the cluster, so a cohesive functional label cannot be assigned.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0034620","count":1},{"id":"GO:0048515","count":1},{"id":"GO:0035311","count":1},{"id":"GO:0038005","count":1}]},{"hash":"1198979170321494847","title":"Plant Hormone Biosynthesis and Fruit Ripening","description":"The cluster centers on multiple plant hormone pathways (auxin, ethylene, gibberellin, salicylic acid), including their biosynthesis and catabolic processes, and connects to fruit ripening and related secondary metabolism, suggesting a module of hormone-driven development and maturation in plants.","confidence":"Medium","size":15,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":9},{"id":"GO:0009852","count":5},{"id":"GO:0009835","count":5},{"id":"GO:0009693","count":5},{"id":"GO:0045487","count":5}]},{"hash":"1178815996192447751","title":"Neuronal vesicle trafficking and endosome-lysosome transport","description":"The cluster centers on Rab signaling and vesicle trafficking, including protein transport, synaptic vesicle budding, calcium-regulated exocytosis, and endosome-to-lysosome transport, plus lysosomal membrane organization and related localization processes. This points to a cohesive function in neuronal vesicle trafficking and membrane dynamics, with some neuronal development context reflected by axonogenesis terms.","confidence":"High","size":15,"edges":22,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0050771","count":3},{"id":"GO:0032482","count":3},{"id":"GO:0015031","count":3},{"id":"GO:1902824","count":3},{"id":"GO:0045176","count":3}]},{"hash":"2297479049944220340","title":"Plant Metabolic Diversity and Plasmodesmata Transport","description":"The cluster lists multiple metabolic processes (fructose biosynthesis, fatty acid biosynthesis, retinol metabolism, oxalate metabolism, estrogen catabolic and biphenyl catabolic processes) and includes a GO term for plasmodesmata-mediated intercellular transport, suggesting proteins involved in diverse plant metabolism with intercellular transport functions.","confidence":"Medium","size":15,"edges":40,"triangles":32,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0046370","count":3},{"id":"GO:0042572","count":3},{"id":"GO:0006633","count":3},{"id":"GO:0033609","count":3}]},{"hash":"193656158656045642","title":"Nuclear RNA Processing and SnoRNA Maturation","description":"The top GO terms cluster around nuclear RNA processing activities (mRNA decay via RNase MRP, tRNA processing, snoRNA processing, and general RNA phosphodiester bond hydrolysis), indicating a focus on RNA maturation and turnover in the nucleus. Some plant developmental terms are present but appear incidental; the dominant theme is RNA processing and maturation.","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000294","count":3},{"id":"GO:0030261","count":3},{"id":"GO:0008033","count":3},{"id":"GO:0090502","count":3},{"id":"GO:0034965","count":3}]},{"hash":"685702076593055727","title":"Plant stress response and autophagy","description":"This cluster is enriched for plant defense/stress terms (salicylic acid signaling, camalexin biosynthesis, aerenchyma formation, trehalose response) and intracellular turnover (piecemeal microautophagy of the nucleus, vacuolar protein processing, pectin and lipid catabolism). The combination points to stress-response remodeling with autophagy/vacuolar degradation as a unifying theme; a couple of terms (endocannabinoid signaling, neuroblast proliferation) are less directly aligned and may reflect annotation noise.","confidence":"Medium","size":15,"edges":12,"triangles":0,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0034727","count":3},{"id":"GO:0010618","count":3},{"id":"GO:0006624","count":3},{"id":"GO:0080151","count":3},{"id":"GO:2000124","count":3}]},{"hash":"771570690339725766","title":"Lipopolysaccharide Core and Heptose Biosynthesis","description":"The top GO terms are dominated by lipopolysaccharide biosynthetic processes, especially core-region biosynthesis and ADP-L-glycero-beta-D-manno-heptose biosynthesis, indicating proteins involved in LPS assembly; other terms appear incidental.","confidence":"High","size":15,"edges":34,"triangles":29,"max_degree":11,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0009103","count":7},{"id":"GO:1902987","count":6},{"id":"GO:0006825","count":5},{"id":"GO:0097171","count":5},{"id":"GO:0009244","count":5}]},{"hash":"1691284824502863791","title":"Developmental signaling and fate regulation","description":"This cluster centers on regulators of development and cell fate, including modulation of signaling pathways (notably Wnt), apoptosis, and cell migration, along with differentiation cues (lung induction, midbrain dopaminergic neuron differentiation). It also includes layers of gene regulation (ncRNA-mediated silencing, splicing) and extracellular matrix-related processes (heparan sulfate biosynthesis), suggesting a cohesive theme of coordinating development through signaling and gene regulation. Proton transport is a more general cellular function that may tag along but is not the core driver of this cluster\u2019s theme. ","confidence":"Medium","size":15,"edges":8,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0015991","count":5},{"id":"GO:0008285","count":3},{"id":"GO:0090090","count":3},{"id":"GO:0043065","count":3},{"id":"GO:0016477","count":3}]},{"hash":"1444998616037792791","title":"ERAD-linked protein degradation and membrane proteolysis","description":"The top GO terms point to intracellular protein quality control and turnover, including ER-associated degradation (glycoprotein trimming in ERAD), vacuolar protein catabolism, and proteolysis of membrane proteins. This suggests a cohesive theme of protein processing and degradation within secretory/endomembrane pathways, hence the chosen label. Some outlier terms (metal ion transport and LDL receptor regulation) appear, but the proteolysis-focused terms dominate the cluster\u2019s signal.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070574","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0007039","count":2},{"id":"GO:0010989","count":2},{"id":"GO:0006879","count":2}]},{"hash":"264740370418989394","title":"Plant cell wall polysaccharide biosynthesis","description":"The top GO terms cluster around plant cell wall components and biogenesis (homogalacturonan, glucuronoxylan, mucilage, plant-type secondary cell wall biogenesis) and related glycosylation processes, indicating proteins involved in synthesizing and organizing cell wall glycans. Some general sugar metabolism terms appear but the dominant signal is plant cell wall biosynthesis.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0005978","count":3},{"id":"GO:0016266","count":2},{"id":"GO:0010289","count":2},{"id":"GO:0006012","count":2},{"id":"GO:0010192","count":2}]},{"hash":"1828025768454887631","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0090615","count":4},{"id":"GO:0090617","count":4},{"id":"GO:0042793","count":4},{"id":"GO:1905639","count":4},{"id":"GO:1900865","count":4}]},{"hash":"1118620434146847733","title":"Organelle inheritance and cytoskeletal organization","description":"Most terms point to inheritance of cellular compartments (mitochondria, peroxisomes, Golgi) and cytoskeletal/trafficking processes (spindle organization, actin-based vesicle transport, filopodium assembly). A unifying theme is intracellular organization and propagation of cellular components, with a secondary emphasis on developmental processes. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000001","count":1},{"id":"GO:1904970","count":1},{"id":"GO:0007051","count":1},{"id":"GO:0021592","count":1},{"id":"GO:0030050","count":1}]},{"hash":"2080045022960555239","title":"Developmental Gene Regulation and Neural Development","description":"This cluster is dominated by GO terms for DNA-templated transcription and mRNA processing, combined with multiple developmental processes such as forebrain development, neural tube closure, skeletal system development, and multicellular organism development, indicating a coherent theme of developmental gene expression and neural development. Some stress- and defense-related terms appear but do not outweigh the primary developmental signature.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":11},{"id":"GO:0006397","count":10},{"id":"GO:0070059","count":10},{"id":"GO:0030900","count":10},{"id":"GO:0050830","count":10}]},{"hash":"739010409508507762","title":"Plant photosynthesis and ER protein processing","description":"The top terms cluster around photosynthesis and chloroplast-associated assembly (photosystem II, photosynthesis) and ER protein handling (unfolded protein response, N-linked glycosylation), with cytokinin response reinforcing a plant-specific context; the other terms seem more divergent annotations, but the core theme is plant chloroplast and ER-related functions.","confidence":"Medium","size":15,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030968","count":1},{"id":"GO:0006487","count":1},{"id":"GO:0010270","count":1},{"id":"GO:0015979","count":1},{"id":"GO:0009735","count":1}]},{"hash":"1716880704482817822","title":"Microtubule dynamics in mitosis and vesicle transport","description":"The top GO terms cluster around microtubule-associated processes: spindle/microtubule attachments to kinetochores, centrosome separation, and metaphase chromosome recapture all point to mitotic microtubule dynamics, while plus-end-directed vesicle transport along microtubules and regulation of microtubule-based processes highlight transport along the cytoskeleton. Stress granule disassembly and signals related to cell growth and stem cell homeostasis are also connected to cytoskeletal organization and cellular architecture, supporting a cohesive theme centered on microtubule-guided mitosis and intracellular transport.","confidence":"High","size":15,"edges":66,"triangles":142,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000742","count":6},{"id":"GO:0035617","count":6},{"id":"GO:1990535","count":5},{"id":"GO:0099607","count":5},{"id":"GO:0007100","count":5}]},{"hash":"1047456773469095798","title":"Unknown","description":"The top GO terms are scattered across RNA processing, lipopolysaccharide biosynthesis, various obsolete methylation/chromatin terms, and plant development processes, with no single cohesive function tying the proteins together. The absence of edges and the presence of many obsolete terms suggest no clear cluster theme to name confidently.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0090309","count":1},{"id":"GO:0090116","count":1},{"id":"GO:0010069","count":1}]},{"hash":"1464022178464627904","title":"Genome maintenance and organelle trafficking","description":"The cluster features nuclear processes (DNA replication, base-excision repair, mRNA export) alongside organelle-related protein handling (ER-to-Golgi transport, mitochondrial inner membrane insertion, and chaperone-mediated assembly), suggesting a cohesive theme of cellular maintenance spanning nucleus and organelles.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0006888","count":3},{"id":"GO:0006284","count":3},{"id":"GO:0006406","count":2},{"id":"GO:2001171","count":2}]},{"hash":"2144560237615337744","title":"Plant jasmonate/oxylipin signaling and lipid metabolism","description":"Top GO terms cluster around jasmonate/oxylipin biosynthesis, sterol and fatty acid metabolism, and stress responses (ozone, toxic substances), with a note of development (stamen). This combination strongly suggests a plant lipid-derived signaling module centered on the jasmonate/oxylipin pathway.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0009695","count":1},{"id":"GO:0031408","count":1},{"id":"GO:0009636","count":1},{"id":"GO:0033543","count":1}]},{"hash":"818899216152861360","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0090617","count":10},{"id":"GO:1905639","count":10},{"id":"GO:1900865","count":10},{"id":"GO:0042793","count":10},{"id":"GO:0010019","count":10}]},{"hash":"2020580082570965840","title":"Cell cycle regulation and mitosis","description":"This cluster centers on mitotic processes and DNA replication, with strong hits for mitotic cell cycle, G2/M transition, DNA replication, kinetochore localization, and regulation of CDK activity, pointing to cell cycle control as the core theme. Some terms (ABA signaling, visual perception, Schwann cell development, muscle response) appear less directly connected and may reflect broad annotations or incidental associations.","confidence":"High","size":15,"edges":49,"triangles":67,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045736","count":12},{"id":"GO:0034501","count":12},{"id":"GO:0000278","count":10},{"id":"GO:0006260","count":10},{"id":"GO:0009738","count":9}]},{"hash":"1464121334950760673","title":"Cerebellar development and neuronal signaling","description":"The cluster is strongly enriched for terms related to cerebellar development and neuronal connectivity, including cerebellar cortex formation, Bergmann glial differentiation, dendritic spine morphogenesis, and regulation of axon regeneration, suggesting a focus on cerebellar neural development and synaptic remodeling. Additional terms like insulin receptor signaling and T cell receptor signaling appear but seem less central to the core cerebellar theme; some cell-cycle related terms may reflect broader regulatory context rather than a single pathway. Overall, the dominant theme is cerebellar neural development and signaling.","confidence":"Medium","size":15,"edges":62,"triangles":161,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045736","count":12},{"id":"GO:0034501","count":12},{"id":"GO:0050852","count":12},{"id":"GO:0008285","count":12},{"id":"GO:0060997","count":12}]},{"hash":"1993285783747781125","title":"Ubiquitin-Dependent Proteolysis in Oocyte Maturation","description":"The cluster is dominated by GO terms for ubiquitin-dependent protein catabolic processes and SCF-dependent proteasomal degradation, together with oocyte maturation and spindle assembly in female meiosis I, indicating a focus on ubiquitin-proteasome\u2013mediated proteolysis during oocyte meiosis. Some neural development terms appear less related, but the strongest theme is proteolysis in meiosis/oocyte maturation. ","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:0031146","count":7},{"id":"GO:0051436","count":5},{"id":"GO:0001556","count":5},{"id":"GO:0070544","count":5}]},{"hash":"24888739335982708","title":"Broad Developmental Morphogenesis","description":"The top GO terms point to development and morphogenesis across multiple tissues and organ systems (neural, renal, hepatic, craniofacial, roots, etc.), with additional general transcription activity supporting developmental programs. This suggests the cluster represents broad developmental processes rather than a single pathway, so a label reflecting cross-tissue development and morphogenesis is appropriate.","confidence":"High","size":15,"edges":96,"triangles":347,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0031290","count":4},{"id":"GO:0045617","count":4},{"id":"GO:0006366","count":4},{"id":"GO:0009737","count":3},{"id":"GO:0080022","count":3}]},{"hash":"2146303829370679170","title":"Stress Response and Transcription Regulation","description":"This cluster centers on transcription-related processes (DNA-templated transcription) and multiple stress-response signals (response to toxic substances, ER-stress\u2013induced apoptotic signaling, cellular response to cadmium), suggesting a theme of stress sensing coupled with transcriptional control. Some development and immune-defense terms appear, indicating multifunctional roles or broad gene membership, but the dominant signal ties stress response to transcriptional regulation. The lack of network edges within the cluster points to dispersed, context-dependent functions rather than a single cohesive pathway.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0009636","count":3},{"id":"GO:0043547","count":2},{"id":"GO:0070059","count":2},{"id":"GO:0007568","count":2}]},{"hash":"358477805287889804","title":"Brain development and synaptic vesicle exocytosis regulation","description":"The top GO terms center on regulation of synaptic vesicle exocytosis and brain development, with related hints of intracellular trafficking (endosome to lysosome transport, apical protein localization) and gene expression control, suggesting a neuronally focused cluster tied to synaptic function and development. Some terms (e.g., androgen receptor signaling) are peripheral, but the main theme fits neuronal development and vesicle regulation.","confidence":"Medium","size":15,"edges":47,"triangles":35,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000300","count":5},{"id":"GO:0010796","count":5},{"id":"GO:0007420","count":5},{"id":"GO:0031384","count":5},{"id":"GO:0008333","count":4}]},{"hash":"111256610686848742","title":"Biosynthesis and RNA Methylation","description":"Top terms point to diverse biosynthetic processes (biotin, antibiotic, sterol, ubiquinone, polyamine) together with RNA modification activities (guanine-N7 methylation, 7-methylguanosine mRNA capping). This pattern suggests the cluster reflects general biosynthetic/metabolic functions intertwined with RNA modification processes, rather than a single specific pathway; the absence of edges supports a broad, diffuse functional grouping rather than a tight complex. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0030961","count":3},{"id":"GO:0016126","count":3},{"id":"GO:0043985","count":3}]},{"hash":"2225337583726633928","title":"Organelle Inheritance and Cytoskeletal Transport","description":"The set of top GO terms is dominated by organelle inheritance (mitochondrion, peroxisome, Golgi) and spindle organization, along with vesicle transport along actin filaments. This suggests a common theme of coordinating organelle segregation with cytoskeletal dynamics and intracellular trafficking during cell division and transport, with some additional development-related terms present but not defining the cluster\u2019s core function.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0000001","count":2},{"id":"GO:1904970","count":2},{"id":"GO:0007051","count":2},{"id":"GO:0021592","count":2}]},{"hash":"1930448906502141393","title":"Gene Expression Regulation and Chromatin Dynamics","description":"The cluster\u2019s top GO terms span RNA modification (RNA guanine-N7 methylation), translation initiation and reinitiation, transcription, chromatin organization, and protein ubiquitination, with links to nutrient signaling and development. This pattern suggests a broad regulatory program controlling gene expression at multiple levels (RNA processing, transcription, translation) and chromatin state, rather than a single metabolic pathway. The absence of tight interconnected edges does not negate this regulatory theme.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0036265","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0007584","count":3},{"id":"GO:0007275","count":3}]},{"hash":"152307420966894684","title":"Unknown","description":"This cluster has no GO terms or interactions (Edges: 0, Triangles: 0, Max Degree: 0) and no top terms to guide a label, so there is no clear shared function to define a thematic name for these proteins.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"543431359904758171","title":"Plant cell wall biosynthesis and pollen exine formation","description":"This cluster is characterized by GO terms tied to plant cell wall components and biosynthesis (glucuronoxylan, chondroitin/heparan sulfate proteoglycan biosynthesis), and processes like cell wall organization and plant-type secondary cell wall biogenesis, plus pollen exine formation. The common theme is synthesis and organization of plant cell walls and pollen wall structures.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010584","count":1},{"id":"GO:0050651","count":1},{"id":"GO:0030204","count":1},{"id":"GO:0050650","count":1},{"id":"GO:0010417","count":1}]},{"hash":"1290709876772048503","title":"Plant cell wall biosynthesis and plasmodesmata organization","description":"The terms cluster around plant cell wall biology: cell wall organization, plant-type secondary cell wall biogenesis, and regulation of cellulose biosynthesis, plus plasmodesma organization, suggesting proteins involved in cell wall construction and intercellular transport in plants. A few other terms (e.g., meiotic cohesion, P granule assembly) appear incidental and do not drive the main theme.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":2},{"id":"GO:0009834","count":2},{"id":"GO:0016266","count":2},{"id":"GO:0009831","count":1},{"id":"GO:0009663","count":1}]},{"hash":"1308428822773056866","title":"Lipid signaling and stress response","description":"The top terms cluster around lipid-derived signaling and stress responses: oxylipin and jasmonic acid biosynthesis, fatty acid beta-oxidation, and responses to ozone/toxic substances. Immune signaling terms (NF-kappaB regulation, T cell cytokine production) may reflect shared stress-response pathways, while some terms like stamen development appear as plant-specific noise. Overall, the cluster most coherently ties to lipid metabolism and stress signaling.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002724","count":3},{"id":"GO:0006486","count":2},{"id":"GO:0043123","count":2},{"id":"GO:0009695","count":2},{"id":"GO:0031408","count":2}]},{"hash":"927699517343655208","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000132","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0090114","count":3},{"id":"GO:0090615","count":2},{"id":"GO:0090617","count":2}]},{"hash":"1543183833821102791","title":"Unknown","description":"The protein set includes neural-related terms (neuron apoptosis, astrocyte differentiation, glial growth) but also DNA integration, dormancy, vitamin transport, and smooth muscle development, with no single unifying function.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":2},{"id":"GO:0085014","count":1},{"id":"GO:0006950","count":1},{"id":"GO:0035023","count":1},{"id":"GO:0042066","count":1}]},{"hash":"709677742031011922","title":"Aromatic amino acid metabolism and alkaloid biosynthesis","description":"This cluster shows several GO terms tied to catabolism of L-phenylalanine and L-tyrosine, plus biosynthetic processes for cinnamic acid, alkaloids, antibiotics, and other secondary metabolites, suggesting a shared theme of aromatic compound metabolism and secondary metabolite production. Some terms (like zinc stress and tetramerization) are peripheral, and there are no interactions, so the support is moderate.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006559","count":2},{"id":"GO:0009403","count":2},{"id":"GO:0006572","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0009821","count":2}]},{"hash":"105275071568190475","title":"Drosophila oogenesis RNA processing and ribosome maturation","description":"These proteins appear linked to ovarian germline development (fusome organization, germ-line cyst formation, oocyte maturation) and to RNA metabolism and ribosome biogenesis (mRNA processing, rRNA maturation, decapping/deadenylation, exoribonuclease activity), suggesting a coordinated role in RNA processing and ribosome assembly during oogenesis.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030723","count":1},{"id":"GO:0050779","count":1},{"id":"GO:0071035","count":1},{"id":"GO:0006397","count":1},{"id":"GO:0031087","count":1}]},{"hash":"1489200327674260292","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0090615","count":15},{"id":"GO:0090617","count":15},{"id":"GO:1905639","count":15},{"id":"GO:1900865","count":15},{"id":"GO:0042793","count":15}]},{"hash":"991066182347244726","title":"Metabolic Growth and Redox Regulation","description":"The terms cluster around glucose metabolism, pentose phosphate pathway, and ROS regulation, with adipose tissue development and multicellular growth; corticosterone response and metal ion responses suggest hormonal and redox-linked metabolic activity, supporting a label focused on metabolic growth and redox control.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":1},{"id":"GO:0035264","count":1},{"id":"GO:0035934","count":1},{"id":"GO:0060612","count":1},{"id":"GO:0010269","count":1}]},{"hash":"1275980212909894998","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071050","count":1},{"id":"GO:0033621","count":1},{"id":"GO:0048451","count":1},{"id":"GO:0006378","count":1},{"id":"GO:0031440","count":1}]},{"hash":"2006402262249021326","title":"Plant secondary cell wall biogenesis","description":"The cluster\u2019s top GO terms are dominated by plant-type secondary cell wall biogenesis and its positive regulation, pointing to a core function in plant cell wall formation. Chromatin remodeling could relate to regulation of this process, but other terms (neuronal, metabolic) suggest annotation noise or multi-function proteins. Overall, the strongest shared theme is plant secondary cell wall biosynthesis.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901348","count":3},{"id":"GO:0009834","count":3},{"id":"GO:0043044","count":3},{"id":"GO:0035249","count":2},{"id":"GO:0065009","count":2}]},{"hash":"1098532434417358855","title":"Synaptic translation and AMPA receptor clustering","description":"The top GO terms point to translation (including positive regulation), neurotransmitter secretion, and AMPA receptor clustering, suggesting proteins involved in local protein synthesis and organization of postsynaptic receptors at synapses. While a few terms reference polarized epithelia and microvilli, the strongest signal is synaptic protein synthesis and receptor organization, supporting this label.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0007269","count":2},{"id":"GO:0045727","count":1},{"id":"GO:1905373","count":1},{"id":"GO:0097113","count":1}]},{"hash":"574938547548311630","title":"Proteostasis and Development Regulation","description":"The cluster centers on ubiquitination and proteasome-mediated protein catabolic processes, and on regulation of enzymatic activity related to protein turnover (negative regulation of endopeptidase activity and CDK kinase activity). Several development-related terms (cochlea morphogenesis, mammillary axonal complex development, somitogenesis, melanocyte migration) suggest a link between protein turnover control and developmental morphogenesis, while lipid transport and defense against fungus appear ancillary. Overall, the common theme is how regulated protein degradation and enzyme activity shape development and cell-cycle processes.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010951","count":2},{"id":"GO:0006869","count":2},{"id":"GO:0050832","count":2},{"id":"GO:0045736","count":2},{"id":"GO:0000209","count":1}]},{"hash":"1202844199339661330","title":"Lipid biosynthesis and ER-Golgi trafficking","description":"The cluster is dominated by lipid metabolism and vesicle transport terms (ceramide biosynthesis; serine palmitoyltransferase regulation) and ER-related processes (ER organization; ER-to-Golgi transport), which point to a membrane biogenesis/trafficking theme. A few items touch on developmental mRNA localization and axis specification, but the core signal is lipid production linked to ER-Golgi trafficking.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000105","count":1},{"id":"GO:0007029","count":1},{"id":"GO:0046513","count":1},{"id":"GO:1904222","count":1},{"id":"GO:0045451","count":1}]},{"hash":"622777763091996246","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":47,"triangles":60,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":3},{"id":"GO:0090617","count":3},{"id":"GO:0042793","count":3},{"id":"GO:1905639","count":3},{"id":"GO:1900865","count":3}]},{"hash":"1683334665331831303","title":"Alkaloid and lipid metabolism","description":"The top GO terms point to catabolic and metabolic processing of diverse organic compounds, especially alkaloids (alkaloid catabolic, isoquinoline alkaloid metabolic, camphor catabolic) and lipids (bile acid biosynthetic, triglyceride metabolic, retinoic acid catabolic). While a couple terms about ion responses appear, the central theme is degradation/processing of alkaloids and lipids, suggesting a cohesive metabolic cluster.","confidence":"Medium","size":14,"edges":9,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009822","count":10},{"id":"GO:0006641","count":10},{"id":"GO:0071615","count":10},{"id":"GO:0034653","count":10},{"id":"GO:0033076","count":10}]},{"hash":"181097809388658334","title":"RNA processing and silencing machinery","description":"The cluster is rich in RNA-related processes: tRNA processing, miRNA processing, and RISC complex assembly, plus translation and ribosome biogenesis terms, which together suggest involvement in RNA metabolism and gene silencing pathways. While other terms like motor neuron apoptotic process and negative regulation of proliferation appear, the strongest and most coherent signal is RNA processing/silencing together with translation machinery.","confidence":"High","size":14,"edges":75,"triangles":237,"max_degree":13,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0042254","count":3},{"id":"GO:0045071","count":3},{"id":"GO:0097049","count":3},{"id":"GO:0008033","count":3}]},{"hash":"1379503823320134332","title":"Neuronal development and dendrite morphogenesis","description":"This cluster is dominated by nervous system development terms, including CNS neuron development and dendrite morphogenesis, pointing to a neuronal development theme. While other terms (cholesterol biosynthesis, DNA replication/repair) are general cellular processes, the neural-associated terms are most representative of the cluster\u2019s function.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006695","count":5},{"id":"GO:0000435","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0031100","count":4},{"id":"GO:0007399","count":4}]},{"hash":"259191303257728629","title":"Diverse small-molecule xenobiotic and lipid metabolism","description":"This cluster is enriched for catabolic and metabolic processes across a range of small molecules, notably alkaloids (isoquinoline, camphor, other alkaloids) and lipid-related pathways (triglyceride metabolism, bile acid biosynthesis, retinoic acid catabolism). The common theme appears to be detoxification and biotransformation of xenobiotics and lipids, with a few unrelated ion-response terms that are likely incidental. Overall, the proteins likely participate in diverse metabolic processing rather than a single, narrow function.","confidence":"Medium","size":14,"edges":10,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009822","count":10},{"id":"GO:0006641","count":10},{"id":"GO:0071615","count":10},{"id":"GO:0034653","count":10},{"id":"GO:0033076","count":10}]},{"hash":"1288285853594434441","title":"RNA Pol II Transcription Regulation & Chromatin","description":"The top GO terms predominantly reflect regulation of transcription by RNA polymerase II, including preinitiation complex assembly and transcriptional control in response to signals, with an additional note on histone H3 acetylation, indicating chromatin-level regulation. Despite some obsolete terms, the convergence on RNAP II\u2013mediated transcription control and chromatin modification suggests the proteins function as transcription regulators linked to chromatin state.","confidence":"Medium","size":14,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043966","count":4},{"id":"GO:0045898","count":3},{"id":"GO:0061408","count":3},{"id":"GO:0000122","count":3},{"id":"GO:2000306","count":3}]},{"hash":"1629715647686398684","title":"Lipid and Alkaloid Metabolism","description":"The set of GO terms centers on metabolism and catabolism of lipids and lipid-derived molecules (prostaglandin biosynthesis; triglyceride and bile acid metabolism; retinoic acid catabolic process), along with alkaloid metabolism (alkaloid and isoquinoline alkaloid metabolic processes). This pattern suggests a cluster focused on lipid- and small-molecule/xenobiotic metabolism rather than a single protein function. A few terms touch on ion response and inflammatory regulation, but the dominant signal is lipid and alkaloid metabolism.","confidence":"Medium","size":14,"edges":26,"triangles":23,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":10},{"id":"GO:0009822","count":8},{"id":"GO:0006641","count":8},{"id":"GO:0071615","count":8},{"id":"GO:0034653","count":8}]},{"hash":"2133322350935302233","title":"Diverse metabolism and signaling","description":"The top GO terms span antibiotic biosynthesis, triglyceride catabolism, iron-sulfur cluster assembly, strigolactone biosynthesis/response, prostaglandin catabolism, chlorophyll catabolism, menaquinone biosynthesis, and regulation of endocannabinoid signaling. This breadth suggests no single cohesive function for the cluster, but rather a collection of enzymes involved in various metabolic and signaling processes across different organisms. Therefore the label is a broad fit, with Low confidence due to heterogeneity.","confidence":"Low","size":14,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0019433","count":3},{"id":"GO:0016226","count":2},{"id":"GO:1902348","count":2},{"id":"GO:1905344","count":2}]},{"hash":"1862803160458952923","title":"Xenobiotic and lipid metabolism","description":"Most of the top GO terms describe catabolic or biosynthetic processes for alkaloids, isoquinoline alkaloids, retinoic acid, triglycerides, and bile acids, pointing to a core role in small-molecule and lipid metabolism. A few terms pertain to ion responses or inflammatory regulation, which are less central to the main theme. Taken together, the cluster is best captured by a label reflecting metabolism of xenobiotics and lipids.","confidence":"High","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009822","count":13},{"id":"GO:0006641","count":13},{"id":"GO:0071615","count":13},{"id":"GO:0034653","count":13},{"id":"GO:0033076","count":13}]},{"hash":"1759573127696461386","title":"Chromatin Remodeling and Histone Modification","description":"Most terms point to chromatin state regulation and histone modification (histone acetylation, H2A deubiquitination, chromatin remodeling, heterochromatin formation) and to genome maintenance (DSB repair during replication and meiotic recombination). A few terms relate to plant development, but the predominant signal is chromatin dynamics governing genome stability, justifying a label centered on chromatin modification/remodeling.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0035066","count":5},{"id":"GO:0000183","count":5},{"id":"GO:0010520","count":5},{"id":"GO:1990414","count":5},{"id":"GO:0035522","count":5}]},{"hash":"764188914787289346","title":"Chromatin Regulation in Development","description":"The cluster is enriched for chromatin- and transcription-related terms (negative regulation of transcription by RNA polymerase II, rDNA heterochromatin formation, nucleosome assembly, histone methylation regulation) alongside several developmental processes (brain development, male gonad development, pro-B cell differentiation, single fertilization). This pattern suggests the proteins function together to control chromatin state and gene expression during development. Some other terms (tRNA modification, Rho signal regulation) may reflect additional regulatory roles but do not outweigh the core chromatin- and development-focused theme.","confidence":"Medium","size":14,"edges":8,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":5},{"id":"GO:0000183","count":5},{"id":"GO:0007420","count":4},{"id":"GO:0007338","count":4},{"id":"GO:0051572","count":4}]},{"hash":"59532827338166459","title":"Developmental signaling and cell fate","description":"The terms cluster around developmental pathways (hippo signaling, canonical Wnt signaling), and developmental processes (forebrain development, keratinocyte differentiation) as well as apoptosis, indicating a theme of cell fate regulation during development. Some metabolic biosynthesis and catabolic terms appear incidental, but the dominant signal is developmental signaling and differentiation.","confidence":"Medium","size":14,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":3},{"id":"GO:0030216","count":3},{"id":"GO:0035329","count":3},{"id":"GO:0030900","count":3},{"id":"GO:0090263","count":3}]},{"hash":"2218000097197617519","title":"Transsulfuration and Cysteine Biosynthesis","description":"The cluster\u2019s top GO terms cluster around serine/homocysteine catabolism and transsulfuration, including L-serine catabolic process, L-homocysteine catabolic process, transsulfuration, L-cysteine biosynthetic process from L-serine, and hydrogen sulfide biosynthetic process, all pointing to sulfur amino acid metabolism and cysteine/H2S production. Some terms like \u201cresponse to morphine\u201d are likely incidental noise. Overall, the proteins appear to participate in a cohesive sulfur metabolism pathway, particularly cysteine biosynthesis via transsulfuration.","confidence":"High","size":14,"edges":86,"triangles":308,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006535","count":3},{"id":"GO:0043418","count":3},{"id":"GO:0019346","count":3},{"id":"GO:0019295","count":3},{"id":"GO:0006565","count":3}]},{"hash":"2092839041745811403","title":"RNA Processing and Translation Initiation","description":"This cluster centers on RNA maturation and translation readiness: ribosome biogenesis, formation of the preinitiation complex, regulation of translational initiation, and mRNA processing/export/splicing. The presence of regulatory ncRNA-mediated silencing and protein ubiquitination suggests broader regulatory control of RNA metabolism and translation. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0006406","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0048026","count":2},{"id":"GO:1900363","count":2}]},{"hash":"1646775870997462496","title":"Biosynthesis of secondary metabolites","description":"This cluster is enriched for multiple secondary-metabolite biosynthesis terms (sporopollenin, chalcone, flavonoid, clavulanic acid, antibiotic biosynthesis), along with related lipid-derived biosynthesis (long-chain fatty-acyl-CoA, carnitine). While there are a few catabolic terms present, the predominant signal is production of diverse small molecules rather than general metabolism or signaling, justifying a secondary-metabolite biosynthesis label.","confidence":"High","size":14,"edges":8,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0035336","count":4},{"id":"GO:0080110","count":4},{"id":"GO:0045329","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0006151","count":3}]},{"hash":"2290830183196885843","title":"Light-Driven Transcription and Chlorophyll Regulation","description":"The cluster centers on transcription-related GO terms (DNA-templated transcription and its regulation) alongside light- and pigment-associated processes (detection of visible light, detection of hypoxia, regulation of chlorophyll catabolic process, and chromophore linkage), suggesting proteins involved in light sensing and chlorophyll/chromophore metabolism, potentially spanning photosynthetic organisms including cyanobacteria. Some terms are plant-specific (ethylene signaling) or immune-related, but the core theme ties to light-responsive transcription and chlorophyll regulation.","confidence":"Medium","size":14,"edges":9,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0018298","count":3},{"id":"GO:0043158","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0070483","count":2},{"id":"GO:1903660","count":2}]},{"hash":"1218221454149139507","title":"Plant flavonoid and lignin biosynthesis","description":"The top GO terms center on flavonoid glycoside biosynthesis (kaempferol, quercetin, cyanidin) and lignin metabolism, indicating a cluster of proteins involved in plant phenylpropanoid secondary metabolism rather than animal signaling; some other terms appear as broad metabolic annotations but do not override the main flavonoid/lignin biosynthesis theme.","confidence":"High","size":14,"edges":4,"triangles":0,"max_degree":2,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0016999","count":5},{"id":"GO:0030259","count":5},{"id":"GO:0006711","count":4},{"id":"GO:0052696","count":4},{"id":"GO:0070980","count":4}]},{"hash":"2067725562328328448","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":3},{"id":"GO:0090617","count":3},{"id":"GO:0042793","count":3},{"id":"GO:1905639","count":3},{"id":"GO:1900865","count":3}]},{"hash":"1717728679590695603","title":"Translation machinery and tRNA charging","description":"The cluster is dominated by GO terms for translation and tRNA aminoacylation (leucyl-, methionyl-, isoleucyl-, valyl-tRNA charging) plus translation-related regulation and frameshifting, indicating a cohesive group of proteins involved in protein synthesis and tRNA charging/processing. A few intron-splicing terms may reflect tRNA processing rather than mRNA splicing, but the overall signal points to translation machinery. ","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0006450","count":2},{"id":"GO:0010102","count":1},{"id":"GO:0000373","count":1},{"id":"GO:0006429","count":1}]},{"hash":"1493158457818371519","title":"Ribosome biogenesis and RNA processing","description":"This cluster is enriched for translation- and RNA-processing terms (mitochondrial translation, translation, ribosome biogenesis, mRNA splicing, ribosomal large subunit export), indicating membership in the protein synthesis and RNA-processing machinery. While a few plant-development terms are present, the dominant pattern centers on RNA biology rather than development.","confidence":"Medium","size":14,"edges":10,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0032543","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0000055","count":1}]},{"hash":"450421034752222396","title":"Cofactor Biosynthesis and Antiviral Defense","description":"This cluster combines several biosynthetic pathways for cofactors (menaquinone, biotin, pyrroloquinoline quinone) and related metabolic redox processes (triglyceride catabolism, oxidant detoxification), with immune-related terms such as defense/innate responses to virus and viral process. The strongest signal is metabolic/cofactor biosynthesis, complemented by a notable set of antiviral/innate immune terms, suggesting a cluster that links metabolism with host defense against viruses. Confidence: Medium","confidence":"","size":14,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":4},{"id":"GO:0009234","count":3},{"id":"GO:0009102","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0055114","count":3}]},{"hash":"2260974508374676545","title":"Microtubule dynamics and mitosis","description":"Most representative terms are microtubule nucleation and mitotic spindle pole body duplication, which point to cytoskeletal organization during cell division. Although other GO terms in the set appear diverse (immune, plant-specific, translation), the core cluster signal centers on microtubule-based processes and mitosis, justifying the label as Microtubule dynamics and mitosis. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002181","count":2},{"id":"GO:1903087","count":2},{"id":"GO:0007020","count":2},{"id":"GO:0035167","count":1},{"id":"GO:0042129","count":1}]},{"hash":"2235133338744893334","title":"Splicing and mRNA Regulation","description":"This cluster is dominated by post-transcriptional RNA processing terms\u2014spliceosome-mediated and alternative splicing, mRNA export, modification, and stability regulation\u2014together with regulatory ncRNA-mediated gene silencing. The combination points to a cohesive role in RNA maturation and control of gene expression at the mRNA level, with a few secondary terms like blastocyst formation or viral translation reinitiation likely representing broader functional contexts.","confidence":"High","size":14,"edges":67,"triangles":164,"max_degree":13,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":8},{"id":"GO:0048026","count":8},{"id":"GO:0010610","count":7},{"id":"GO:0045292","count":7},{"id":"GO:0006378","count":7}]},{"hash":"1410137950658533942","title":"Nuclear transcription and chromatin regulation","description":"The cluster centers on nuclear processes: DNA-templated transcription, regulation of transcription, chromatin organization, and spliceosomal snRNP assembly, with supporting signals from ubiquitination/proteasomal degradation and related regulatory pathways. While a couple of terms touch on broader signaling or development, the dominant theme is transcriptional control and chromatin dynamics with coordinated protein turnover.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":2},{"id":"GO:0000387","count":2},{"id":"GO:0070262","count":1},{"id":"GO:0031497","count":1}]},{"hash":"916273587323247106","title":"Ribosome Biogenesis and Translation","description":"This cluster shows strong enrichment for rRNA maturation (SSU/LSU and 5.8S), and for translation, pointing to a core role in ribosome assembly and protein synthesis. While there are additional terms related to apoptosis and development, the predominant signal supports ribosome biogenesis and translation as the defining theme of this group.","confidence":"High","size":14,"edges":41,"triangles":57,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":3},{"id":"GO:0000462","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0006915","count":2}]},{"hash":"1561012044574283403","title":"Spliceosome-Mediated RNA Processing and mRNA Regulation","description":"The terms cluster around RNA splicing (spliceosome), mRNA stability and export, and regulatory ncRNA-mediated silencing, pointing to a group of proteins involved in post-transcriptional RNA processing and regulation, especially splicing decisions and stability control. Peripheral terms like blastocyst formation and viral translation reinitiation are less central to the core function.","confidence":"High","size":14,"edges":18,"triangles":1,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":6},{"id":"GO:0048026","count":6},{"id":"GO:0010610","count":5},{"id":"GO:0000398","count":5},{"id":"GO:0016556","count":4}]},{"hash":"1977154072418825178","title":"Cell cycle, DNA replication, and nuclear transport","description":"This cluster is dominated by mitotic cell cycle and DNA replication terms, complemented by nuclear transport (protein export from nucleus) and ER polarization, pointing to a core theme of cell-cycle\u2013linked DNA metabolism and nuclear organization. Some terms reflect development and immune signaling, but they appear as secondary associations.","confidence":"Medium","size":14,"edges":32,"triangles":24,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":14},{"id":"GO:0006260","count":14},{"id":"GO:0043277","count":13},{"id":"GO:0046641","count":13},{"id":"GO:0060709","count":13}]},{"hash":"765487589889297452","title":"Post-transcriptional RNA processing and silencing","description":"This cluster centers on RNA-based regulation after transcription, including ncRNA/miRNA-mediated gene silencing, splicing regulation via the spliceosome, mRNA modification, export, and stabilization, all pointing to coordinated post-transcriptional control rather than transcriptional regulation.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":8},{"id":"GO:0048026","count":8},{"id":"GO:0016556","count":7},{"id":"GO:0006406","count":7},{"id":"GO:0000381","count":7}]},{"hash":"1364307763619153156","title":"Dendritic Cell Antigen Presentation and T Cell Activation","description":"The top GO terms are dominated by adaptive immune functions: T cell cytokine production, T cell proliferation, MHC class II biosynthesis, and positive regulation of dendritic cell antigen processing and presentation, all pointing to dendritic cell\u2013mediated activation of T cells. Additional terms related to respiratory burst and metal ion transport suggest supporting roles of phagocytes and metalloproteins, but the core signal centers on antigen presentation and T cell activation. Confidence: High","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002369","count":2},{"id":"GO:0002309","count":2},{"id":"GO:0030026","count":2},{"id":"GO:0045342","count":2},{"id":"GO:0015707","count":2}]},{"hash":"687529553681981779","title":"Ubiquitin-Proteasome Proteostasis and PTMs","description":"The top GO terms cluster around ubiquitin-proteasome\u2013dependent protein degradation (SCF-dependent proteasomal pathways, ERAD) and post-translational modification regulation (deneddylation, desumoylation). There are also signals related to cell division and chromatin regulation, which fit a broader theme of controlled protein turnover and modification during the cell cycle and chromatin dynamics. A few placental development terms appear but are likely incidental to the broader proteostasis/PTM pattern. Confidence: High.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0060712","count":2},{"id":"GO:1904333","count":2}]},{"hash":"1509712476916086876","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0090615","count":7},{"id":"GO:0090617","count":7},{"id":"GO:1905639","count":7},{"id":"GO:1900865","count":7},{"id":"GO:0042793","count":7}]},{"hash":"1793707073486904971","title":"Phosphorylation-regulated growth signaling","description":"The top GO terms cluster around regulation and signaling, especially serine/threonine phosphorylation and kinase activity, along with growth-related processes (cell growth, skin and liver regeneration) and regulation of transcription/translation. This suggests a theme of growth control via phosphorylation-driven signaling, even though there are no observed protein\u2013protein interactions in this cluster.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030307","count":2},{"id":"GO:0043588","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0080163","count":1},{"id":"GO:0018107","count":1}]},{"hash":"92174823798193384","title":"Cysteine and sulfur amino acid metabolism and sulfhydration","description":"The top GO terms point to cysteine- and sulfur-containing amino acid metabolism (cysteine catabolic and biosynthetic processes, L-homocysteine biosynthesis) and protein sulfhydration, which is a sulfur/ H2S\u2013dependent post-translational modification on cysteine residues. Although some terms relate to stress signaling (response to glucocorticoid, response to cAMP) and other amino acids (glycine catabolism), the core signal is sulfur amino acid metabolism and sulfhydration, with a plausible link to sulfur-driven signaling and metabolism in this cluster.","confidence":"Medium","size":14,"edges":19,"triangles":6,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0050832","count":2},{"id":"GO:0006546","count":1},{"id":"GO:0051591","count":1},{"id":"GO:0044524","count":1},{"id":"GO:0071269","count":1}]},{"hash":"29001885556860370","title":"Proteostasis and Chromatin Regulation","description":"The cluster centers on protein turnover via ubiquitination and the proteasome (autoubiquitination, SCF-dependent degradation, ERAD) and on post-translational regulation via neddylation. It also features chromatin organization and heterochromatin maintenance, with links to DNA repair, suggesting a theme where proteostasis interfaces with chromatin state and genome integrity.","confidence":"High","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051865","count":14},{"id":"GO:0030433","count":14},{"id":"GO:1903955","count":11},{"id":"GO:0031497","count":11},{"id":"GO:0016032","count":11}]},{"hash":"926823527795367997","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":9},{"id":"GO:0090617","count":9},{"id":"GO:0042793","count":9},{"id":"GO:1905639","count":9},{"id":"GO:1900865","count":9}]},{"hash":"1796331554285071772","title":"Unknown","description":"These proteins appear linked to a highly diverse set of GO terms, including multiple biosynthetic processes (biotin, antibiotic, strigolactone), oxidation-reduction and various metabolic activities (prostaglandin catabolic, methionine biosynthesis), transcription regulation, and even a behavioral term (fear response). There is no clear, shared function or pathway connecting these terms, and the absence of edges supports a lack of cohesive biological theme. Therefore the cluster cannot be assigned a specific, representative name with confidence.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0009102","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2}]},{"hash":"2194939957989612949","title":"Metabolic Regulation and Signaling","description":"The cluster includes GO terms for lipid biosynthesis, glycolytic and gluconeogenic processes, cellular responses to cAMP, regulation of PKC signaling, and protein trafficking/localization, plus ion transport. This spread suggests a grouping around how metabolism and signaling pathways are regulated, rather than a single, tight pathway. A broad label capturing metabolism with coordinated signaling fits best across the terms observed.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008654","count":1},{"id":"GO:0045821","count":1},{"id":"GO:0009627","count":1},{"id":"GO:0006094","count":1},{"id":"GO:0071320","count":1}]},{"hash":"1135157459091580482","title":"Flavonoid Glycoside Biosynthesis and Phenylpropanoid Metabolism","description":"This cluster is dominated by GO terms for flavonoid biosynthesis and glycosylation (kaempferol and quercetin O-glucosides, cyanidin 3-O-glucoside) and related phenylpropanoid processes like lignin metabolism, indicating a coherent theme of plant secondary metabolite production. Some terms appear noisy (e.g., estrogen catabolic process, paranode localization) and may reflect annotation spillover, but the core signal points to flavonoid glycoside biosynthesis and phenylpropanoid metabolism.","confidence":"High","size":14,"edges":46,"triangles":60,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006711","count":11},{"id":"GO:0030259","count":11},{"id":"GO:0052696","count":11},{"id":"GO:0070980","count":11},{"id":"GO:0033330","count":11}]},{"hash":"1149875501369598659","title":"Unknown","description":"The top terms span immune signaling (T cell proliferation, tolerance induction, viral response) as well as broad developmental and cellular processes (placental differentiation, ER polarization, nuclear export, meiosis, endocrine secretion). There isn\u2019t a single cohesive function tying these proteins together, so a precise label isn\u2019t justifiable.","confidence":"","size":14,"edges":13,"triangles":3,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043277","count":4},{"id":"GO:0046641","count":4},{"id":"GO:0060709","count":4},{"id":"GO:0006611","count":4},{"id":"GO:0061167","count":4}]},{"hash":"631884644406611039","title":"Innate Immune TLR Signaling and Cytokine Production","description":"The GO terms center on Toll-like receptor signaling (MyD88-dependent, TLR2), NF-kappaB activation, and production/regulation of cytokines and chemokines (IL-6, IL-15, IL-18, CCL5), plus antifungal peptide production. This points to a shared function in innate immune sensing and downstream inflammatory responses, indicating a cohesive module of TLR-driven cytokine signaling and antimicrobial defense.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032738","count":1},{"id":"GO:0090073","count":1},{"id":"GO:0002755","count":1},{"id":"GO:0045410","count":1},{"id":"GO:0071651","count":1}]},{"hash":"1435463631483784204","title":"Immune Regulation and Development","description":"The top GO terms show strong immune-related activities (apoptotic cell clearance, T cell proliferation, tolerance induction, response to virus) alongside developmental and regenerative processes (placental development, organ regeneration, ER polarization, nuclear transport, meiotic DSB processing). This suggests a cluster of proteins involved in immune regulation with ancillary roles in development and tissue remodeling, rather than a single, tightly defined pathway.","confidence":"Medium","size":14,"edges":23,"triangles":11,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043277","count":13},{"id":"GO:0046641","count":13},{"id":"GO:0060709","count":13},{"id":"GO:0006611","count":13},{"id":"GO:0061167","count":13}]},{"hash":"841682286328762229","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1900865","count":6},{"id":"GO:0031426","count":6},{"id":"GO:0031425","count":6},{"id":"GO:0016554","count":6},{"id":"GO:0080156","count":6}]},{"hash":"192159851054831602","title":"Flavonoid and phenylpropanoid biosynthesis","description":"This cluster is dominated by GO terms for flavonoid and anthocyanin biosynthesis (anthocyanin-containing compound biosynthetic process; kaempferol and quercetin O-glucoside biosynthesis; lignin metabolic process), which are core parts of the phenylpropanoid pathway. Other terms like biphenyl catabolic and antibiotic metabolism suggest broader secondary metabolism, while the paranode localization term appears as an outlier. Overall, the shared theme is plant secondary metabolite biosynthesis, especially flavonoids and lignin-related pathways.","confidence":"High","size":14,"edges":9,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009718","count":9},{"id":"GO:0006711","count":6},{"id":"GO:0030259","count":6},{"id":"GO:0052696","count":6},{"id":"GO:0070980","count":6}]},{"hash":"1711512860637695611","title":"Golgi-Endosome Vesicle Transport","description":"The terms cluster around intracellular trafficking to and from the Golgi and endosomes\u2014COPII loading, endosome-to-Golgi, recycling endosome-to-Golgi, retrograde transport, vesicle fusion regulation, and Rab/Rap signaling\u2014indicating a cohesive vesicle trafficking function. A couple of outliers (lens morphogenesis, host-mediated activation of viral genome replication) do not define the core theme but do not override it.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051534","count":1},{"id":"GO:0090110","count":1},{"id":"GO:0034499","count":1},{"id":"GO:0070309","count":1},{"id":"GO:0044829","count":1}]},{"hash":"2095745789824869232","title":"Plant metabolism and development","description":"The terms point to plant-specific biology, including reproduction (pollination, seed coat development) and secondary/metabolic pathways (phenylpropanoid metabolism, various carbon metabolism terms) along with aluminum transport, suggesting a broad plant metabolism/development theme rather than a single unified function.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015690","count":3},{"id":"GO:0009856","count":3},{"id":"GO:0019427","count":1},{"id":"GO:0008218","count":1},{"id":"GO:0090410","count":1}]},{"hash":"406257022066259813","title":"TLR\u2013NF-\u03baB Innate Immune Signaling","description":"The proteins are annotated with GO terms centered on toll-like receptor signaling (TLR4, TLR10), NF-\u03baB activation (I-kappaB phosphorylation), and cytokine production (TNF, IFN-\u03b1), along with LPS and fungal component sensing and dendritic cell regulation, indicating a cohesive theme of innate immune sensing and inflammatory signaling that can bias toward Th1 responses.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042535","count":1},{"id":"GO:0002730","count":1},{"id":"GO:0034142","count":1},{"id":"GO:0007252","count":1},{"id":"GO:0034166","count":1}]},{"hash":"2301373375747794780","title":"Ubiquitin-Dependent Protein Degradation","description":"The top GO terms are dominated by ubiquitin-mediated degradation: ubiquitin-dependent protein catabolic process, autoubiquitination, and K48-linked ubiquitination, indicating a module of proteins involved in tagging substrates for proteasomal turnover. Additional terms related to ERAD, peroxisomal import, and receptor downregulation (e.g., Wnt receptor catabolic process) support a broader theme of proteostasis and regulated protein turnover. Confidence: High","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":9},{"id":"GO:0051865","count":5},{"id":"GO:0070936","count":5},{"id":"GO:0016558","count":5},{"id":"GO:0046621","count":5}]},{"hash":"1268862340783181445","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090617","count":3},{"id":"GO:0042793","count":3},{"id":"GO:1905639","count":3},{"id":"GO:1900865","count":3},{"id":"GO:0010019","count":3}]},{"hash":"1558600892793215126","title":"Transmembrane Transporters (Ion and Metabolite)","description":"The top GO terms cluster around transport across membranes for various substrates: ions (K+, Na+, phosphate, nitrate), sugars (galactose, fucose), xenobiotics, and even neurotransmitter loading into vesicles. This pattern strongly suggests a group of membrane transporter proteins handling diverse substrates, with a vesicular transport-related example included. Confidence here is High.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":5},{"id":"GO:0006855","count":4},{"id":"GO:0042128","count":4},{"id":"GO:0006004","count":3},{"id":"GO:0098700","count":3}]},{"hash":"1296984777334622057","title":"Auxin-driven plant development and patterning","description":"This cluster centers on auxin response and signaling, plus meristem development, leaf vascular patterning, axis specification, and transcriptional regulation, suggesting proteins that coordinate auxin-mediated plant growth and tissue patterning.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010047","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0009733","count":1},{"id":"GO:0009942","count":1}]},{"hash":"407967379492843602","title":"Mitochondrial translation and transcription","description":"The cluster shows strong signals for translation and ribosome biogenesis/assembly (GO:0006412, GO:0042273, GO:0000027) together with mitochondrial transcription processes (GO:0006391, GO:1903108). Additionally, ubiquinone biosynthesis and related metabolic terms point to mitochondrial metabolism, supporting a mitochondria-centered gene expression theme. A few other terms are peripheral, but the core pattern aligns with mitochondrial protein synthesis and transcription control, hence this label. ","confidence":"Medium","size":13,"edges":77,"triangles":275,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0042273","count":3},{"id":"GO:0000027","count":2},{"id":"GO:0030961","count":2},{"id":"GO:0016126","count":2}]},{"hash":"865348290941717797","title":"Chloroplast Translation and Photosynthesis","description":"This cluster centers on chloroplast functions: translation and ribosome biogenesis (LSU rRNA maturation) alongside photosynthesis and light-harvesting processes (PS I and II, light responses). The inclusion of far-red, UV-A, and high-light response terms indicates a stress-related regulation of chloroplast activity, including programmed cell death. Together, these terms point to a cohesive theme of chloroplast translation machinery coupled with photosynthetic activity and light-stress responses.","confidence":"High","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0000463","count":1},{"id":"GO:0009768","count":1}]},{"hash":"1079137083113410937","title":"DNA Maintenance and Proteostasis","description":"The cluster centers on DNA metabolism (repair, replication, transcription, cell cycle) and proteostasis-related processes (protein catabolic processing, ERAD, peroxisome matrix import), suggesting a functional core around genome maintenance and protein quality control.","confidence":"Medium","size":13,"edges":18,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0030163","count":2},{"id":"GO:0016558","count":2},{"id":"GO:0030433","count":2}]},{"hash":"1707052936856945464","title":"Neural and organ development","description":"This cluster is characterized by GO terms related to development of neural tissues (midbrain dopaminergic neuron differentiation) and organ formation (lung induction, renal inner medulla development), suggesting a shared theme of cell fate specification and organogenesis. Additional terms like NLS-bearing protein import into nucleus and intermediate filament bundle assembly reflect cellular architecture and transport underlying differentiation. Some terms are obsolete or less related, contributing to heterogeneity.","confidence":"Medium","size":13,"edges":55,"triangles":114,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":7},{"id":"GO:0010909","count":5},{"id":"GO:0060492","count":5},{"id":"GO:1904948","count":5},{"id":"GO:0072053","count":5}]},{"hash":"1131581127719702340","title":"Unknown","description":"The top GO terms span several unrelated themes: aromatic compound catabolic processes (carbazole, toluene, alkaloids) alongside energy/photoreaction terms (photosynthesis, nonphotochemical quenching, proton transmembrane transport), plus prostaglandin biosynthesis and female gonad development. With no inferred shared pathway and no edges connecting the proteins, there isn\u2019t a coherent function to name as a cluster. This likely reflects diverse annotations rather than a single biological module.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046232","count":4},{"id":"GO:0008585","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0001516","count":3},{"id":"GO:1902600","count":2}]},{"hash":"828751140933733460","title":"Steroid and lipid metabolism","description":"The cluster is driven by GO terms for testosterone biosynthesis, bile acid biosynthesis, and triglyceride metabolism, pointing to a core theme of lipid and steroid metabolic pathways. Other terms about alkaloid metabolism suggest broader small-molecule processing, while ion-response and inflammatory-regulation terms appear less central. Overall, the dominant signal is lipid/steroid metabolism with ancillary small-molecule processing.","confidence":"Medium","size":13,"edges":8,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0061370","count":6},{"id":"GO:0009822","count":5},{"id":"GO:0006641","count":5},{"id":"GO:0071615","count":5},{"id":"GO:0034653","count":5}]},{"hash":"556191034816523952","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":8,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1901621","count":2},{"id":"GO:0006260","count":2},{"id":"GO:1905259","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0097428","count":2}]},{"hash":"321090757654331928","title":"Auxin Signaling and Fatty Acid Metabolism","description":"These GO terms cluster around auxin biology (response to auxin, auxin-activated signaling, auxin polar transport, regulation of organ growth) and fatty acid metabolism (biosynthetic and catabolic processes, palmitic acid biosynthesis, long-chain fatty-acyl-CoA processes), with phylloquinone biosynthesis also represented. This suggests proteins that coordinate auxin-regulated growth with lipid metabolism in plants. The link is plausible but not tightly unified by a single dominant function, so confidence is Medium.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006633","count":1},{"id":"GO:0009733","count":1},{"id":"GO:0009734","count":1},{"id":"GO:0046620","count":1},{"id":"GO:0009926","count":1}]},{"hash":"1137246562663998556","title":"Sugar Transport and Glucose Response","description":"This cluster is enriched for GO terms describing transport of sugars (glucose, fructose, xylose, trehalose) and related uptake, plus cellular responses to glucose availability (glucose starvation, insulin-stimulated glucose import). A few terms relate to general transport and other processes, but the dominant signal is membrane sugar transport and glucose handling, which justifies a sugar transport/glucose response label.","confidence":"Medium","size":13,"edges":44,"triangles":68,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0042149","count":5},{"id":"GO:1990539","count":5},{"id":"GO:0043252","count":5},{"id":"GO:0015771","count":5},{"id":"GO:0052106","count":5}]},{"hash":"845348698580086044","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":17,"triangles":0,"max_degree":6,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0090617","count":6},{"id":"GO:0042793","count":6},{"id":"GO:1905639","count":6},{"id":"GO:1900865","count":6},{"id":"GO:0031426","count":6}]},{"hash":"554768167756116060","title":"Chemical Metabolism and Stress Response","description":"The top GO terms indicate metabolism of various chemicals (retinoic acid, ethanol, furaldehyde, copper handling) and stress/defense responses (response to lipopolysaccharide, nitrosative stress, extracellular regulation of signal transduction). Although terms span different organisms, the shared theme is processing of xenobiotics/metabolites and cellular responses to chemical stress, suggesting a cohesive cluster around chemical metabolism intertwined with stress signaling.","confidence":"Medium","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0042573","count":13},{"id":"GO:0045777","count":13},{"id":"GO:0043458","count":13},{"id":"GO:0046688","count":13},{"id":"GO:0006068","count":13}]},{"hash":"1175859098882449327","title":"TGF-\u03b2/BMP pathway regulators","description":"The GO terms are dominated by regulation and response related to TGF-\u03b2 signaling and BMP pathways (negative regulation of TGF-\u03b2 receptor signaling, BMP signaling, SMAD assembly, and cellular response to TGF-\u03b2), indicating a cohesive theme of modulation within this pathway. A few other terms touch broader developmental signaling, but the central signal is TGF-\u03b2/BMP regulation.","confidence":"High","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0061191","count":3},{"id":"GO:0046827","count":3},{"id":"GO:0042347","count":3},{"id":"GO:0000173","count":3},{"id":"GO:0042006","count":3}]},{"hash":"1703976624175842455","title":"Steroid and vitamin biosynthesis","description":"The cluster is dominated by biosynthetic processes, notably C21-steroid hormone biosynthesis and vitamin biosynthesis (retinol and ascorbic acid), along with related redox and metabolic pathways, suggesting a theme of steroid and vitamin production. The drought response term is more of a peripheral link via metabolic adjustment, but the core signal points to steroid and vitamin biosynthesis. ","confidence":"Medium","size":13,"edges":70,"triangles":220,"max_degree":12,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0046370","count":8},{"id":"GO:0042572","count":8},{"id":"GO:0055114","count":7},{"id":"GO:0009414","count":5},{"id":"GO:0006699","count":5}]},{"hash":"1722174953906182745","title":"Neurodevelopment and ER-stress apoptosis","description":"The top GO terms cluster around developmental processes (forebrain development, neural tube closure, skeletal system development, multicellular organism development) and transcriptional regulation, with a notable link to intrinsic apoptotic signaling in response to ER stress and other cellular stress responses (cadmium, defense). This suggests a theme of developmental regulation coupled with stress-induced signaling, justifying a label that highlights both neurodevelopment and ER-stress\u2013related apoptosis.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070059","count":3},{"id":"GO:0030900","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0001501","count":3}]},{"hash":"1902726296348762460","title":"Presynaptic vesicle trafficking and SNARE fusion","description":"This cluster centers on presynaptic neurotransmitter release machinery and vesicle trafficking, highlighted by SNARE complex assembly, synaptic vesicle fusion, spontaneous neurotransmitter secretion, and Golgi/ER-Golgi organization and endosome transport terms, suggesting a cohesive vesicle cycling program at the synapse.","confidence":"High","size":13,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1903358","count":4},{"id":"GO:0060291","count":3},{"id":"GO:0035493","count":3},{"id":"GO:1903422","count":3},{"id":"GO:0097352","count":3}]},{"hash":"1111612050853505839","title":"Proliferation and Angiogenesis","description":"This cluster is enriched for DNA replication, which points to cell proliferation, and for angiogenesis-related terms such as endothelial cell migration and placenta-related development, suggesting a tie to vascular formation during development. Additional terms related to immune cell proliferation and general cellular processes indicate a broader developmental program that includes growth and tissue remodeling.","confidence":"Medium","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":11},{"id":"GO:0043536","count":7},{"id":"GO:0009190","count":7},{"id":"GO:0001525","count":7},{"id":"GO:0043277","count":6}]},{"hash":"984906998149708894","title":"Metabolite and sugar transport","description":"The cluster is dominated by GO terms for transport across membranes of various solutes, especially sugars (glucose, fructose, trehalose) and other metabolites (urate, nitrite). This consistent theme indicates a cohesive function in membrane transport of nutrients and metabolites, with several glucose/fructose transport terms reinforcing a sugar-transporter role.","confidence":"High","size":13,"edges":34,"triangles":17,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0015747","count":4},{"id":"GO:0006004","count":4},{"id":"GO:0042149","count":3},{"id":"GO:1990539","count":3},{"id":"GO:0043252","count":3}]},{"hash":"1197540834788756724","title":"RNA processing and translation control","description":"These GO terms cluster around mRNA maturation and handling (splicing via spliceosome, alternative splicing regulation, mRNA export, mRNA modification) and protein synthesis control (translation initiation and reinitiation). The combination suggests a cohesive function in RNA processing and regulation of translation, with a minor note of development via blastocyst formation.","confidence":"High","size":13,"edges":3,"triangles":0,"max_degree":1,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0001731","count":5},{"id":"GO:0002188","count":5},{"id":"GO:0031047","count":5},{"id":"GO:0048026","count":5},{"id":"GO:0045292","count":5}]},{"hash":"1770887889385667350","title":"Root hair development and membrane transport","description":"This cluster centers on membrane transport of small molecules (calcium, amino acids, phosphoglycerate, UDP-glucose) and includes root-specific development terms (root hair and lateral root development). The combination suggests proteins involved in nutrient transport and epidermal root cell differentiation, particularly in root hairs, with some broader signaling processes. The lack of network connectivity reinforces a functional grouping rather than a single pathway, so the label emphasizes both transport activity and root-hair development themes.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990034","count":3},{"id":"GO:0032973","count":2},{"id":"GO:0000160","count":2},{"id":"GO:0043123","count":2},{"id":"GO:0035690","count":2}]},{"hash":"1264844895579382499","title":"Splicing and mRNA processing cluster","description":"The top GO terms are dominated by mRNA processing and spliceosome-related activities (cis splicing, mRNA modification, export, and regulation of alternative splicing), plus mRNA stabilization and general splicing regulation. This points to a cohesive group of proteins involved in post-transcriptional handling of mRNA, especially splicing and export. A few terms like regulatory ncRNA-mediated gene silencing align with RNA regulatory pathways, while one outlier (blastocyst formation) may reflect developmental context rather than core function. Overall, the cluster appears to represent proteins centered on spliceosome-mediated mRNA processing and related post-transcriptional regulation.","confidence":"High","size":13,"edges":11,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":3},{"id":"GO:0016556","count":2},{"id":"GO:0006406","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0048026","count":2}]},{"hash":"2295397244580645020","title":"Developmental transcriptional regulation","description":"The cluster centers on transcription control (DNA-templated transcription; regulation of transcription by RNA Pol II; regulation of DNA binding) and includes several development-related processes (myoblast development, ureter morphogenesis, epithalamus development) plus signaling responses (TGF-\u03b2, steroid hormone). This pattern suggests proteins that regulate gene expression during development and differentiation, rather than a single pathway.","confidence":"High","size":13,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0043388","count":3},{"id":"GO:0021538","count":2},{"id":"GO:0048545","count":2}]},{"hash":"1255851404361767356","title":"RNA processing and translation","description":"The top terms are dominated by translation and RNA-related processes (mRNA processing, tRNA processing, RNA splicing), with additional but weaker signals for RNA-templated DNA biosynthesis and intron homing. This points to a module enriched in RNA metabolism and protein synthesis machinery, with some extra terms reflecting trafficking or cell polarity context. Confidence: Medium","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0015031","count":2},{"id":"GO:0006397","count":1},{"id":"GO:0008033","count":1},{"id":"GO:0006278","count":1}]},{"hash":"2130216658311495659","title":"Viral Life Cycle and Host Interaction","description":"Based on GO terms including symbiont entry into host, establishment of integrated proviral latency, virion assembly, viral release from host cell, and host-mediated activation of viral genome replication, the cluster is dominated by viral infection and virus\u2013host interaction processes across entry, replication, and assembly stages. Some terms touch on host signaling or stress responses during infection, but the overarching theme is viral life cycle.","confidence":"High","size":13,"edges":27,"triangles":6,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0030260","count":2},{"id":"GO:0075713","count":2},{"id":"GO:0019076","count":2},{"id":"GO:1901407","count":2},{"id":"GO:0019068","count":2}]},{"hash":"1475551639268208160","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0015979","count":3},{"id":"GO:0018298","count":3},{"id":"GO:0016032","count":1},{"id":"GO:1903762","count":1}]},{"hash":"554951175570028774","title":"RNA metabolism and translation control","description":"Based on the Top Terms, the proteins are enriched for translation (GO:0006412), various RNA processing steps (GO:0016556 mRNA modification; GO:0006406 mRNA export from nucleus), and RNA-mediated gene silencing (GO:0031047 regulatory ncRNA-mediated gene silencing). Additional terms about translation initiation (IRES-dependent viral translational initiation) and stress responses to translation inhibitors (cycloheximide) support a theme centered on post-transcriptional control of gene expression. A few terms about plant development may reflect gene pleiotropy rather than a separate function of the cluster. Therefore, 'RNA metabolism and translation control' best captures the main shared function of this cluster.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0075522","count":2},{"id":"GO:0046898","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0009908","count":1}]},{"hash":"1677682462099598461","title":"Nuclear transcription and telomere regulation","description":"The top GO terms cluster around core nuclear functions: DNA-templated transcription, mRNA processing, and regulation of protein export from the nucleus, as well as telomere maintenance/capping. This suggests the proteins collectively participate in nuclear gene expression control and telomere biology. Other terms like cell migration and response to muscle stretch may reflect broader signaling roles but do not redefine the central nuclear-focused theme.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0045444","count":3},{"id":"GO:0032212","count":3},{"id":"GO:1904355","count":3},{"id":"GO:0045736","count":3}]},{"hash":"1812790292656770370","title":"Chromatin assembly and mitotic chromosome segregation","description":"The cluster is enriched for nuclear processes like CENP-A\u2013containing chromatin assembly, DNA replication, transcription, and microtubule severing, all central to chromosome maintenance and segregation during cell division; ER-associated terms appear as noise rather than defining features.","confidence":"High","size":13,"edges":9,"triangles":3,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0030433","count":6},{"id":"GO:0034975","count":5},{"id":"GO:0006260","count":4},{"id":"GO:0018279","count":4}]},{"hash":"1347666277287510046","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":69,"triangles":203,"max_degree":12,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":10},{"id":"GO:0031047","count":10},{"id":"GO:0000398","count":9},{"id":"GO:0006369","count":9},{"id":"GO:0000393","count":8}]},{"hash":"1164401313913076257","title":"DNA Damage Response & Repair","description":"The cluster shows strong representation of DNA damage sensing and repair processes (interstrand cross-link repair, cisplatin and X-ray responses, replication-born DSB repair via sister chromatid exchange, mitotic recombination-dependent fork processing, and camptothecin/hydroxyurea responses), suggesting a cohesive DDR/repair module; the inclusion of protein homooligomerization hints at assembly of repair complexes. Oocyte maturation is less central but may reflect meiotic recombination links, not a dominant theme.","confidence":"High","size":13,"edges":24,"triangles":21,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":2},{"id":"GO:0072719","count":2},{"id":"GO:0036297","count":2},{"id":"GO:0010165","count":2},{"id":"GO:1990414","count":2}]},{"hash":"1878221104250537901","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001731","count":6},{"id":"GO:0002188","count":6},{"id":"GO:0000209","count":5},{"id":"GO:0000462","count":5},{"id":"GO:0048568","count":5}]},{"hash":"1199874813883344707","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051344","count":1},{"id":"GO:0097421","count":1},{"id":"GO:1903629","count":1},{"id":"GO:1903611","count":1},{"id":"GO:0019853","count":1}]},{"hash":"1747916616175293921","title":"Mitotic spindle dynamics and microtubule transport","description":"The cluster is enriched with GO terms tied to mitosis and microtubule function\u2014centrosome separation, metaphase chromosome alignment, spindle\u2013kinetochore attachments, and regulation of microtubule-based processes\u2014as well as plus-end-directed vesicle transport along microtubules, indicating a cohesive role in spindle dynamics and cytoskeletal regulation. Some terms also touch on development and stem cell homeostasis, but the dominant signal centers on mitotic microtubule activity.","confidence":"High","size":13,"edges":68,"triangles":201,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0007100","count":9},{"id":"GO:0007080","count":9},{"id":"GO:1990535","count":8},{"id":"GO:0099607","count":8},{"id":"GO:1990942","count":8}]},{"hash":"2093466362741445079","title":"Mitotic regulation and organelle distribution","description":"This cluster's top GO terms center on regulation of the mitotic cell cycle and maintenance of centrosome location, complemented by intracellular distribution of mitochondria and related protein-folding/complex-assembly processes. While a few development terms are present (e.g., atrial septum, striatum, ureter development), the dominant signal ties to cell division and intracellular organization, suggesting a module of mitotic control and organelle positioning.","confidence":"Medium","size":13,"edges":12,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051291","count":2},{"id":"GO:0051661","count":2},{"id":"GO:0003283","count":2},{"id":"GO:0007346","count":2},{"id":"GO:0048312","count":2}]},{"hash":"1439251127867572107","title":"Calcium-Responsive Signaling","description":"The cluster is dominated by GO:0071277 (cellular response to calcium ion) with multiple connected terms such as negative regulation of protein kinase activity, ERBB2 signaling, stomatal closure, dendrite extension, and transcriptional regulation, pointing to a core theme of calcium-mediated signal transduction and downstream gene regulation. Some terms like DNA replication and ubiquitin-dependent ERAD appear ancillary, suggesting the core function centers on calcium-responsive signaling rather than a single pathway. Overall, a calcium-driven signaling and transcriptional control theme fits best.","confidence":"Medium","size":13,"edges":60,"triangles":145,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0071277","count":5},{"id":"GO:0006260","count":3},{"id":"GO:0006469","count":3},{"id":"GO:0080148","count":3},{"id":"GO:0060548","count":3}]},{"hash":"1832482453408001942","title":"RNA processing and translation control with protein turnover","description":"This cluster is dominated by RNA processing and translation-related terms (formation of translation preinitiation complex, translation reinitiation, mRNA splicing) and by protein turnover (polyubiquitination, SCF-dependent proteasomal degradation), pointing to a core theme of gene expression regulation and protein homeostasis. Additional terms touch on chromatin organization and signaling/development contexts, but the strongest signal centers on RNA processing and translation with ubiquitin-mediated turnover.","confidence":"Medium","size":13,"edges":4,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001731","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0000398","count":4},{"id":"GO:0070262","count":3},{"id":"GO:0031497","count":3}]},{"hash":"890214990298360991","title":"Immune activation and antiviral stress responses","description":"The top GO terms point to immune-related activities: apoptotic cell clearance, positive regulation of T cell proliferation, cellular response to virus, and positive regulation of tolerance induction to self antigen. While there are also terms tied to general cellular trafficking and organ development, the strongest signal is immune signaling and host defense, with tolerance and clearance aspects suggesting coordinated immune regulation alongside stress responses.","confidence":"Medium","size":13,"edges":7,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043277","count":13},{"id":"GO:0046641","count":13},{"id":"GO:0060709","count":13},{"id":"GO:0006611","count":13},{"id":"GO:0061167","count":13}]},{"hash":"531465801279989884","title":"Flavonoid Biosynthesis and Phenylpropanoid Metabolism","description":"Most top GO terms point to biosynthesis and modification of flavonoids and related phenylpropanoids (kaempferol/quercetin/cyanidin glycosides, lignin metabolism). There are supportive glycosylation/ glucuronidation themes and a few outliers (e.g., axon localization) that seem noise. Overall, the cluster represents flavonoid and related phenylpropanoid metabolic processes.","confidence":"High","size":13,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006711","count":10},{"id":"GO:0030259","count":10},{"id":"GO:0052696","count":10},{"id":"GO:0070980","count":10},{"id":"GO:0033330","count":10}]},{"hash":"1729123452062942366","title":"Neural development and synaptic signaling","description":"This cluster is dominated by neural-related terms: substantia nigra development, regulation of branching morphogenesis of a nerve, and excitatory postsynaptic potential, pointing to neuronal development and synaptic activity. The ER-to-Golgi transport term supports secretory functions typical of neurons. Immune-related terms (T-helper 1 response, IL-12 production) and xenobiotic response appear as ancillary annotations and may reflect multifunctionality or annotation noise. Overall, the core theme is neural development and synaptic signaling with some immune associations.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042088","count":3},{"id":"GO:0006888","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0021762","count":2},{"id":"GO:0030437","count":2}]},{"hash":"2266416512982469421","title":"Trafficking and cytoskeleton dynamics","description":"This cluster centers on intracellular membrane trafficking (Golgi organization, endosome-to-Golgi transport, vacuole fusion) and cytoskeletal regulation (cell shape, Rho signaling), with supporting links to autophagy and cell division. The GO terms point to coordinated organelle dynamics and membrane traffic influenced by cytoskeletal signals, suggesting a coherent functional theme around trafficking coupled to cytoskeletal remodeling.","confidence":"Medium","size":13,"edges":18,"triangles":8,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":4},{"id":"GO:1903358","count":3},{"id":"GO:0008360","count":3},{"id":"GO:0034498","count":3},{"id":"GO:0042144","count":3}]},{"hash":"1120638170776602039","title":"Drosophila development and signaling","description":"The top GO terms point to tissue-specific development in an insect (cuticle, retina, nurse cell\u2013oocyte transport) alongside signaling and regulatory processes (response to cAMP, protein dephosphorylation) and stress responses, suggesting a module that coordinates morphogenesis and signaling during development. Confidence: Medium","confidence":"","size":13,"edges":13,"triangles":1,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0051591","count":3},{"id":"GO:0050665","count":3},{"id":"GO:0008365","count":3},{"id":"GO:0042403","count":3},{"id":"GO:0042554","count":3}]},{"hash":"1258600380435584741","title":"Unknown","description":"The top GO terms span immune-related processes (apoptotic cell clearance, positive regulation of T cell proliferation, tolerance induction to self antigen, cellular response to virus) alongside development and cellular processes (placenta differentiation, organ regeneration, protein export from nucleus, ER polarization, meiotic DSB processing, parathyroid hormone secretion). The terms do not coalesce into a single clear function or pathway, and the disconnected themes suggest no cohesive label can capture the cluster beyond Unknown.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043277","count":13},{"id":"GO:0046641","count":13},{"id":"GO:0060709","count":13},{"id":"GO:0006611","count":13},{"id":"GO:0061167","count":13}]},{"hash":"1080079425369480980","title":"RNA methylation and translation initiation","description":"This cluster is dominated by RNA modification and protein synthesis signals, including RNA (guanine-N7)-methylation, tRNA methylation, rRNA methylation, and translation preinitiation/reinitiation. While there are some vesicle trafficking and actin-regulation terms present, these are less represented. Therefore, the core theme appears to be RNA maturation/modification feeding into translation initiation.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034316","count":3},{"id":"GO:0070262","count":3},{"id":"GO:0036265","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0001731","count":3}]},{"hash":"1266635542190965045","title":"Chromatin regulation and transcription control","description":"The cluster is enriched for nuclear gene-expression processes: DNA-templated transcription, chromatin organization and histone modification (H3K27 methylation), plus ribosome biogenesis and translation, and ubiquitin-proteasome\u2013dependent protein turnover. This combination suggests a cohesive theme around regulation of transcription and chromatin state, with associated proteostasis mechanisms.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0061087","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0000122","count":2},{"id":"GO:0006412","count":2}]},{"hash":"389980930741240553","title":"Neuronal signaling and mitochondrial regulation","description":"The top GO terms include neural-function related processes (neuron-neuron synaptic transmission, behavioral fear response, CNS myelin maintenance) and mitochondrial-related processes (protein import into mitochondrial matrix, calcium import into the mitochondrion, regulation of ROS). This points to a cohesive theme where neuronal signaling depends on mitochondrial function and calcium/ROS handling. Some epithelial differentiation and lipid metabolism terms appear less connected, but do not override the dominant neural-mitochondrial pattern.","confidence":"High","size":13,"edges":13,"triangles":6,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0001949","count":3},{"id":"GO:0032286","count":3},{"id":"GO:0006675","count":3},{"id":"GO:0030150","count":3},{"id":"GO:2000378","count":3}]},{"hash":"1649193462913119142","title":"Flavonoid Biosynthesis and Lignin Metabolism","description":"The top GO terms point strongly to flavonoid pathway activities (anthocyanin-containing compounds, kaempferol/quercetin O-glucoside biosynthesis, flavonoid glycosylation) and related phenylpropanoid derivatives, including lignin biosynthesis. A cohesive theme across these terms is plant secondary metabolism centered on flavonoids and lignin, with some broader metabolic associations. Confidence: High","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009718","count":9},{"id":"GO:0006711","count":7},{"id":"GO:0030259","count":7},{"id":"GO:0052696","count":7},{"id":"GO:0070980","count":7}]},{"hash":"122873531240909005","title":"Xenobiotic response and detoxification","description":"The top GO terms are dominated by cellular response to xenobiotic stimulus and response to toxic substances, with supporting detoxification activity (oxidant detoxification). Although some metabolic processes appear (glycogen regulation, biotin biosynthesis), the xenobiotic/toxic response theme best represents the cluster.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000082","count":3},{"id":"GO:0005981","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0042220","count":2},{"id":"GO:0005979","count":2}]},{"hash":"1984088570059880321","title":"N-terminal peptide methyltransferases","description":"The top GO terms are dominated by various N-terminal peptidyl methylation reactions (glycine, alanine, serine, lysine) and related methylation activities, with a few other methylation-centric processes (e.g., rRNA methylation). This pattern suggests a cluster of methyltransferase enzymes targeting N-terminal residues, alongside broader methylation pathways, rather than a single biosynthetic pathway.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018013","count":3},{"id":"GO:0009102","count":3},{"id":"GO:0009236","count":3},{"id":"GO:0018012","count":3},{"id":"GO:0031167","count":3}]},{"hash":"1045648646568600617","title":"Immunoglobulin diversification and DNA recombination","description":"This cluster is dominated by terms related to immunoglobulin gene diversification, including isotype switching to IgG and IgA and somatic hypermutation, along with several DNA recombination/repair processes (interstrand cross-link repair, removal of nonhomologous ends, negative regulation of DNA recombination). Some terms like oxidative phosphorylation and mating-type gene conversion are less aligned and may reflect background noise, but the core theme centers on antibody gene diversification via recombination and repair.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006119","count":1},{"id":"GO:0048304","count":1},{"id":"GO:0043570","count":1},{"id":"GO:0007534","count":1},{"id":"GO:0048298","count":1}]},{"hash":"396377971495828746","title":"Apoptosis and Growth Signaling","description":"The cluster's terms include apoptotic process and apoptotic cell clearance, pathways like Hippo and Wnt signaling that regulate cell proliferation, and GO terms for DNA replication and transcription, as well as differentiation processes (keratinocyte differentiation) and cell fate decisions (sperm capacitation, chemotaxis). This mix points to proteins tied to controlling cell survival, division, and development through signaling networks, and thus a theme of apoptosis coupled with growth/fate signaling.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006915","count":5},{"id":"GO:0006935","count":5},{"id":"GO:0030216","count":5},{"id":"GO:0035329","count":5},{"id":"GO:0006260","count":5}]},{"hash":"1086460490435095341","title":"mRNA Decapping and NMD with Stress Granule Localization","description":"This cluster is driven by GO terms related to mRNA processing, deadenylation-dependent and -independent decapping, nonsense-mediated decay, and miRNA-mediated post-transcriptional gene silencing, plus a term for localization to cytoplasmic stress granules. These collectively point to a shared role in mRNA turnover and translational control under stress, with a few seemingly unrelated terms present as noise. Confidence: High","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006891","count":1},{"id":"GO:0009860","count":1},{"id":"GO:0032258","count":1},{"id":"GO:0000290","count":1},{"id":"GO:0006397","count":1}]},{"hash":"2085935862531057271","title":"Organellar RNA Processing and Translation Regulation","description":"This cluster is dominated by GO terms related to chloroplast/plastid RNA processing, plastid transcription, chloroplast RNA processing, mitochondrial mRNA processing, and regulation of mitochondrial translation, along with RNA editing and snoRNP assembly. These collectively point to RNA metabolism and expression control in plant organelles (chloroplasts/plastids and mitochondria), suggesting a cohesive functional theme across the proteins.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0000492","count":3},{"id":"GO:0010019","count":2},{"id":"GO:0031426","count":2},{"id":"GO:0016554","count":2}]},{"hash":"1638375432659737424","title":"Plant cell wall biogenesis and remodeling","description":"The cluster is dominated by GO terms tied to plant cell wall construction and modification (cell wall biogenesis, plant-type cell wall modification, xyloglucan metabolism, fungal-type cell wall organization). While there are additional plant-specific developmental and photosynthesis terms, the prevailing signal centers on plant cell wall biosynthesis and remodeling, supporting a cohesive functional theme for this cluster.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032491","count":3},{"id":"GO:0009831","count":3},{"id":"GO:0006037","count":3},{"id":"GO:0080086","count":3},{"id":"GO:0010411","count":3}]},{"hash":"44124312675344816","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":9},{"id":"GO:0090617","count":9},{"id":"GO:0042793","count":9},{"id":"GO:1905639","count":9},{"id":"GO:1900865","count":9}]},{"hash":"2160343222627882080","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051291","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000480","count":2}]},{"hash":"403626948232463955","title":"Unknown","description":"The GO terms are highly heterogeneous: several apoptosis-related terms (positive regulation of neuron apoptotic process, apoptotic DNA fragmentation, ectopic germ cell programmed cell death) occur alongside stress-related terms (response to antibiotic, response to TNF) but others point to plant/biochemical processes (pectin catabolic process, cell wall modification) and differentiation (erythrocyte differentiation). This lack of a single cohesive theme makes a concise, representative label unreliable. ","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0009405","count":1},{"id":"GO:0042545","count":1},{"id":"GO:0045490","count":1},{"id":"GO:0035234","count":1}]},{"hash":"1166153257113200268","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090617","count":3},{"id":"GO:1905639","count":3},{"id":"GO:1900865","count":3},{"id":"GO:0042793","count":3},{"id":"GO:0010019","count":3}]},{"hash":"734694746015903349","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090617","count":1},{"id":"GO:0042793","count":1},{"id":"GO:1905639","count":1},{"id":"GO:1900865","count":1},{"id":"GO:0070129","count":1}]},{"hash":"2107316139269525765","title":"Unknown","description":"The terms span transcriptional regulation and chromatin modification, proteolysis, endocytosis, and several metabolism processes with no clear common theme and no protein\u2013protein edges, so a specific, representative label cannot be assigned.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0000183","count":2},{"id":"GO:0007039","count":1},{"id":"GO:0006879","count":1}]},{"hash":"94571291721138982","title":"Nucleotide metabolism and salvage","description":"The cluster is dominated by GO terms for nucleotide phosphorylation, nucleotide biosynthesis (ADP/AMP/ITP), CDP biosynthesis, and purine ribonucleotide interconversion, pointing to a shared role in nucleotide metabolism and energy-currency turnover. Brain and liver development terms appear as potential tissue associations rather than core functions.","confidence":"High","size":12,"edges":46,"triangles":83,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0046939","count":4},{"id":"GO:0046940","count":4},{"id":"GO:0046705","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0001889","count":3}]},{"hash":"527251824604858024","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051291","count":3},{"id":"GO:0015979","count":2},{"id":"GO:0006189","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006564","count":2}]},{"hash":"794454708030047277","title":"Amino acid catabolism and hormonal signaling","description":"This cluster is enriched for several amino acid catabolic processes (serine, alanine, glycine, cysteine, kynurenine/tryptophan) and signaling responses (cAMP, glucocorticoid), with Notch signaling also represented. The common theme appears to be amino acid metabolism linked to cellular signaling pathways, suggesting a metabolic-hormonal signaling module.","confidence":"Medium","size":12,"edges":34,"triangles":60,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006564","count":5},{"id":"GO:0042853","count":4},{"id":"GO:0009436","count":4},{"id":"GO:0097053","count":4},{"id":"GO:0007219","count":4}]},{"hash":"339395709085644940","title":"Retinoid, lipid, and sugar metabolism","description":"The cluster centers on broad metabolic pathways, including retinol/retinoic acid metabolism, fatty acid biosynthesis, and fructose metabolism, with related ethanol metabolism. The presence of stress-response terms (copper ion, LPS) may reflect regulation under challenging conditions, but the dominant signal is core metabolism across lipids, sugars, and retinoids, justifying a metabolism-focused label.","confidence":"Medium","size":12,"edges":64,"triangles":201,"max_degree":11,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0046370","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0042572","count":5},{"id":"GO:0006633","count":5},{"id":"GO:0042573","count":4}]},{"hash":"2028418323758638013","title":"Alkaloid and lipid metabolism","description":"The cluster centers on metabolism of diverse organic compounds, especially alkaloids (isoquinoline, camphor catabolic) and lipids (triglyceride metabolism, bile acid biosynthesis), indicating a general metabolic processing theme. Some ion-response terms are present but do not override the dominant metabolic pattern.","confidence":"Medium","size":12,"edges":15,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009822","count":10},{"id":"GO:0006641","count":10},{"id":"GO:0071615","count":10},{"id":"GO:0034653","count":10},{"id":"GO:0033076","count":10}]},{"hash":"1752129168720118346","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":4},{"id":"GO:0090617","count":4},{"id":"GO:1905639","count":4},{"id":"GO:1900865","count":4},{"id":"GO:0042793","count":4}]},{"hash":"2084588745150782338","title":"mRNA Splicing and Processing Regulation","description":"The dominant GO terms indicate involvement in splicing via the spliceosome, polyadenylation, mRNA export, modification, and regulation of mRNA stability and alternative splicing, all pointing to a cluster of proteins dedicated to mRNA maturation and post-transcriptional control. The combination of spliceosome activity and regulatory processes suggests a cohesive role in RNA processing rather than a single enzymatic function.","confidence":"High","size":12,"edges":6,"triangles":0,"max_degree":3,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":8},{"id":"GO:0045292","count":7},{"id":"GO:0010610","count":6},{"id":"GO:0006376","count":5},{"id":"GO:0098789","count":5}]},{"hash":"2071524413286601297","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030154","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0090615","count":1},{"id":"GO:0090617","count":1}]},{"hash":"747450090517792040","title":"Flavonoid Glycoside Biosynthesis and Polyphenol Metabolism","description":"This cluster is driven by GO terms for biosynthesis of flavonoid glycosides (kaempferol, quercetin, cyanidin), as well as related phenolic metabolism (lignin) and glycosylation/xenobiotic processes, suggesting a module focused on polyphenol production and modification. One term about axon paranode localization appears unrelated and may reflect annotation noise.","confidence":"Medium","size":12,"edges":61,"triangles":180,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006711","count":8},{"id":"GO:0030259","count":8},{"id":"GO:0052696","count":8},{"id":"GO:0070980","count":8},{"id":"GO:0033330","count":8}]},{"hash":"1565469829602682592","title":"Mitochondrial Transporters","description":"The cluster is strongly enriched for transmembrane transport functions, especially mitochondrial ATP transport and related nucleotide transport (ADP, NAD) as well as other small-molecule transports (TPP, glycine, thiosulfate). This pattern points to mitochondrial carrier proteins that mediate metabolite exchange across the mitochondrial membrane. A few terms related to development or stress responses are tangential, but the dominant theme is mitochondrial transport. ","confidence":"High","size":12,"edges":18,"triangles":1,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:1990544","count":7},{"id":"GO:0097421","count":7},{"id":"GO:0032869","count":7},{"id":"GO:0007565","count":7},{"id":"GO:0030974","count":7}]},{"hash":"936250347392697754","title":"Plant Hormone Signaling and Metabolism","description":"This cluster centers on plant hormone signaling (cytokinin-activated pathway) and related metabolic responses, including hormone biosynthesis regulation and plant-specific catabolic processes (glucosinolates, cellulose).","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009736","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0019762","count":3},{"id":"GO:0019512","count":3},{"id":"GO:0008286","count":3}]},{"hash":"161388395270539162","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":3},{"id":"GO:0090617","count":3},{"id":"GO:0042793","count":3},{"id":"GO:1905639","count":3},{"id":"GO:1900865","count":3}]},{"hash":"1878436152073994423","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":12,"triangles":6,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000398","count":5},{"id":"GO:0048026","count":4},{"id":"GO:0031047","count":4},{"id":"GO:0071035","count":3},{"id":"GO:0000467","count":3}]},{"hash":"375486129010422763","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010019","count":5},{"id":"GO:0031426","count":5},{"id":"GO:0016554","count":5},{"id":"GO:0090615","count":5},{"id":"GO:0070129","count":5}]},{"hash":"2162658090254717895","title":"Ubiquitin-Dependent Protein Degradation","description":"The top GO terms reveal a strong emphasis on ubiquitination and proteasomal protein catabolism (protein ubiquitination, polyubiquitination, autoubiquitination, SCF-dependent ubiquitin-dependent protein catabolic process, and K6-linked ubiquitination). This indicates a cohesive cluster centered on tagging proteins with ubiquitin for degradation, including histone turnover via ubiquitination. A few other terms (response to vitamin D, TNF signaling) appear as peripheral associations rather than core functions.","confidence":"High","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042787","count":8},{"id":"GO:0016567","count":5},{"id":"GO:0000209","count":5},{"id":"GO:1903265","count":5},{"id":"GO:0051865","count":5}]},{"hash":"480047818050528457","title":"Neural development and innate immune signaling","description":"This cluster combines strong neural development signals (regulation of branching morphogenesis of a nerve, axonal fasciculation, synapse assembly) with innate immune cues (TLR4/10 signaling, detection of lipopolysaccharide, I-kappaB phosphorylation), suggesting a set of proteins involved in neuroimmune signaling during development. The theme is coherent, though the immune terms may reflect cross-talk rather than classical neuronal roles.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":4},{"id":"GO:0007275","count":2},{"id":"GO:2000172","count":2},{"id":"GO:0002730","count":2},{"id":"GO:0007413","count":2}]},{"hash":"616071812515815473","title":"Ribosome biogenesis and translation with mRNA decay","description":"The cluster centers on rRNA maturation (SSU/LSU/5.8S) and translation processes (initiation, termination), with additional RNA surveillance and decay pathways (no-go decay, non-stop decay) and a note of ubiquitination, suggesting a group involved in ribosome assembly/translation and associated quality control 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:0016567","count":2},{"id":"GO:0000462","count":1},{"id":"GO:0071025","count":1},{"id":"GO:0070966","count":1},{"id":"GO:0006412","count":1}]},{"hash":"1747052382753000596","title":"Chitin and peptidoglycan cell-wall metabolism","description":"This cluster centers on cell-wall metabolism, especially chitin and peptidoglycan turnover, including both biosynthesis and catabolic processes. A few outlier terms (transcription/repair) are present but do not override the core cell-wall theme.","confidence":"High","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035948","count":2},{"id":"GO:0070816","count":1},{"id":"GO:0006360","count":1},{"id":"GO:0006289","count":1},{"id":"GO:0016998","count":1}]},{"hash":"1222248938551322357","title":"Neural and Visual System Development","description":"The top GO terms cluster around development of the nervous and visual systems\u2014forebrain and cerebellum development, retinal ganglion cell axon guidance, visual perception, and motor neuron axon guidance\u2014indicating proteins involved in neural and sensory tissue formation and guidance during embryogenesis. Some terms also reflect general embryonic development, but the neural/sensory pattern is the strongest signal.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":2},{"id":"GO:0031290","count":2},{"id":"GO:0048701","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0001890","count":2}]},{"hash":"1125171587345367369","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":22,"triangles":11,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0046444","count":1},{"id":"GO:0006747","count":1},{"id":"GO:0019350","count":1},{"id":"GO:1990966","count":1}]},{"hash":"2197813276591696840","title":"Spliceosome-Mediated mRNA Processing","description":"This cluster is dominated by GO terms related to mRNA maturation and processing\u2014splicing via the spliceosome, polyadenylation, export from the nucleus, modification, and stabilization\u2014suggesting a cohesive group of proteins involved in RNA processing and regulation of alternative splicing. A couple of outlier terms (blastocyst formation, viral translation termination-reinitiation) do not obscure the central theme.","confidence":"High","size":12,"edges":30,"triangles":37,"max_degree":10,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":11},{"id":"GO:0006378","count":11},{"id":"GO:0016556","count":10},{"id":"GO:0006406","count":10},{"id":"GO:0031047","count":10}]},{"hash":"1250599729372417559","title":"Nuclear transcription and chromatin regulation","description":"The listed terms cluster around nuclear gene expression processes: transcription initiation/ regulation (DNA-templated transcription), chromatin-related activities (SAGA complex localization, histone deubiquitination), mRNA processing/export, and genome maintenance (proteasome-related assembly; homologous recombination repair). Development terms appear less central but may reflect broader regulation roles, not a distinct pathway. Overall, these proteins seem to function in nuclear gene expression and chromatin/genome maintenance. ","confidence":"Medium","size":12,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043248","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0006406","count":1},{"id":"GO:0040025","count":1},{"id":"GO:0072742","count":1}]},{"hash":"541245196449250421","title":"Ubiquitin-Mediated Protein Regulation","description":"The top GO terms are all centered on ubiquitination and ubiquitin-dependent processes (protein ubiquitination, autoubiquitination, ubiquitin-dependent ERAD, K48- and K6-linked ubiquitination, and ubiquitin-dependent catabolic processes). This suggests the cluster members are primarily involved in tagging proteins for degradation or in ubiquitin signaling pathways, with additional links to peroxisomal protein import and NF-kappaB signaling, both of which can be regulated via ubiquitination. Overall, a cohesive theme is ubiquitin-mediated control of protein fate.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":6},{"id":"GO:0016567","count":6},{"id":"GO:0030433","count":6},{"id":"GO:1903762","count":5},{"id":"GO:0042787","count":5}]},{"hash":"1865804031528372407","title":"Cell Division and Growth Machinery","description":"The top GO terms point to cellular proliferation and development, including cell division, mitotic cell cycle, cell septum assembly, spermatid development, and multicellular organism growth. Additional terms for ribosomal subunit biogenesis and tRNA modification reflect essential biosynthetic processes that support growth, while the cytokinin-activated signaling pathway suggests plant-specific growth regulation. Altogether, the cluster appears to group proteins involved in cell proliferation and the core biosynthetic machinery needed for growth and division.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0007286","count":2},{"id":"GO:0035264","count":2},{"id":"GO:0009736","count":2},{"id":"GO:0000278","count":2}]},{"hash":"1793412396067493603","title":"Cellular Stress Response and Protein Quality Control","description":"This cluster is enriched for stress-response GO terms (response to heat, hydrogen peroxide, xenobiotic stimulus, estradiol) and the ubiquitin-dependent ERAD pathway, plus regulation of peptidase activity, suggesting a common theme of cellular stress management and protein quality control in ER/mitochondrial contexts; some signaling/adhesion terms (SREBP pathway, cadherin-mediated adhesion) may reflect downstream adaptive responses.","confidence":"Medium","size":12,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0032355","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0042542","count":2},{"id":"GO:0009408","count":2}]},{"hash":"2050226250831733555","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0010923","count":1},{"id":"GO:0000472","count":1},{"id":"GO:0000480","count":1},{"id":"GO:0001708","count":1}]},{"hash":"1323934616401382447","title":"Chromatin Remodeling and Histone Modification","description":"Reason: The cluster\u2019s top GO terms cluster around nucleosome assembly/disassembly and regulation of histone acetylation, indicating chromatin remodeling as the central theme. While there are also hints of cell-cycle and cytoskeletal processes, the recurring chromatin-related terms best define the group.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007117","count":1},{"id":"GO:0015031","count":1},{"id":"GO:0006337","count":1},{"id":"GO:0071442","count":1},{"id":"GO:0031116","count":1}]},{"hash":"1006737788902569064","title":"Vesicle trafficking and cell cycle control","description":"The top GO terms cluster around ER-to-Golgi and inter-Golgi vesicle transport, along with ubiquitin-dependent ERAD, and core cell cycle processes (cell division, cell cycle). This points to a functional module centered on intracellular trafficking linked to proliferation control. Some terms like chitin-based larval cuticle pattern formation and root development appear as noise, but the dominant signal supports vesicle trafficking integrated with cell cycle regulation.","confidence":"Medium","size":12,"edges":13,"triangles":4,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0007049","count":2},{"id":"GO:0043547","count":2}]},{"hash":"893221658261280549","title":"Plant Development and Cuticle Biosynthesis Regulation","description":"The dominant GO terms point to plant development processes (multicellular organism development, floral meristem growth, bract and seed development) along with cuticle biosynthesis (wax and cutin) and ABA signaling, plus transcriptional regulation. This suggests a cluster of regulatory proteins coordinating reproductive/seed development and epidermal barrier formation, potentially transcription factors governing these pathways. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:1904276","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:1901959","count":2}]},{"hash":"1478816426313929894","title":"Cell Division and Vesicle Trafficking","description":"The proteins cluster around mitotic processes (mitotic cell cycle, cell division) and multiple vesicle trafficking and secretion pathways (endosome to lysosome transport, regulation of the secretory pathway, synaptic vesicle exocytosis), with supporting terms on organelle inheritance and protein complex assembly. This pattern suggests a shared function in coordinating cell division with intracellular transport and secretion activities.","confidence":"Medium","size":12,"edges":10,"triangles":2,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010796","count":5},{"id":"GO:0031384","count":5},{"id":"GO:0000278","count":4},{"id":"GO:0051301","count":4},{"id":"GO:2000300","count":3}]},{"hash":"1927936446254808986","title":"Cellular trafficking and motility","description":"Top GO terms indicate multiple aspects of cellular movement and trafficking, including cell migration, adherens junction assembly, and centriole-related processes, along with transport activities such as nucleocytoplasmic import/export and vesicle/ERAD trafficking, and regulation of GTPase signaling. While not all terms point to a single function, the unifying theme is proteins involved in moving cargo and coordinating cell movement within tissues, via cytoskeletal dynamics and membrane trafficking. Therefore the cluster is best named 'Cellular trafficking and motility'.","confidence":"Medium","size":12,"edges":32,"triangles":34,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0016477","count":5},{"id":"GO:0006607","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0015991","count":5},{"id":"GO:0006406","count":5}]},{"hash":"1956789780236613136","title":"DNA replication, transcription, and cell cycle control","description":"This cluster shows enrichment for nuclear processes: DNA replication, DNA-templated transcription, and cell cycle regulation (including mitotic cell cycle and G1/S transition control). The presence of dephosphorylation indicates broader regulatory control. Some terms (ER-Golgi transport, forebrain development, lymphangiogenesis, lipopolysaccharide biosynthesis) may reflect annotation noise or multifunctional roles, but the core terms point to gene expression and DNA replication/cell cycle machinery.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0016311","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0006351","count":2}]},{"hash":"505753878006273175","title":"Ubiquitin-proteasome regulation and chromatin organization","description":"The top GO terms center on ubiquitination and proteasomal degradation (polyubiquitination, SCF-dependent proteasomal degradation), together with chromatin organization and related regulation (dephosphorylation, cell cycle transitions). While there are additional signaling and developmental terms, the core pattern points to protein turnover intertwined with chromatin dynamics.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0070317","count":3},{"id":"GO:0070262","count":2},{"id":"GO:0031497","count":2},{"id":"GO:0000209","count":2}]},{"hash":"149276520519812300","title":"RNA methylation and tRNA modification enzymes","description":"The top GO terms are dominated by RNA-related methylation processes: RNA guanine-N7 methylation, mRNA capping, tRNA methylation, wobble uridine modification, and arginine methylation, which together suggest a cluster enriched for methyltransferase and RNA modification activities. Other terms (biosynthesis and stress/response genes) are more diverse and less central to this theme, so the label centers on RNA methylation/modification.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036265","count":4},{"id":"GO:0006370","count":4},{"id":"GO:0030488","count":4},{"id":"GO:0009877","count":4},{"id":"GO:0002098","count":4}]},{"hash":"1740043620238527537","title":"Autophagy and organelle turnover","description":"The top GO terms are dominated by autophagy-related processes (nucleophagy, mitophagy, autophagy in response to ER overload, and mitochondrial autophagy), plus supporting steps like protein lipidation and membrane targeting for autophagosome formation. Rho signaling and cilium assembly regulation appear ancillary. Overall, the cluster centers on autophagy-driven turnover of organelles.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":2},{"id":"GO:0034263","count":1},{"id":"GO:0034727","count":1},{"id":"GO:0006612","count":1},{"id":"GO:0006501","count":1}]},{"hash":"1624427775239465293","title":"Plant hormone signaling in defense and development","description":"The top GO terms include cytokinin-activated signaling, gibberellin-mediated signaling, defense responses, nodulation, and pollen development, indicating a theme of hormone-driven regulation of growth, reproduction, and biotic interactions in plants. Other terms about DNA maintenance appear incidental to the main function represented by this cluster.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009607","count":1},{"id":"GO:0009736","count":1},{"id":"GO:0006952","count":1},{"id":"GO:0009877","count":1},{"id":"GO:0009740","count":1}]},{"hash":"1231696465805711367","title":"Ubiquitin-regulated NF-kappaB/TNF immune signaling","description":"This cluster centers on protein ubiquitination with key roles in activating NF-kappaB and TNF-mediated signaling, along with an adaptive immune response. Additional terms point to antiviral regulation (RIG-I pathway and intracellular transport of viral material) and necroptosis control, suggesting a cohesive theme of ubiquitin-driven modulation of innate/adaptive immune signaling in antiviral defense.","confidence":"High","size":12,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":2},{"id":"GO:0007250","count":2},{"id":"GO:1901253","count":2},{"id":"GO:0033209","count":2},{"id":"GO:0039536","count":2}]},{"hash":"10598439661031989","title":"Amino acid biosynthesis and cofactor metabolism","description":"The cluster\u2019s top GO terms cluster around biosynthetic pathways for amino acids (lysine, tryptophan) and cofactors (biotin), plus related metabolite pathways like porphyrin/heme biosynthesis and central carbon metabolism (oxaloacetate). While there are also entries tied to transcription regulation and insulin response, the strongest, coherent theme is amino acid metabolism and cofactor biosynthesis, with several pathways tied to the production of essential metabolites. This suggests a metabolic instead of a purely regulatory cluster.","confidence":"Medium","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0033512","count":5},{"id":"GO:0009102","count":5},{"id":"GO:0019878","count":5},{"id":"GO:0006782","count":5},{"id":"GO:0019441","count":4}]},{"hash":"9254700687081101","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":8,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030150","count":2},{"id":"GO:0019805","count":2},{"id":"GO:0034354","count":2},{"id":"GO:0043420","count":2},{"id":"GO:0000105","count":2}]},{"hash":"1777944187718705700","title":"Organelle Cofactor Biosynthesis","description":"The cluster is enriched for various cofactor biosynthesis processes (heme O, menaquinone, ubiquinone, phylloquinone, chlorophyll, vitamin K), suggesting a shared role in organelle-based production of essential cofactors. While there are mitochondrial-specific terms, the dominant theme centers on biosynthesis of cofactors across organelles. Confidence: Medium","confidence":"","size":11,"edges":27,"triangles":24,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0045041","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0042407","count":1},{"id":"GO:0051560","count":1},{"id":"GO:0009234","count":1}]},{"hash":"542061481424059514","title":"Organ Development and Stress Response","description":"The top GO terms include multiple organ development processes (ovarian follicle, retina, placenta, thymus) alongside DNA replication/repair and stress responses (hydrogen peroxide, cadmium, SOS). This suggests proteins involved in developmental pathways that also participate in cellular stress responses, so the label reflects the combined themes without overfitting to a single function.","confidence":"Medium","size":11,"edges":7,"triangles":4,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0001541","count":3},{"id":"GO:0042542","count":3},{"id":"GO:0001895","count":3},{"id":"GO:0000187","count":3}]},{"hash":"1029656181235240793","title":"Redox Detoxification and Antioxidant Metabolism","description":"This cluster centers on oxidative stress management and detox pathways, with strong signals for cellular oxidant detoxification, redox homeostasis, toxin catabolic processes, arsenic response, and L-ascorbic acid metabolism. The presence of mitochondrial membrane potential and calcium release regulation suggests links to mitochondrial and calcium signaling in stress responses, while prostaglandin biosynthesis and germ cell regulation appear more peripheral but could reflect broader signaling context. Overall, the common theme is redox balance and detoxification.","confidence":"Medium","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":8},{"id":"GO:0045454","count":8},{"id":"GO:0001516","count":6},{"id":"GO:2000255","count":5},{"id":"GO:0010880","count":5}]},{"hash":"1897911861348919489","title":"Central carbon metabolism and energy production","description":"These proteins map to core carbon metabolism and energy production. Dominant GO terms cover glycolysis, the TCA cycle, gluconeogenesis, and the pentose phosphate pathway, with supportive terms for nutrient response and leucine catabolism, indicating a cluster of enzymes and regulators coordinating carbohydrate flux and energy generation. ","confidence":"High","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":7},{"id":"GO:0006096","count":6},{"id":"GO:0006094","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0007584","count":4}]},{"hash":"1542334492542452781","title":"RNA and protein methylation enzymes","description":"This cluster is dominated by methylation-related terms: rRNA methylation, guanine-N7 methylation, peptidyl-lysine dimethylation, and protein methylation, plus cobalamin biosynthesis which involves methyltransferases. While redox and other metabolism terms appear, the shared function centers on methyltransferase activities modifying RNA and proteins, making this label representative. ","confidence":"Medium","size":11,"edges":17,"triangles":8,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0009236","count":3},{"id":"GO:0018027","count":3},{"id":"GO:0031167","count":3},{"id":"GO:0070476","count":2}]},{"hash":"855346149734892155","title":"Alkaloid and lipid metabolism","description":"The GO terms cluster around the metabolism and catabolism of diverse small molecules, including alkaloids (carbazole, isoquinoline alkaloids), retinoic acid, bile acids, and triglycerides. This points to a broader theme of alkaloid and lipid-derived compound metabolism rather than a single precise pathway, with some peripheral terms (ion response, inflammation) being less central. Confidence in this thematic connection is Moderate.","confidence":"Medium","size":11,"edges":8,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046232","count":8},{"id":"GO:0009822","count":7},{"id":"GO:0006641","count":7},{"id":"GO:0071615","count":7},{"id":"GO:0034653","count":7}]},{"hash":"950422728178895983","title":"Unknown","description":"The GO terms span transcription, several lipid/metabolic processes, hormone and stress responses, RNA processing, and development, with no single dominant function tying the proteins together. The lack of a cohesive shared theme suggests the cluster is not functionally cohesive, so Unknown is appropriate.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0019395","count":2},{"id":"GO:0071375","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0071372","count":2}]},{"hash":"398339891506109555","title":"Ubiquitin-Proteasome System","description":"The Top Terms are dominated by ubiquitin-dependent proteolysis, including SCF-dependent proteasomal ubiquitin-mediated catabolic processes, K11-linked ubiquitination, autoubiquitination, and the ERAD pathway, with additional signals for sumoylation. This strongly points to a core function in tagging and degrading proteins (proteostasis). Some meiosis and signaling terms appear, but they are likely substrates or regulatory intersections rather than forming a separate module. Overall, the cluster centers on ubiquitin-mediated protein turnover.","confidence":"High","size":11,"edges":28,"triangles":32,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031146","count":7},{"id":"GO:0042787","count":7},{"id":"GO:0070979","count":5},{"id":"GO:0051865","count":5},{"id":"GO:0030433","count":5}]},{"hash":"1680729699772926827","title":"Neurodevelopment and cell junction formation","description":"Top terms indicate neural development and morphogenesis (cochlea morphogenesis, convergent extension in neural plate elongation, Rho signaling) and epithelial barrier assembly (bicellular tight junction assembly). Some outlier terms (aba biosynthesis, bile acid secretion) may reflect annotation noise or multifunctionality, but the dominant theme is neural development and cell junction organization, justifying this label.","confidence":"Medium","size":11,"edges":14,"triangles":8,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0009688","count":3},{"id":"GO:0035750","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0007266","count":2}]},{"hash":"1026275897366123594","title":"Lipid and small-molecule metabolism","description":"This cluster's terms cluster around metabolism of lipids (triglyceride metabolism, bile acid biosynthesis) and various small molecules (retinoic acid, alkaloid metabolism), with some ion-response terms that may reflect signaling rather than metabolism. The uterus development term appears as noise, suggesting possible annotation noise. Overall, the dominant theme is lipid and small-molecule metabolic processes.","confidence":"Medium","size":11,"edges":8,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0060065","count":7},{"id":"GO:0009822","count":6},{"id":"GO:0006641","count":6},{"id":"GO:0071615","count":6},{"id":"GO:0034653","count":6}]},{"hash":"2223848747001333886","title":"Amino sugar and polyamine metabolism","description":"The proteins show enrichment in metabolic processes involving amino sugars (glucosamine, N-acetylglucosamine) and polyamines (putrescine, spermidine, spermine), including their acetylation and catabolism, plus related pathways like mycothiol biosynthesis and N-terminal propionylation. A sporulation term is present but not dominant, so the core theme appears to be metabolism of amino-sugar and polyamine pathways. ","confidence":"Medium","size":11,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030435","count":4},{"id":"GO:0045150","count":3},{"id":"GO:0046208","count":3},{"id":"GO:0006041","count":3},{"id":"GO:0032918","count":3}]},{"hash":"604394930833329746","title":"Unknown","description":"The top GO terms are highly heterogeneous, including viral process, transcription, cell differentiation, receptor internalization, fruit ripening, and flavonoid biosynthesis, with several terms labeled obsolete. This mix spans plant- and animal-related processes and lacks a clear, cohesive theme, so a single interpretable label cannot be confidently assigned.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0048333","count":2}]},{"hash":"1524799875273622191","title":"DNA replication and transcription regulation","description":"Top terms center on cell division and DNA replication, plus transcription initiation regulation and mRNA export, with supporting energy metabolism terms. This points to a nuclear program coordinating genome duplication with gene expression, making this label representative of the cluster.","confidence":"Medium","size":11,"edges":15,"triangles":9,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0006260","count":5},{"id":"GO:0070389","count":5},{"id":"GO:0046034","count":4},{"id":"GO:0006406","count":4}]},{"hash":"1663754870270480228","title":"DNA Transcription Regulation","description":"The cluster is centered on DNA-templated transcription and regulation of transcription (with related DNA processes like recombination), suggesting a core theme of gene expression control; developmental terms likely reflect downstream effects of transcription factors. Some terms appear incidental, but the transcription-focused terms are the strongest signal.","confidence":"Medium","size":11,"edges":14,"triangles":7,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0007286","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0032508","count":2},{"id":"GO:0006310","count":2}]},{"hash":"920726670860606600","title":"Neuronal synapse assembly and vesicle trafficking","description":"This cluster is dominated by GO terms for brain development, synapse assembly, dendritic spine development, and vesicle transport/regulation of exocytosis, suggesting a cohesive role in neuronal synapse formation and intracellular vesicle dynamics.","confidence":"High","size":11,"edges":6,"triangles":0,"max_degree":2,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0007420","count":4},{"id":"GO:0007416","count":3},{"id":"GO:0060999","count":3},{"id":"GO:0043001","count":3},{"id":"GO:0006886","count":3}]},{"hash":"1864918286785525241","title":"Plant oxidative stress and cell wall remodeling","description":"This cluster is dominated by GO terms for oxidative stress response, detoxification of oxidants, and lignin-related cell wall organization in plants, pointing to roles in stress defense and cell wall remodeling; translation/transcription terms likely reflect general gene expression processes rather than a unifying function of the cluster.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0046274","count":1},{"id":"GO:0006979","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0042744","count":1}]},{"hash":"1577276969312952315","title":"Glycogen, starch, and trehalose metabolism","description":"Top GO terms cluster around alpha-glucan metabolism, including glycogen, starch, and trehalose biosynthesis and catabolism, as well as related sucrose breakdown. This indicates a cohesive theme of polysaccharide metabolism among the proteins, despite no observed interactions. ","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030980","count":1},{"id":"GO:0044245","count":1},{"id":"GO:0005978","count":1},{"id":"GO:0005983","count":1},{"id":"GO:0030979","count":1}]},{"hash":"997307329393104040","title":"Cell Cycle and Growth Regulation","description":"The leading GO terms cluster around cell proliferation and growth, with clear signals for cell cycle and cell division (cell cycle, cell division, budding cell apical bud growth) and kinase-regulated growth signaling (positive regulation of peptidyl-threonine phosphorylation). While terms like angiogenesis, retina vasculature development, defense response, and metabolic pathways appear, they are more peripheral annotations to broader growth and signaling roles. Overall, the proteins likely participate in cell cycle control and growth-related signaling.","confidence":"Medium","size":11,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0007118","count":2},{"id":"GO:0010800","count":2},{"id":"GO:0014068","count":2}]},{"hash":"1608721925546419220","title":"Ribosome biogenesis and rRNA processing","description":"The Top Terms point strongly to ribosome assembly and RNA maturation, with multiple terms for preribosome/large subunit assembly, maturation of LSU and 5.8S rRNA, cytosolic ribosome assembly, and rRNA/base methylation. The presence of transcription-related terms is peripheral; the core theme is ribosome biogenesis and rRNA processing, possibly with some linkage to mitochondrial translation. ","confidence":"High","size":11,"edges":14,"triangles":5,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:1902626","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0070131","count":2}]},{"hash":"1749505369941135347","title":"Wnt-regulated neurodevelopment and migration","description":"The top GO terms point to developmental signaling with Wnt pathway inhibition, controlling cell proliferation and promoting apoptosis, alongside cell migration/chemotaxis and neural differentiation (including midbrain dopaminergic neurons). While cell cycle terms (DNA replication, cell division) appear, the strongest cohesive theme is developmental signaling linked to neurodevelopment and neuronal positioning/migration, modulated by Wnt. Confidence: Medium","confidence":"","size":11,"edges":6,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0008285","count":5},{"id":"GO:0090090","count":5},{"id":"GO:0043065","count":5},{"id":"GO:0016477","count":5},{"id":"GO:0006260","count":4}]},{"hash":"2145639747765776236","title":"Neural development and actin remodeling","description":"The top GO terms cluster around brain development, neural axis specification, and regulation of synaptic vesicle exocytosis, together with multiple actin cytoskeleton processes (formin-nucleated assembly, polymerization, stress fiber assembly) and Rho signaling. This pattern suggests a functional module coordinating neural development with actin-driven neuronal morphology and synaptic regulation.","confidence":"High","size":11,"edges":47,"triangles":110,"max_degree":10,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:2000300","count":8},{"id":"GO:0010796","count":6},{"id":"GO:0007420","count":6},{"id":"GO:0031384","count":6},{"id":"GO:0090338","count":4}]},{"hash":"627515692591466539","title":"Ribosome Assembly and Translation","description":"This cluster is dominated by GO terms related to ribosomal large subunit assembly and translation, indicating involvement in protein synthesis machinery. The other terms appear sporadic (e.g., heart development, olfactory nerve development, transcription regulation), suggesting they are not representative of the core function for these proteins. Overall, the strongest signal points to ribosome assembly and translation.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000027","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0003226","count":1},{"id":"GO:2000270","count":1},{"id":"GO:2001229","count":1}]},{"hash":"619857107457930756","title":"Endosomal trafficking and iron transport","description":"The terms point to intracellular handling of proteins via endocytic/lysosomal pathways (receptor-mediated endocytosis, transferrin transport, vacuolar proteolysis) and iron homeostasis, with supporting roles from deubiquitination and ERAD-related maintenance that can regulate trafficking and turnover. The cluster thus seems to reflect coordinated protein turnover and iron handling within the endolysosomal system.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044313","count":2},{"id":"GO:0035523","count":2},{"id":"GO:1904378","count":2},{"id":"GO:0007039","count":2},{"id":"GO:0006879","count":2}]},{"hash":"1618410784562432816","title":"RNA Maturation and Modification","description":"The top GO terms cluster around RNA processing and chemical modifications: rRNA processing (ITS1 cleavage), RNA guanine-N7 methylation, mRNA capping, and tRNA methylation, which together point to RNA maturation and modification as the core theme. The other terms (sterol/ubiquinone/polyamine biosynthesis) appear peripheral, suggesting additional housekeeping metabolism but not forming a cohesive alternative core. Hence this label is a reasonable, though not exclusive, representation of the cluster\u2019s function.","confidence":"Medium","size":11,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030961","count":1},{"id":"GO:0016126","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0043985","count":1},{"id":"GO:0001300","count":1}]},{"hash":"1293699610600935678","title":"Oxidative Stress Response","description":"Dominated by terms for hydrogen peroxide response and ROS regulation, with additional links to light-induced stress; overall points to a function in managing oxidative stress and light-related damage, despite a few unrelated terms (e.g., lens morphogenesis) appearing in the set.","confidence":"High","size":11,"edges":23,"triangles":19,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0042542","count":5},{"id":"GO:2000378","count":4},{"id":"GO:0032355","count":3},{"id":"GO:0007568","count":3},{"id":"GO:0014070","count":3}]},{"hash":"893002667571713208","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":6},{"id":"GO:1903762","count":5},{"id":"GO:0042787","count":5},{"id":"GO:0061158","count":5},{"id":"GO:0002635","count":5}]},{"hash":"296550244803304855","title":"Plant organ development and senescence regulation","description":"The top terms point to a broad set of plant development processes (timing of organ formation, fruit dehiscence, protoxylem development, root cap and sieve element formation, callus formation) plus transcriptional regulation, and also include leaf senescence and age-related resistance. This suggests a cluster of proteins involved in coordinating plant organogenesis and aging/defense programs rather than a single specific pathway.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090709","count":1},{"id":"GO:0010047","count":1},{"id":"GO:0090059","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0006355","count":1}]},{"hash":"1990048070780290003","title":"Neurodevelopment and DNA maintenance","description":"These proteins appear linked to neural development processes (forebrain development, neural tube closure, embryonic cranial skeleton morphogenesis, dendrite morphogenesis, multicellular development) and also to genome maintenance (DNA replication, DNA repair, DNA-templated transcription), suggesting a cluster of factors involved in neural development with roles in DNA maintenance during replication/proliferation.","confidence":"Medium","size":11,"edges":8,"triangles":0,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":11},{"id":"GO:0048701","count":10},{"id":"GO:0006281","count":10},{"id":"GO:0048813","count":10},{"id":"GO:0070059","count":10}]},{"hash":"275871166921819201","title":"Lignan biosynthesis","description":"The top GO terms are dominated by phenylpropanoid and lignan-related processes, especially pinoresinol and secoisolariciresinol biosynthesis, indicating a shared function in lignan production. A few terms relate to bacterial LPS core or sporopollenin biosynthesis, which may reflect annotation noise or broad biosynthetic roles, but the strongest signal centers on lignan biosynthesis. ","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0009699","count":2},{"id":"GO:1902123","count":2},{"id":"GO:0097171","count":2},{"id":"GO:0006541","count":2}]},{"hash":"816521647971814235","title":"Carbohydrate transport and sugar metabolism","description":"The top GO terms point to transport and metabolism of carbohydrates (glucose, fructose, trehalose) and related nutrients (nitrite, organic anions), as well as a cellular response to glucose starvation, suggesting a coherent theme around nutrient uptake and carbohydrate handling. There are additional, less central terms about transcription initiation, mRNA capping, and sterol biosynthesis, likely reflecting broader metabolic context, but the strongest signal is carbohydrate transport/metabolism. ","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006367","count":2},{"id":"GO:0006370","count":2},{"id":"GO:0016126","count":2},{"id":"GO:0042149","count":2},{"id":"GO:1990539","count":2}]},{"hash":"2245456728742641709","title":"Neural development and synaptic vesicle regulation","description":"The top terms center on neural development and presynaptic function\u2014regulation of synaptic vesicle exocytosis, brain development, and neural patterning\u2014with supporting signals from calcium handling and Rho signaling, suggesting a cohesive cluster of proteins involved in neural development and synaptic vesicle regulation rather than unrelated processes.","confidence":"High","size":11,"edges":47,"triangles":107,"max_degree":10,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:2000300","count":5},{"id":"GO:0010796","count":5},{"id":"GO:0007420","count":5},{"id":"GO:0031384","count":5},{"id":"GO:0035023","count":4}]},{"hash":"627039460040031249","title":"Plant stress-responsive transcription regulation","description":"The dominant term is regulation of DNA-templated transcription, indicating transcriptional control. The presence of plant-relevant terms such as auxin biosynthesis, hormone biosynthetic regulation, and cell wall organization, along with responses to herbicide and selenium ion, suggests the cluster centers on how gene expression is modulated in plants under hormonal and environmental stresses. NAD+ biosynthesis and apoptotic terms are less central but compatible with stress contexts, supporting a cohesive theme of plant stress-responsive transcriptional regulation.","confidence":"High","size":11,"edges":2,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0006950","count":1},{"id":"GO:0009435","count":1},{"id":"GO:0009635","count":1},{"id":"GO:0046886","count":1}]},{"hash":"1617199865071411458","title":"TGF-\u03b2/BMP-SMAD signaling regulation","description":"This cluster centers on transforming growth factor-beta family signaling, with multiple terms for cellular response to TGF-\u03b2, BMP signaling regulation, and SMAD pathway regulation, including TGF-\u03b2 receptor signaling. This suggests a coherent theme of TGF-\u03b2/BMP pathway control in development, with a couple of outlier terms that are less central to the core theme.","confidence":"High","size":11,"edges":14,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0061191","count":3},{"id":"GO:0046827","count":3},{"id":"GO:0042347","count":3},{"id":"GO:0000173","count":3},{"id":"GO:0042006","count":3}]},{"hash":"1433757057101768253","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":9,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:1905639","count":8},{"id":"GO:1900865","count":8},{"id":"GO:0042793","count":8},{"id":"GO:0031425","count":8},{"id":"GO:0016554","count":8}]},{"hash":"1356783822476123138","title":"Neural development and hormonal response","description":"The top GO terms point to neural functions (brain development, adult locomotory behavior) and hormonal/stress signaling (response to estradiol, xenobiotic stimulus), with apoptotic regulation and proliferation control that support neural development and circuit refinement. A stray term like cellulose catabolic process suggests annotation noise, but overall the cluster centers on neural development and behavioral regulation influenced by hormones and stress.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0008344","count":2},{"id":"GO:0030245","count":2},{"id":"GO:0031667","count":1}]},{"hash":"1942741632442211360","title":"Neural development and glial apoptosis regulation","description":"This cluster is dominated by nervous system\u2013related terms, including forebrain development, neural tube closure, and negative regulation of glial cell apoptosis, along with potassium ion transport and an intrinsic apoptotic ER-stress pathway. These co-occurring terms suggest a shared theme around neural development and glial cell survival under cellular stress, despite some metabolic/cell-cycle terms that are less central to this theme.","confidence":"Medium","size":11,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0034351","count":8},{"id":"GO:0001501","count":8},{"id":"GO:0000278","count":8},{"id":"GO:0001403","count":8},{"id":"GO:0071276","count":8}]},{"hash":"1202954362842917836","title":"Methylation and DNA modification","description":"The terms are dominated by methylation-related processes, including protein methylation and multiple DNA methylation activities, plus a DNA restriction-modification system item. Although there are some unrelated terms (protein turnover and homeostasis), the common thread across the top terms is methylation-based modification of proteins or DNA, justifying this label.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042220","count":3},{"id":"GO:0090124","count":3},{"id":"GO:0006479","count":3},{"id":"GO:0032775","count":3},{"id":"GO:0009307","count":3}]},{"hash":"643992648782999754","title":"Flavonoid glycoside biosynthesis and lignin metabolism","description":"The top GO terms strongly point to plant phenylpropanoid pathways, with kaempferol/quercetin/cyanidin O-glucoside biosynthesis and lignin metabolism forming a cohesive theme, i.e., flavonoid biosynthesis and lignin formation. Some other terms appear as broad xenobiotic or related processes, but the core signal is plant secondary metabolism and modification.","confidence":"Medium","size":11,"edges":24,"triangles":19,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006711","count":10},{"id":"GO:0030259","count":10},{"id":"GO:0052696","count":10},{"id":"GO:0070980","count":10},{"id":"GO:0033330","count":10}]},{"hash":"347970527925106807","title":"Gluconeogenesis and sugar metabolism","description":"The cluster shows a clear emphasis on carbohydrate metabolism: gluconeogenesis, regulation of gluconeogenesis, fructose-6-phosphate metabolic process, and sucrose biosynthesis, plus cellular responses tied to glucose availability. These together suggest a coherent theme around sugar production and homeostasis. Minor terms related to xenobiotic response, dephosphorylation, and Ras signaling likely reflect broader regulatory roles rather than a primary function of the cluster.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":2},{"id":"GO:0006111","count":1},{"id":"GO:0042149","count":1},{"id":"GO:0005986","count":1},{"id":"GO:0016311","count":1}]},{"hash":"1762844377843472712","title":"Unknown","description":"The terms include cellulose catabolic process, antibiotic biosynthetic process, rDNA heterochromatin formation, regulation of collagen catabolic process, and various proliferation, adhesion, and immune-related terms. The collection spans microbial metabolism and mammalian cellular signaling, with no clear shared function or pathway across all proteins. With zero edges and a highly heterogeneous GO profile, it is not possible to assign a coherent label beyond Unknown.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0000183","count":3},{"id":"GO:0010710","count":2},{"id":"GO:0008284","count":2}]},{"hash":"1898564995842684331","title":"Seed development and lipid metabolism","description":"This cluster centers on plant-specific seed processes, with terms for seed coat development and positive regulation of seed germination, alongside multiple fatty-acid and acetyl-CoA\u2013related metabolic pathways (medium-, long-, and other fatty-acyl-CoA metabolism, acetyl-CoA biosynthesis, and pyruvate fermentation to acetate). While there are a few outliers (bioluminescence, bile acid metabolism), the dominant signal ties seed development to lipid metabolism and secondary metabolism (phenylpropanoids). Confidence: Medium","confidence":"","size":11,"edges":26,"triangles":28,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0019427","count":6},{"id":"GO:0008218","count":6},{"id":"GO:0090410","count":6},{"id":"GO:0008206","count":6},{"id":"GO:0036112","count":6}]},{"hash":"790705273992744430","title":"Membrane Transport of Metabolites and Cofactors","description":"The dominant GO terms describe transmembrane transport of ATP/ADP, NAD, thiamine pyrophosphate, glycine, thiosulfate, and related metabolites, suggesting a cohesive cluster of proteins involved in moving energy-related molecules and cofactors across membranes (primarily mitochondrial and plasma membranes). Other terms about insulin response and pregnancy likely reflect broader metabolic regulation rather than changing the core transport theme.","confidence":"High","size":11,"edges":6,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1990544","count":9},{"id":"GO:0097421","count":9},{"id":"GO:0032869","count":9},{"id":"GO:0007565","count":9},{"id":"GO:0030974","count":9}]},{"hash":"1282262033698758086","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0090615","count":11},{"id":"GO:0090617","count":11},{"id":"GO:0042793","count":11},{"id":"GO:1905639","count":11},{"id":"GO:1900865","count":11}]},{"hash":"881583195264376956","title":"Yeast pseudohyphal growth and secretion","description":"The top GO terms point to yeast-specific morphological responses to nutrient limitation (pseudohyphal and invasive growth in response to glucose limitation) as well as secretion/trafficking processes (protein exit from ER and localization to the cell surface) and associated sterol biosynthesis, suggesting a theme of yeast adaptive morphogenesis coupled with secretion. Some terms are obsolete or noisy, but the core signal centers on nutrient-driven morphological change and trafficking in yeast.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000010","count":1},{"id":"GO:0061060","count":1},{"id":"GO:0007124","count":1},{"id":"GO:0070863","count":1},{"id":"GO:0001403","count":1}]},{"hash":"527475767705181475","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006361","count":1},{"id":"GO:0006366","count":1},{"id":"GO:0070816","count":1},{"id":"GO:0006362","count":1},{"id":"GO:0006296","count":1}]},{"hash":"72990387289908542","title":"Developmental signaling and morphogenesis","description":"This cluster is enriched for GO terms related to development and morphogenesis (BMP signaling, embryonic fin morphogenesis, skeletal joint development, olfactory bulb development), suggesting a common theme around developmental signaling and tissue patterning. Additional terms on glycan biosynthesis and endomembrane organization hint at supporting cellular processes, but the dominant signal is developmental. With no observed protein-protein edges, the label emphasizes functional theme rather than interaction networks.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008101","count":3},{"id":"GO:0035118","count":3},{"id":"GO:0035884","count":3},{"id":"GO:0021772","count":3},{"id":"GO:0072498","count":3}]},{"hash":"1402424262498766908","title":"Development and Ion Homeostasis","description":"The cluster combines developmental signals (multicellular organism development, fat cell differentiation, cell migration) with ion transport/homeostasis (sodium/potassium transport and potassium homeostasis), suggesting a theme around development that requires ionic regulation. Some terms (mRNA processing, telomere maintenance) are broader housekeeping processes but do not dominate the set. Overall, development plus ion regulation best captures the core pattern.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019233","count":5},{"id":"GO:0007275","count":5},{"id":"GO:0098719","count":4},{"id":"GO:0097623","count":4},{"id":"GO:0030007","count":4}]},{"hash":"2127500771209812553","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":1},{"id":"GO:0090617","count":1},{"id":"GO:1905639","count":1},{"id":"GO:1900865","count":1},{"id":"GO:0042793","count":1}]},{"hash":"1381712766605186180","title":"Translation machinery and translational regulation","description":"Dominant GO terms cover core translation stages\u2014initiation, elongation, termination\u2014and regulation of translation, plus mRNA binding and frameshifting, pointing to a cluster of translation machinery and its regulators. A few outlier terms about viral transport and neuronal activity are present but do not override the main theme.","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0045901","count":2},{"id":"GO:0006413","count":2},{"id":"GO:0006415","count":2},{"id":"GO:0006452","count":1}]},{"hash":"335349883126843898","title":"Glycolysis and ATP metabolism with insulin/cAMP signaling","description":"The top GO terms point to core energy pathways (canonical glycolysis, ATP and pyruvate biosynthesis) and responses to glucose, insulin stimulus, and cAMP, indicating a cluster centered on energy production and its regulation. Additional terms for heat and lithium ion responses and programmed cell death reflect stress signaling linked to energy status, reinforcing the overall energy-metabolism theme.","confidence":"High","size":10,"edges":35,"triangles":77,"max_degree":8,"top_function":"programmed cell death","top_go_terms":[{"id":"GO:0061621","count":9},{"id":"GO:0032869","count":7},{"id":"GO:0006754","count":7},{"id":"GO:0012501","count":7},{"id":"GO:0051591","count":7}]},{"hash":"67392800875049972","title":"Developmental Signaling and Morphogenesis","description":"The top GO terms cluster around signaling pathways (auxin-activated signaling, estradiol response, ERK cascade regulation) that drive developmental programs and morphogenesis, including endothelial and retina vasculature morphogenesis and organ regeneration. Some terms reflect detoxification/metabolic processes, which may add noise, but the core theme points to signaling controlling development and tissue formation. ","confidence":"Medium","size":10,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032355","count":3},{"id":"GO:0009734","count":3},{"id":"GO:0009635","count":3},{"id":"GO:0001886","count":3},{"id":"GO:0031100","count":3}]},{"hash":"1538020871236045665","title":"Hormone-Regulated Amino Acid Metabolism","description":"The top GO terms cluster around biosynthesis and catabolism of amino acids (serine, glycine, cysteine) and related central metabolites (pyruvate, quinolinate), plus cellular responses to insulin, cAMP, and glucocorticoids. This suggests a cohesive module of metabolic processes that are modulated by hormonal signaling, focusing on amino acid metabolism and broader central carbon metabolism. Therefore, the label reflects both the chemical themes and the regulatory context.","confidence":"High","size":10,"edges":35,"triangles":66,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0042866","count":4},{"id":"GO:0051591","count":3},{"id":"GO:0006564","count":3},{"id":"GO:0032869","count":2},{"id":"GO:0006546","count":2}]},{"hash":"2234172132572246208","title":"Redox Homeostasis and Oxidative Stress Response","description":"Most GO terms describe redox biology: oxidative stress response, redox homeostasis, oxidant detoxification, and protein deglutathionylation, which together point to regulation of cellular redox state. A couple of terms are broader regulatory processes but don't override the redox theme.","confidence":"High","size":10,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1903026","count":2},{"id":"GO:0034599","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0080058","count":2},{"id":"GO:0098869","count":2}]},{"hash":"2009058097135875320","title":"Plant cell wall biosynthesis and growth regulation","description":"This cluster is dominated by GO terms for cell wall polysaccharide biosynthesis, cell wall organization, and regulation of cell shape, with inclusion of cell cycle terms, suggesting roles in cell growth and wall construction. Hormone turnover (cytokinin catabolic process) reinforces growth regulation, while other metabolic terms point to general plant metabolism supporting these processes.","confidence":"Medium","size":10,"edges":13,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0035884","count":9},{"id":"GO:0009823","count":9},{"id":"GO:0019853","count":9},{"id":"GO:0019516","count":9},{"id":"GO:1903457","count":9}]},{"hash":"507000326993383134","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":30,"triangles":41,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":9},{"id":"GO:0031047","count":8},{"id":"GO:0000393","count":6},{"id":"GO:0071035","count":6},{"id":"GO:0000467","count":6}]},{"hash":"364554646702184092","title":"Ribosome biogenesis and translation","description":"The top GO terms are strongly centered on translation and ribosome biogenesis\u2014cytoplasmic translation, ribosome assembly, and maturation of SSU/LSU rRNA, plus selenocysteine incorporation during translation\u2014indicating a core function in ribosome-related processes. A few outliers (fertilization, JNK signaling) are present but do not dominate the cluster. Confidence: High","confidence":"","size":10,"edges":40,"triangles":86,"max_degree":9,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0042254","count":3},{"id":"GO:0000462","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0046330","count":1}]},{"hash":"1488543863904507399","title":"Plant defense and nodulation signaling","description":"The top terms emphasize defense responses and biotic stimulus, with strong representation of cytokinin-activated signaling and gibberellin-mediated signaling, plus nodulation, all of which point to plant hormone signaling governing defense and nodulation processes. Some terms like synapse assembly appear as outliers, but the core theme is plant immune and hormone signaling linked to nodulation. ","confidence":"Medium","size":10,"edges":7,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009607","count":2},{"id":"GO:0009736","count":2},{"id":"GO:0006952","count":2},{"id":"GO:0009877","count":2},{"id":"GO:0009740","count":2}]},{"hash":"649436570593397327","title":"Biosynthesis of diverse metabolites","description":"The top GO terms point to multiple biosynthetic pathways across distinctly different metabolite classes (fructose, retinol, anthocyanin, bile acids, ascorbic acid, glucuronate), suggesting the cluster groups proteins involved in diverse metabolite production rather than a single pathway; a few stress-related terms appear but do not override the central biosynthetic theme. ","confidence":"Medium","size":10,"edges":36,"triangles":66,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0046370","count":5},{"id":"GO:0042572","count":5},{"id":"GO:0009718","count":4},{"id":"GO:0009414","count":3}]},{"hash":"749130209010002284","title":"DNA replication and cell cycle control","description":"The dominant GO terms are DNA replication and cell cycle, with related regulation of telomere maintenance and CDK activity, pointing to a core function in replication-associated cell cycle progression. Some terms on mRNA processing and differentiation/physiology (fat cell differentiation, cell migration, response to muscle stretch) appear but are less central to the cluster\u2019s primary signal.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0045444","count":2},{"id":"GO:0032212","count":2},{"id":"GO:1904355","count":2}]},{"hash":"528160171263572423","title":"Plant Nitrate/Peptide Transport and Hormone Signaling","description":"The top GO terms cluster around nitrate and peptide transport and assimilation, plus hormone-related signaling (auxin, gibberellin) and herbicide response, indicating a cohesive plant module for nutrient uptake connected to hormone regulation.","confidence":"High","size":10,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0080055","count":3},{"id":"GO:0009734","count":3},{"id":"GO:0009635","count":3},{"id":"GO:0035672","count":3},{"id":"GO:0042938","count":3}]},{"hash":"930175520082688766","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":7},{"id":"GO:0090617","count":7},{"id":"GO:0042793","count":7},{"id":"GO:1905639","count":7},{"id":"GO:1900865","count":7}]},{"hash":"2205332688809324532","title":"Spliceosome Assembly and mRNA Splicing","description":"The cluster is strongly enriched for GO terms tied to RNA processing via the spliceosome, including cis splicing, spliceosomal snRNP/snoRNP assembly, and spliceosomal complex assembly, indicating a core spliceosome machinery module. Additional terms for nuclear import and translation align with general RNA processing and ribonucleoprotein function, while stress-related terms (response to water deprivation, abscisic acid) suggest regulatory links to stress-induced splicing changes. Overall, this cluster represents RNA splicing machinery with assembly/regulation components.","confidence":"High","size":10,"edges":44,"triangles":112,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":3},{"id":"GO:0048025","count":2},{"id":"GO:0000492","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0009414","count":2}]},{"hash":"1409703400231396845","title":"Ribosome biogenesis and translation","description":"The set is dominated by GO terms for translation (cytoplasmic and mitochondrial) and ribosome biogenesis processes (large and small subunit assembly/export, rRNA maturation). This suggests the cluster comprises proteins involved in ribosome assembly and protein synthesis.","confidence":"High","size":10,"edges":28,"triangles":35,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0002181","count":2},{"id":"GO:0000055","count":1},{"id":"GO:0042273","count":1},{"id":"GO:0000028","count":1}]},{"hash":"1059090027843581877","title":"Unknown","description":"The top terms span diverse themes (transcription by RNA Pol II, multiple tissue developmental processes across muscle, neuron, pancreas, plant, circadian entrainment, and signaling regulation) with no single unifying function, so a coherent, specific label cannot be inferred.","confidence":"","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":9},{"id":"GO:2000323","count":7},{"id":"GO:0007518","count":7},{"id":"GO:0048658","count":7},{"id":"GO:0009649","count":7}]},{"hash":"1730182597191975976","title":"Transmembrane Metabolite Transporters","description":"The top GO terms indicate a strong enrichment for transport activities across membranes, including mitochondrial ATP/ADP transport, NAD transport, thiosulfate and thiamine pyrophosphate transport, and amino acid transport (glycine). While the cluster also touches on insulin response and liver-related processes, those likely reflect metabolic regulation in support of transport functions rather than a different primary role. Therefore, labeling this cluster as membrane-transporters for diverse metabolites and cofactors best captures the shared function of the proteins.","confidence":"High","size":10,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1990544","count":7},{"id":"GO:0097421","count":7},{"id":"GO:0032869","count":7},{"id":"GO:0007565","count":7},{"id":"GO:0030974","count":7}]},{"hash":"354132950500796354","title":"Peroxisome Biogenesis and Inheritance","description":"Top terms describe peroxisome fission, membrane biogenesis, organization, import, and inheritance, pointing to a shared function in peroxisome assembly and maintenance; the presence of ER-dependent peroxisome organization and protein import supports a biogenesis/inheritance cluster, while an outlier term (positive regulation of acrosome reaction) is unrelated.","confidence":"High","size":10,"edges":9,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0016559","count":1},{"id":"GO:0016557","count":1},{"id":"GO:0050821","count":1},{"id":"GO:0032527","count":1},{"id":"GO:0032581","count":1}]},{"hash":"565842469384535777","title":"Mitotic Division and Intracellular Trafficking","description":"The cluster is dominated by mitosis-related terms (mitotic cell cycle, cell division, mitotic spindle assembly, mitochondrion inheritance), suggesting a core tie to cell division. The presence of trafficking-related terms (endosome to lysosome transport, positive regulation of secretory pathway) and adhesion-related processes implies coordination between division and intracellular transport/organization, and organelle inheritance during mitosis, giving a cohesive though multi-faceted functional theme.","confidence":"Medium","size":10,"edges":12,"triangles":7,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0060263","count":3},{"id":"GO:0090307","count":3},{"id":"GO:0090394","count":3}]},{"hash":"790559350481350778","title":"RNA Transcription Initiation and Processing","description":"The prominent GO terms cluster around transcription initiation (RNA Pol II promoter), preinitiation complex assembly, DNA-templated transcription, and RNA processing/spliceosome activity, suggesting a nuclear transcription and RNA maturation role. A few terms like proteasome assembly, urate transport, and lithium response may be peripheral noise.","confidence":"Medium","size":10,"edges":8,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0015747","count":2},{"id":"GO:1900370","count":1},{"id":"GO:1901092","count":1},{"id":"GO:0043923","count":1},{"id":"GO:0006367","count":1}]},{"hash":"659257422919891916","title":"Nuclear gene expression and genome maintenance","description":"The top GO terms cluster around nuclear functions: transcription (DNA-templated transcription; RNA Pol I initiation), mRNA transport, proteasome assembly (protein turnover affecting gene expression), DNA repair by homologous recombination, and cell division, with TORC1 signaling and GTPase regulation suggesting growth-control links to these processes. Pigmentation appears as a minor outlier. Overall, this set points to coordinated nuclear gene expression and genome maintenance activities.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043248","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0000724","count":2},{"id":"GO:0070262","count":2},{"id":"GO:0043547","count":2}]},{"hash":"397387939007964483","title":"Diverse membrane transporters","description":"The top GO terms cluster around transmembrane transport of diverse substrates (glycerophosphodiesters, molybdate, phospholipids, teichoic acids, methionine) and related transport processes such as bacteriocin transport. While a few terms are unrelated, the common theme is membrane transporter activity across substrates, making this the most representative label despite heterogeneity.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045796","count":2},{"id":"GO:0001407","count":2},{"id":"GO:0015689","count":2},{"id":"GO:0043213","count":2},{"id":"GO:0031288","count":2}]},{"hash":"668108469414037624","title":"Unknown","description":"The top GO terms span energy production (photosynthesis light reactions; mitochondrial electron transport and ATP synthesis), various catabolic processes (xylan and glucomannan catabolism; lipid catabolism), plus reproductive and autophagy-related terms (spermatogenesis; acrosome reaction; positive regulation of macroautophagy) with no clear single functional theme connecting all proteins. Therefore there isn\u2019t a cohesive, interpretable function for this cluster.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006810","count":1},{"id":"GO:0019684","count":1},{"id":"GO:0042775","count":1},{"id":"GO:0006120","count":1},{"id":"GO:0045493","count":1}]},{"hash":"908958268777502671","title":"Flavonoid Biosynthesis","description":"Most terms point to flavonoid biosynthesis and modification: kaempferol and quercetin O-glucoside biosynthesis, anthocyanin-containing compound biosynthetic process, and related glycosylation. Additional terms reflect general xenobiotic/antibiotic metabolism, which can accompany secondary metabolite pathways in plants. One outlier (axon paranode localization) seems unrelated. Thus the cluster likely represents a flavonoid biosynthetic module.","confidence":"High","size":10,"edges":8,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0016999","count":6},{"id":"GO:0030259","count":6},{"id":"GO:0009718","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0006711","count":4}]},{"hash":"152426524215369637","title":"APC/C-Driven Mitosis and Ubiquitination","description":"This cluster is dominated by mitotic cell cycle and cell division terms, plus APC/C-dependent proteolysis and K11-linked ubiquitination, pointing to regulation of protein turnover during mitosis. The histone methylation terms are labeled obsolete and likely less informative here, while the cadmium and drug-response terms appear as peripheral stress-related signals rather than core functions.","confidence":"High","size":10,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2001162","count":3},{"id":"GO:0061087","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0031145","count":3},{"id":"GO:0000278","count":3}]},{"hash":"760630806091498623","title":"Unknown","description":"The terms are highly heterogeneous, ranging from nodulation and morphogenesis to various transport and pigment-related processes, with no clear common function tying the cluster together. With 0 edges and no cohesive pathway, the set does not map to a single biological theme, so a definite label is not supported.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009877","count":3},{"id":"GO:0051260","count":2},{"id":"GO:0045796","count":2},{"id":"GO:0001407","count":2},{"id":"GO:0015689","count":2}]},{"hash":"1918093862071230923","title":"TLR-driven innate immune activation","description":"The proteins are dominated by Toll-like receptor signaling terms (TLR4, TLR8, TLR10) and downstream inflammatory/cytokine responses, including dendritic cell cytokine production, chemokines, and antiviral defense, indicating a focus on TLR-mediated innate immunity with related inflammatory regulation.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006963","count":6},{"id":"GO:0002756","count":6},{"id":"GO:0034158","count":6},{"id":"GO:0002730","count":6},{"id":"GO:0034142","count":6}]},{"hash":"490903191092278892","title":"Unknown","description":"The top terms are mixed: some translation-related terms appear, but many terms point to plant development and metabolism (leaf formation, jasmonic acid response, flavonol biosynthesis), while others reference viral processes or chromatin. With no interactions (Edges 0), there is no clear common function linking these proteins, so Unknown.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0002184","count":1},{"id":"GO:1903770","count":1},{"id":"GO:1900386","count":1},{"id":"GO:0010338","count":1}]},{"hash":"1476085638013204280","title":"Sugar and Solute Transporters","description":"The top GO terms are dominated by membrane transport activities for sugars and related solutes (glucose, fructose, trehalose, dehydroascorbic acid, nitrite) and related responses, suggesting a cluster of transporter proteins handling carbohydrate and other solute transport across membranes.","confidence":"High","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042149","count":2},{"id":"GO:1990539","count":2},{"id":"GO:0043252","count":2},{"id":"GO:0015771","count":2},{"id":"GO:0052106","count":2}]},{"hash":"979617849033778481","title":"Neural development and dendrite morphogenesis","description":"The top GO terms are dominated by brain and nervous system development, along with neuron maturation and synaptic/dendrite formation (brain development 4, nervous system development 4, dendrite morphogenesis 3, regulation of neuron maturation 3, branching morphogenesis of a nerve 2). This pattern points to a coherent theme of neural development and dendritic patterning, despite a few outlier terms. Confidence: High","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":4},{"id":"GO:0007399","count":4},{"id":"GO:0071560","count":3},{"id":"GO:0014041","count":3},{"id":"GO:0048813","count":3}]},{"hash":"907236762402266431","title":"Transcriptional Regulation and Signaling","description":"Dominated by DNA-templated transcription and its regulation, with a phosphorelay signaling term connecting transcriptional control to signal transduction; other terms appear diverse and may reflect noise or multifunctionality.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0000160","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0033160","count":3},{"id":"GO:0006006","count":3}]},{"hash":"1663619708881131098","title":"Mitotic cell cycle regulation","description":"The cluster repeatedly features terms tied to mitosis and cell-cycle control, including negative regulation of CDK activity, kinetochore localization, spindle pole localization, and DNA replication, suggesting proteins involved in coordinating chromosome segregation and cell-cycle progression. Supporting processes like mRNA capping and vesicle transport may reflect broader proliferative roles but do not override the central mitotic theme.","confidence":"High","size":10,"edges":41,"triangles":91,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045736","count":7},{"id":"GO:0034501","count":7},{"id":"GO:0035729","count":6},{"id":"GO:0006351","count":4},{"id":"GO:0006260","count":4}]},{"hash":"590346995339589107","title":"Plant development and flowering regulation","description":"The top GO terms are dominated by plant developmental processes linked to growth and flowering (seed growth, floral meristem determinacy, vernalization, photoperiodism), with supportive roles for transcriptional control and calcium signaling, suggesting a cluster focused on plant development and flowering regulation despite an outlier embryonic term.","confidence":"Medium","size":10,"edges":11,"triangles":6,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0090009","count":5},{"id":"GO:0071277","count":4},{"id":"GO:0000122","count":3},{"id":"GO:0080112","count":3},{"id":"GO:0006351","count":3}]},{"hash":"529527316377058348","title":"Diverse biosynthesis of secondary metabolites and lipids","description":"The Top Terms show multiple biosynthetic processes spanning plant pigments (chalcone, flavonoid), pollen wall polymer (sporopollenin), DIF-1, antibiotic biosynthesis, and lipid pathways (fatty acids, acetyl-CoA, cholesterol). This pattern indicates proteins in this cluster participate in a range of biosynthesis pathways across secondary metabolites and lipids, justifying a label that captures diverse biosynthetic activity.","confidence":"High","size":10,"edges":24,"triangles":24,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0009715","count":4},{"id":"GO:0009813","count":4},{"id":"GO:0071770","count":4},{"id":"GO:0031148","count":4},{"id":"GO:0080110","count":4}]},{"hash":"434167114367445593","title":"Diverse metabolite and lipid biosynthesis","description":"This cluster is dominated by GO terms for biosynthetic processes of secondary metabolites (chalcone and flavonoid biosynthesis), sporopollenin, DIF-1, and fatty acids/LUCA long-chain acyl-CoA metabolism, plus cell wall layer assembly, pointing to a core theme of biosynthesis across metabolites, lipids, and structural polymers. A couple of terms (neuron projection maintenance, mitotic spindle/centrosome events) are less directly related, likely representing broader cellular roles.","confidence":"Medium","size":10,"edges":13,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0009715","count":1},{"id":"GO:0009813","count":1},{"id":"GO:0071770","count":1},{"id":"GO:0031148","count":1},{"id":"GO:0035336","count":1}]},{"hash":"1564145174766040388","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000462","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0000480","count":3}]},{"hash":"1202247573477558772","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":2},{"id":"GO:0090617","count":2},{"id":"GO:0042793","count":2},{"id":"GO:1905639","count":2},{"id":"GO:1900865","count":2}]},{"hash":"1846212779333022010","title":"Developmental signaling and gene regulation","description":"Top GO terms suggest involvement in developmental processes (multicellular organism and skin development) along with regulation of signaling (GTPase and kinase activities) and gene expression (transcription and mRNA transport). The cluster appears to group proteins connected to developmental signaling that modulates transcriptional/ post-transcriptional processes, hence a label that combines signaling and gene regulation is appropriate. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0043588","count":4},{"id":"GO:0051260","count":3},{"id":"GO:0071902","count":3}]},{"hash":"1250888464498753615","title":"Unknown","description":"The top GO terms span immune regulation (apoptotic cell clearance, T cell proliferation, tolerance induction), development (placental differentiation, organ regeneration), and general cellular processes (protein export from nucleus, ER polarization, cellular response to virus, meiosis), with no single dominant function, so a cohesive label is not apparent.","confidence":"","size":10,"edges":4,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043277","count":7},{"id":"GO:0046641","count":7},{"id":"GO:0060709","count":7},{"id":"GO:0006611","count":7},{"id":"GO:0061167","count":7}]},{"hash":"815054188766512848","title":"Terpenoid and Sterol Biosynthesis","description":"The top GO terms are dominated by isoprenoid/terpenoid biosynthesis (farnesyl, geranyl, and geranylgeranyl diphosphate; monoterpene) and related lipid pathways such as cholesterol and quinone biosynthesis, suggesting a cohesive function in terpenoid/sterol production. A few terms like DNA recombination and xenobiotic response are less aligned and likely noise. ","confidence":"Medium","size":10,"edges":8,"triangles":1,"max_degree":4,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0042493","count":4},{"id":"GO:0006310","count":3},{"id":"GO:0010212","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0045337","count":2}]},{"hash":"367027858781061713","title":"Plant Cell Wall Biosynthesis and Root Hair Development","description":"This cluster is dominated by GO terms related to plant cell wall construction and modification (cell wall organization, RG-II and glucuronoxylan biosynthesis, plant-type secondary cell wall biogenesis) as well as root hair development and pollen-related processes, suggesting a cohesive theme around cell wall biosynthesis supporting root hair and reproductive structures in plants.","confidence":"High","size":10,"edges":32,"triangles":60,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":7},{"id":"GO:0010306","count":6},{"id":"GO:0080147","count":6},{"id":"GO:0016311","count":1},{"id":"GO:0010584","count":1}]},{"hash":"2083472271370612024","title":"DNA replication and cell cycle regulation","description":"The top GO terms show strong enrichment for DNA-templated transcription, DNA replication, G1/S transition of the mitotic cell cycle, and kinetochore localization, all central to cell-cycle control and DNA metabolism. Some terms touch neural signaling and metabolism, but the central signal is nuclear processes driving chromosome duplication and division, so the cluster likely represents cell-cycle/DNA-processing proteins.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000082","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0005981","count":2},{"id":"GO:0051321","count":2},{"id":"GO:0014044","count":2}]},{"hash":"242052676420680831","title":"Embryonic development signaling","description":"The cluster centers on developmental signaling processes, with multiple GO terms pointing to embryonic morphogenesis and signaling pathways (BMP signaling, embryonic fin and skeletal joint development, olfactory bulb development). While there are also terms tied to glycan biosynthesis and endomembrane organization that suggest broader cellular functions, the convergence on embryogenesis-related signaling and tissue development provides the strongest, coherent theme for naming. Confidence: Medium","confidence":"","size":10,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0008101","count":2},{"id":"GO:0035118","count":2},{"id":"GO:0035884","count":2},{"id":"GO:0021772","count":2},{"id":"GO:0072498","count":2}]},{"hash":"34021974341730855","title":"Potassium Ion Homeostasis and Membrane Potential","description":"Top terms show strong enrichment for potassium import/export, stabilization of membrane potential, and intracellular potassium ion homeostasis, with additional signals for calcium release and other ion-related processes. This pattern points to proteins involved in maintaining cellular excitability and ion balance, centered on potassium transport and membrane potential regulation, with some peripheral terms. Confidence: Medium","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990573","count":2},{"id":"GO:0030322","count":2},{"id":"GO:0030007","count":2},{"id":"GO:0097623","count":2},{"id":"GO:0051209","count":2}]},{"hash":"1563955824281462159","title":"Trehalose/glucosylglycerol osmoprotectant biosynthesis","description":"The GO terms cluster around trehalose and glucosylglycerol biosynthesis and cellular responses to desiccation and temperature stress (heat/cold), suggesting osmoprotectant production as a common function; translation/transcription regulation terms appear secondary but may reflect general stress response regulation. Overall, the set points to osmoprotectant biosynthesis under stress as the core theme.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006355","count":2},{"id":"GO:0070413","count":1},{"id":"GO:0071465","count":1},{"id":"GO:0016311","count":1}]},{"hash":"2281160927894180270","title":"Unknown","description":"The top GO terms span disparate organisms and processes (BMP signaling and vertebrate development; plant hormone signaling and cell wall biosynthesis; endomembrane organization), with no clear shared function or pathway linking all proteins, so no coherent label can be assigned.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008101","count":1},{"id":"GO:0035118","count":1},{"id":"GO:0035884","count":1},{"id":"GO:0021772","count":1},{"id":"GO:0072498","count":1}]},{"hash":"2184488527435869360","title":"Ribosome biogenesis and translation","description":"The strongest signals are in translation-related terms (translation, cytoplasmic translation, regulation of translation) and ribosome/rRNA processing and export (LSU-rRNA maturation, nuclear rRNA export). This suggests a cluster of proteins involved in ribosome assembly and protein synthesis, with minor inclusion of transcription-associated terms likely due to multifunctionality.","confidence":"High","size":9,"edges":34,"triangles":71,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0000470","count":1},{"id":"GO:0006417","count":1},{"id":"GO:0000056","count":1},{"id":"GO:0006407","count":1}]},{"hash":"1436144585589897620","title":"Unknown","description":"This cluster's GO terms span immune-related responses (defense against bacteria, cytolysis, viral release) alongside unrelated processes (cold acclimation, ethanol metabolism, mitochondrial ribosome assembly, cell wall catabolic processes, Tat-mediated transport). The terms do not converge on a single cohesive function or pathway, making a concise, representative label difficult. Therefore, Unknown with no confidence.","confidence":"","size":9,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019076","count":2},{"id":"GO:0009631","count":2},{"id":"GO:0016998","count":1},{"id":"GO:0065002","count":1},{"id":"GO:0043953","count":1}]},{"hash":"721434796366822878","title":"Ribosome Biogenesis and Translation","description":"The top GO terms cluster around ribosome production and function: translation, maturation of SSU-rRNA, and ribosome biogenesis, indicating a core role in making and translating ribosomes. Other terms like RNA splicing and folding appear secondary, suggesting additional RNA-processing connections but not dominating the cluster\u2019s theme. Overall, the dominant signal is ribosome biogenesis linked to translation.","confidence":"High","size":9,"edges":34,"triangles":70,"max_degree":8,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0000462","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0046677","count":3},{"id":"GO:0006407","count":3}]},{"hash":"631759010234266232","title":"Chloroplast photosynthesis and light-response","description":"The top GO terms cluster around photosynthesis and light-related processes: photosynthesis in general, light harvesting by photosystems I and II, nonphotochemical quenching, and responses to varying light conditions such as far-red and UV-A exposure. A translation term appears, possibly reflecting chloroplast protein synthesis, but the dominant theme is chloroplast light-dependent energy capture and signaling.","confidence":"High","size":9,"edges":18,"triangles":15,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0009768","count":1},{"id":"GO:1904964","count":1},{"id":"GO:0010218","count":1},{"id":"GO:0071486","count":1}]},{"hash":"924001172177409116","title":"Bacterial energy metabolism and quinone biosynthesis","description":"This cluster is dominated by metabolism-related GO terms, especially menaquinone and phylloquinone biosynthesis, plus central carbon metabolism (TCA cycle, fatty acid beta-oxidation, valine catabolism) and related catabolic processes. The shared theme is bacterial energy generation and quinone-linked metabolism, with transcription/regulation terms likely reflecting regulatory control within metabolic networks.","confidence":"High","size":9,"edges":14,"triangles":11,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0009234","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0010124","count":4},{"id":"GO:0006099","count":3},{"id":"GO:0055114","count":3}]},{"hash":"651247656662843106","title":"Sterol and lipid biosynthesis","description":"This cluster\u2019s top GO terms cluster around sterol and lipid metabolism: cholesterol biosynthesis via lathosterol, ergosterol biosynthesis, ether lipid metabolism, and fatty acid biosynthesis. While a few terms (sebaceous gland differentiation, B cell chemotaxis, CNS myelin maintenance) touch on unrelated processes, the recurring theme is lipid production and membrane lipid homeostasis, justifying a lipid-biosynthesis label.","confidence":"High","size":9,"edges":6,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0033490","count":2},{"id":"GO:0080065","count":2},{"id":"GO:0001949","count":2},{"id":"GO:0080064","count":2},{"id":"GO:0046485","count":2}]},{"hash":"302365962230607236","title":"Chemical stress responses and metabolism","description":"The Top Terms include stress-related responses (lipopolysaccharide, copper ion) alongside a mix of metabolic processes (lignin biosynthesis, retinoic acid, ethanol and furfural metabolism) and transcription. This pattern suggests a cluster enriched for diverse chemical stress responses linked to broad metabolic functions rather than a single cohesive pathway. ","confidence":"Medium","size":9,"edges":27,"triangles":35,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009809","count":4},{"id":"GO:0032496","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0042573","count":3}]},{"hash":"1452837291266843634","title":"Synaptic Vesicle Trafficking and Plasticity","description":"GO terms point to vesicle trafficking and fusion (SNARE complex assembly; endosome-to-Golgi transport) and neuronal signaling (long-term potentiation). This suggests a module involved in synaptic transmission and vesicle management, with additional signals of modulation via channels and metabolic cues in neurons. Overall, the core theme is vesicle trafficking linked to synaptic plasticity.","confidence":"High","size":9,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071307","count":1},{"id":"GO:0007155","count":1},{"id":"GO:1904209","count":1},{"id":"GO:0008283","count":1},{"id":"GO:0042147","count":1}]},{"hash":"1248535511266734902","title":"Microtubule Organization and Mitosis","description":"Based on the top GO terms, the dominant signals are microtubule nucleation, cytoplasmic microtubule organization, spindle pole body duplication, and cytokinesis, which together define a core function in microtubule dynamics and cell division. Some terms touch on mechanosensing and neuron migration, but their presence appears secondary to the central theme of microtubule-based processes.","confidence":"High","size":9,"edges":14,"triangles":12,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007020","count":4},{"id":"GO:1903087","count":4},{"id":"GO:0071353","count":3},{"id":"GO:0090529","count":3},{"id":"GO:1905789","count":3}]},{"hash":"1931752342475967574","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":13,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1901621","count":2},{"id":"GO:0006260","count":2},{"id":"GO:1905259","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0097428","count":2}]},{"hash":"2131734926700062138","title":"Ion transport and membrane potential maintenance","description":"The frequent GO terms point to ion transport (Cu+, K+, Na+), maintenance of membrane electrochemical gradients, calcium homeostasis, and related membrane processes, suggesting a cluster centered on membrane ion transport and excitability rather than a single pathway.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006825","count":2},{"id":"GO:0010248","count":2},{"id":"GO:0031448","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0061092","count":2}]},{"hash":"1280579818415802647","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":3},{"id":"GO:0090617","count":3},{"id":"GO:0042793","count":3},{"id":"GO:1905639","count":3},{"id":"GO:1900865","count":3}]},{"hash":"686235275753107626","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":3},{"id":"GO:0042135","count":2},{"id":"GO:0046718","count":2},{"id":"GO:0015074","count":2},{"id":"GO:0039651","count":2}]},{"hash":"1571358118577482194","title":"Neurodevelopment and immune signaling","description":"The Top terms cluster around neural development (cerebellar cortex formation, Bergmann glial cell differentiation, regulation of axon regeneration) and immune-related signaling (T cell receptor signaling), with additional developmental themes in placenta and thymus and related signaling pathways (insulin receptor). This combination points to a theme of developmental signaling with neural and immune emphasis.","confidence":"Medium","size":9,"edges":20,"triangles":14,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000187","count":6},{"id":"GO:0001890","count":6},{"id":"GO:0048538","count":6},{"id":"GO:0071276","count":6},{"id":"GO:0048679","count":6}]},{"hash":"1451553378869933099","title":"Plant lipid storage and redox regulation","description":"The cluster centers on lipid storage and oilbody biogenesis in plants, with supporting redox-related terms (hydrogen peroxide catabolic process, redox homeostasis, removal of superoxide radicals) and copper ion transport that tie to metal-dependent redox enzymes. Some terms such as pollen hydration and Golgi vesicle fusion appear peripheral but may reflect broader trafficking and reproductive biology in plant cells. Overall, this cluster appears to reflect plant lipid metabolism coupled with oxidative stress management.","confidence":"Medium","size":9,"edges":12,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0048280","count":2},{"id":"GO:0010344","count":1},{"id":"GO:0050826","count":1},{"id":"GO:0019915","count":1},{"id":"GO:0009859","count":1}]},{"hash":"2034477374535334025","title":"Unknown","description":"The GO terms are a mix of biosynthetic and catabolic processes across different systems, plus regulatory terms like Notch signaling and transcription, with several obsolete terms and no shared specific function, so no coherent theme to label.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009718","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0019878","count":3},{"id":"GO:0019388","count":3},{"id":"GO:0009243","count":3}]},{"hash":"6130026434902341","title":"Amine acetylation and amino-sugar metabolism","description":"The terms cluster around acetylation events (peptidyl-lysine N6-acetylation, N-terminal propionylation) and polyamine acetylation (spermidine, putrescine), as well as amino-sugar metabolism (glucosamine, N-acetylglucosamine) and mycothiol biosynthesis, suggesting a cohesive theme of acetylation-modulated amine/sugar pathways.","confidence":"Medium","size":9,"edges":5,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045150","count":3},{"id":"GO:0046208","count":3},{"id":"GO:0006041","count":3},{"id":"GO:0032918","count":3},{"id":"GO:0006044","count":3}]},{"hash":"1325383152581510400","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901621","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0097428","count":1},{"id":"GO:0045454","count":1},{"id":"GO:0006458","count":1}]},{"hash":"2192629257647856170","title":"Developmental gene regulation and signaling","description":"The cluster features regulators of transcription, mRNA transport, and protein phosphorylation, spanning development (multicellular and skin development) and cell cycle processes. The presence of positive regulation of transcription by RNA Pol II, mRNA transport, mitotic cell cycle, and kinase signaling terms suggests a cohesive theme of gene expression control and signaling during development, with ribosomal maturation terms potentially reflecting broader growth/biogenesis context.","confidence":"Medium","size":9,"edges":15,"triangles":11,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045944","count":4},{"id":"GO:0000463","count":4},{"id":"GO:0000466","count":4},{"id":"GO:0043547","count":3},{"id":"GO:0071902","count":3}]},{"hash":"1740952697051267024","title":"Starch, glycogen, and trehalose metabolism","description":"The top GO terms are all carbohydrate metabolism-related, especially alpha-glucans (starch/glycogen) biosynthesis and catabolism and trehalose metabolism (biosynthetic and catabolic processes). This indicates a coherent cluster of enzymes involved in synthesis and breakdown of starch, glycogen, and trehalose, with some related sucrose metabolism signals. Hence the label accurately reflects the dominant function of these proteins.","confidence":"High","size":9,"edges":20,"triangles":20,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0005978","count":3},{"id":"GO:0019252","count":3},{"id":"GO:0005985","count":3},{"id":"GO:0030980","count":2},{"id":"GO:0044245","count":2}]},{"hash":"657339978546433220","title":"Skeletal Muscle Ion Homeostasis and Contraction","description":"The top GO terms show a clear emphasis on ion transport (potassium import, calcium ion homeostasis, electrochemical gradient maintenance) and mechanisms related to muscle contraction, particularly fast-twitch fibers. Glucose metabolism also aligns with energy supply for muscular activity. A few terms (DNA replication, lipopolysaccharide biosynthesis) are less connected and may reflect unrelated/housekeeping functions in the same protein set, but the core signal points to a skeletal-muscle\u2013related theme of ion handling and contraction.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0006006","count":4},{"id":"GO:0006825","count":4},{"id":"GO:0010248","count":4},{"id":"GO:0031448","count":4}]},{"hash":"33241352964629184","title":"Chromatin Regulation and Ubiquitin-Proteasome Turnover","description":"The cluster's GO terms cluster around chromatin organization and heterochromatin regulation, along with ubiquitin-related processes (neddylation, free ubiquitin chains, SCF-dependent ubiquitin-protein turnover) and DNA repair via homologous recombination, implying a shared role in chromatin state control and protein turnover rather than disparate functions.","confidence":"Medium","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1903955","count":9},{"id":"GO:0031497","count":9},{"id":"GO:0016032","count":9},{"id":"GO:0031146","count":9},{"id":"GO:0000724","count":9}]},{"hash":"1292239586506575500","title":"Lysine biosynthesis via aminoadipic acid and DAP","description":"The top GO terms are dominated by lysine biosynthesis pathways (via aminoadipic acid and diaminopimelate), suggesting a cluster centered on lysine production. Other terms point to related metabolism (TCA cycle, purine metabolism) and protein turnover, which can accompany central metabolism in these proteins, but the lysine pathway signal is the most representative. Given some terms are obsolete, interpretation should be cautious, but the Lysine biosynthesis theme remains the clearest label.","confidence":"Medium","size":9,"edges":10,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0019878","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0010136","count":3},{"id":"GO:0006099","count":2},{"id":"GO:0017000","count":2}]},{"hash":"644713541018408663","title":"Ribosome biogenesis and translation initiation","description":"The cluster\u2019s top GO terms are strongly centered on ribosome assembly and function, including maturation of SSU-rRNA, formation of the translation preinitiation complex, and general ribosome biogenesis, which together point to a shared role in producing and initiating ribosomes for protein synthesis. Some secondary terms (chromatin organization, ubiquitination, signaling, development) are present but do not override the ribosome-centric signature.","confidence":"High","size":9,"edges":11,"triangles":3,"max_degree":8,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000462","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0070262","count":2},{"id":"GO:0031497","count":2}]},{"hash":"1351528074265109496","title":"Transcription and RNA Processing with Stress Response","description":"The top terms center on nuclear gene expression: DNA-templated transcription, regulation of alternative splicing, and translation control, plus processes tied to stress signaling (DNA damage response, cellular response to virus) and protein export from the nucleus. This suggests a cohesive theme of coordinated transcriptional and RNA processing regulation under cellular stress, rather than a single enzymatic function. Confidence: Medium","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006977","count":4},{"id":"GO:0045727","count":3},{"id":"GO:0000381","count":3},{"id":"GO:0043277","count":2}]},{"hash":"950366794171371989","title":"Organogenesis Signaling","description":"This cluster shows several developmental terms across different tissues (lung induction, midbrain dopaminergic neuron differentiation, renal inner medulla development) and a link to Wnt signaling, pointing to a general theme of developmental signaling and organogenesis. Additional terms related to nuclear transport and cytoskeletal organization suggest supportive cellular processes that facilitate development. Overall, the dominant pattern is developmental signaling, with miscellaneous maintenance functions co-occurring.","confidence":"Medium","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0010909","count":5},{"id":"GO:0060492","count":5},{"id":"GO:1904948","count":5},{"id":"GO:0072053","count":5},{"id":"GO:0071562","count":5}]},{"hash":"1160668182451140665","title":"Chromatin Remodeling and Transcription Regulation","description":"The top GO terms cluster around chromatin remodeling and transcription control (chromatin remodeling, transcription from RNA Pol II, negative regulation of Pol II transcription), suggesting these proteins act as transcriptional regulators linked to chromatin dynamics. Some terms are obsolete or miscellaneous, but the predominant signal points to gene expression regulation via chromatin processes.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":3},{"id":"GO:0044109","count":2},{"id":"GO:0061412","count":2},{"id":"GO:0031496","count":2},{"id":"GO:1901407","count":2}]},{"hash":"823287638551358012","title":"Ubiquitin-Dependent Protein Degradation","description":"This cluster is dominated by GO terms tied to ubiquitination and proteasomal degradation (ubiquitin-dependent catabolic process, SCF-dependent ubiquitination, K48-linked ubiquitination, protein ubiquitination, autoubiquitination, and neddylation), pointing to a cohesive theme of protein turnover and ubiquitin signaling. Some terms also touch on stress and apoptotic signaling, suggesting connections to TNF signaling and oxidative stress\u2013induced neuronal pathways as downstream responses. Overall, the shared function is ubiquitin-mediated protein degradation and related regulation.","confidence":"High","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0031146","count":3},{"id":"GO:1903265","count":3},{"id":"GO:0051865","count":3},{"id":"GO:1903378","count":3}]},{"hash":"401409407839849169","title":"Ubiquitin-Proteostasis and Autophagy Regulation","description":"The proteins are enriched for deubiquitination and autoubiquitination, and for autophagy-related processes (mitophagy, aggrephagy, aggresome assembly, autophagosome maturation). This points to a theme of ubiquitin-mediated protein turnover coupled with selective degradation pathways, even though a GnRH neuron development term appears less central. Overall, the cluster seems to be driven by ubiquitin-driven proteostasis and autophagic clearance mechanisms.","confidence":"High","size":9,"edges":22,"triangles":24,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":4},{"id":"GO:1902236","count":3},{"id":"GO:0021888","count":3},{"id":"GO:1904049","count":3},{"id":"GO:1901097","count":3}]},{"hash":"2126800028242220756","title":"Protein Folding and Misfolded-Protein Response","description":"Most terms cluster around protein quality control: ER-associated protein folding, general protein processing, and cellular responses to misfolded proteins, plus stress-related processes like stress granule disassembly and heat acclimation. These together point to a cohesive theme of chaperone-assisted folding and stress adaptation, despite a few outlier terms (transcription, competence) that may reflect broader annotation rather than the core function of the group.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904287","count":1},{"id":"GO:0001319","count":1},{"id":"GO:0030420","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0034975","count":1}]},{"hash":"569340942978929275","title":"DNA replication and telomere maintenance","description":"The top GO terms are dominated by DNA replication, DNA repair, and telomere maintenance/capping, indicating a cluster centered on genome maintenance and nucleic acid processing. A few terms related to pollen development and meiosis appear incidental and may reflect organism-specific annotations, but the core signal supports a DNA maintenance theme.","confidence":"Medium","size":9,"edges":9,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0010833","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0016233","count":1},{"id":"GO:0006268","count":1},{"id":"GO:0007141","count":1}]},{"hash":"1155379635670643487","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":8,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:1901621","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0097428","count":2},{"id":"GO:0006458","count":2}]},{"hash":"1391195577377173357","title":"Flavonoid and fatty-acid biosynthesis in plants","description":"The cluster shows strong enrichment for chalcone and flavonoid biosynthesis, sporopollenin biosynthesis, and fatty-acyl-CoA/fatty acid biosynthetic processes, along with DIM/DIP cell wall layer assembly, indicating a cohesive plant secondary metabolism and pollen-wall formation program.","confidence":"High","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0009715","count":4},{"id":"GO:0009813","count":4},{"id":"GO:0071770","count":4},{"id":"GO:0031148","count":4},{"id":"GO:0035336","count":4}]},{"hash":"2046232435680794643","title":"Plant development and secondary metabolism","description":"The terms point to plant-focused biology: leaf formation and vegetative growth (development) and flavonol biosynthesis (secondary metabolism), with jasmonic acid response indicating defense signaling. While there are a few outliers (mitochondrial respiration, antibiotic biosynthesis), the dominant plant development/metabolism theme justifies this label.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":2},{"id":"GO:0034553","count":1},{"id":"GO:0006120","count":1},{"id":"GO:1903770","count":1},{"id":"GO:1900386","count":1}]},{"hash":"1112134119718758640","title":"Diverse Biosynthesis Pathways","description":"The top GO terms are dominated by biosynthetic processes across multiple metabolite classes, including sterol/ergosterol biosynthesis, UDP-sugar (arabinose, rhamnose) biosynthesis, secondary metabolite (phenylpropanoid) biosynthesis, and related lipid and amino metabolism. This suggests a cluster of proteins involved broadly in metabolite production rather than a single, unified function. Some terms (e.g., transcription) are outliers, but the prevailing theme is biosynthesis. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0006351","count":2},{"id":"GO:1902653","count":2},{"id":"GO:0016126","count":2},{"id":"GO:0033358","count":2}]},{"hash":"319789468638491769","title":"DNA Replication and Cell Cycle Regulation","description":"Most of the terms center on DNA replication processes (initiation, elongation, pre-replicative complex assembly), mitotic/replicative DNA replication, and cell cycle control, with related chromatin remodeling (heterochromatin formation) and DNA repair pathways (break-induced replication). A single term about female gamete generation is present but does not override the core replication/cell cycle theme.","confidence":"High","size":9,"edges":7,"triangles":2,"max_degree":5,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0006268","count":7},{"id":"GO:0007292","count":7},{"id":"GO:0030174","count":7},{"id":"GO:0006271","count":7},{"id":"GO:0000727","count":7}]},{"hash":"666047466354010541","title":"Cell division machinery and apoptosis","description":"The dominant GO terms are DNA replication, mitotic cell cycle, and protein localization to kinetochore, all core to cell division. Additional terms like positive regulation of apoptotic process and Schwann cell development support a developmental/differentiation facet tied to cell proliferation. While there are some neuronal terms present, the strongest signal centers on mitosis and DNA replication, so the cluster is best described as relating to cell division machinery (with some ancillary processes).","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0051591","count":3},{"id":"GO:0071872","count":3},{"id":"GO:0014044","count":3},{"id":"GO:0034501","count":3}]},{"hash":"129442680337647222","title":"SMAD-dependent TGF-\u03b2/BMP signaling regulation","description":"The top GO terms cluster around regulation of TGF-\u03b2 and BMP signaling, including SMAD complex assembly, receptor signaling modulation, and cellular responses to TGF-\u03b2, pointing to a common theme of developmental signaling control. Some terms reflect broader developmental contexts (meristem identity, germ-line masculinization), while a few others (nuclear export, vacuole fusion) appear peripheral to the core pathway.","confidence":"High","size":9,"edges":29,"triangles":47,"max_degree":8,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0046827","count":6},{"id":"GO:0061191","count":5},{"id":"GO:0042347","count":5},{"id":"GO:0000173","count":5},{"id":"GO:0042006","count":5}]},{"hash":"1031030885102187383","title":"Dendritic Spine Morphogenesis via Rac/Rho Signaling","description":"This cluster centers on Rac/Rho-driven cytoskeletal remodeling and synaptic maturation, with terms for lamellipodium and ruffle formation, and dendritic spine development/morphogenesis, plus excitatory synaptic signaling. The presence of hippocampus development and membrane trafficking terms further supports a neuronal context where spine formation and synaptic maturation depend on Rac/Rho signaling and actin dynamics.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007266","count":2},{"id":"GO:0010592","count":2},{"id":"GO:0060999","count":2},{"id":"GO:0097178","count":2},{"id":"GO:0016601","count":2}]},{"hash":"1912398858626477241","title":"DNA Repair and Stress Response","description":"The cluster centers on DNA repair and genome maintenance (base-excision repair, DNA repair, telomere maintenance via recombination) with apoptotic signaling, suggesting a core theme of maintaining genome integrity under stress. Additional terms reflect broader cellular stress responses (amino acid starvation, dauer development, proteolysis) that can accompany DNA damage signaling, pointing to a coordinated but broad stress response rather than a single pathway.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":2},{"id":"GO:0072670","count":2},{"id":"GO:0000722","count":2},{"id":"GO:0046944","count":2},{"id":"GO:0006915","count":2}]},{"hash":"712264211572444889","title":"Ubiquitin-Proteasome Pathway","description":"This cluster is dominated by ubiquitin-dependent proteolysis terms (SCF-dependent proteasomal ubiquitin-mediated protein catabolic process, autoubiquitination, and K63-linked ubiquitination), indicating core involvement in tagging proteins for degradation; additional terms touch on NF-kappaB signaling, ERAD, DNA repair, apoptosis, and viral processes, reflecting broader ubiquitin roles in stress responses and regulation.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:0031146","count":6},{"id":"GO:0051865","count":4},{"id":"GO:0070534","count":4},{"id":"GO:1903378","count":4}]},{"hash":"158639084235105781","title":"Wnt/Hippo signaling and skin differentiation regulators","description":"The terms show enrichment in Wnt signaling and Hippo pathway activity, along with keratinocyte differentiation and melanocyte migration, all pointing to regulation of cell fate and behavior in skin-related cell types. Additional terms for apoptosis and immune cell proliferation fit as supporting regulatory processes, suggesting this cluster centers on signaling-driven control of skin cell differentiation and movement, with broader involvement in cell survival and immune interactions.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090263","count":3},{"id":"GO:0006915","count":2},{"id":"GO:0030216","count":2},{"id":"GO:0060044","count":2},{"id":"GO:0035329","count":2}]},{"hash":"797563749628489223","title":"Polyphenol biosynthesis and xenobiotic metabolism","description":"The top GO terms cluster around biosynthesis of flavonoid glucosides (kaempferol, quercetin, cyanidin) and lignin, together with xenobiotic and hormone metabolism (estrogen catabolic process, antibiotic metabolism), suggesting a theme of polyphenol biosynthesis plus related xenobiotic processing; a single outlier term (paranode axon localization) may be noise.","confidence":"Medium","size":9,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006711","count":5},{"id":"GO:0030259","count":5},{"id":"GO:0052696","count":5},{"id":"GO:0070980","count":5},{"id":"GO:0033330","count":5}]},{"hash":"1508464465689619434","title":"Presynaptic vesicle trafficking and secretion","description":"The cluster is enriched for GO terms that center on vesicle trafficking and neurotransmitter release at the presynaptic terminal: SNARE complex assembly, synaptic vesicle fusion to the presynaptic active zone membrane, spontaneous neurotransmitter secretion, and related endosome/ER-Golgi transport processes. Together, these terms point to a cohesive role in presynaptic vesicle cycling and neurotransmitter release, with some broader intracellular trafficking connections. ","confidence":"High","size":9,"edges":4,"triangles":0,"max_degree":4,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006888","count":8},{"id":"GO:0060291","count":7},{"id":"GO:0035493","count":7},{"id":"GO:1903422","count":7},{"id":"GO:0097352","count":7}]},{"hash":"1719149760944229757","title":"Cell Cycle and DNA Replication","description":"The strongest signals are mitotic cell cycle and DNA replication, pointing to a core theme of cellular proliferation and genome maintenance. Additional terms touch on related nuclear processes (protein export from nucleus, meiotic DNA break processing) and various development/immune contexts, suggesting the cluster centers on cell division and DNA metabolism with some peripheral developmental and immune-related signals.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":9},{"id":"GO:0006260","count":9},{"id":"GO:0043277","count":8},{"id":"GO:0046641","count":8},{"id":"GO:0060709","count":8}]},{"hash":"1086901188908382858","title":"Unknown","description":"Top terms span diverse processes (development, cell cycle, signaling, neural regeneration, viral replication, and nuclear export) with no single shared function, and the cluster has no edges or triangles, indicating no cohesive expert-defined module. Therefore a specific label cannot be assigned with confidence.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051534","count":4},{"id":"GO:0045071","count":4},{"id":"GO:0001893","count":4},{"id":"GO:0051298","count":4},{"id":"GO:0042535","count":4}]},{"hash":"1658637299898325024","title":"Potassium Channels Driving Cardiac and Neuronal Excitability","description":"The top GO terms emphasize potassium ion transport across membranes, and membrane depolarization and action potentials in both atrial/AV node and neuronal contexts, pointing to a cluster of potassium channels or subunits that regulate electrical excitability in heart and nervous tissue. The mention of protein homooligomerization supports channel subunit assembly, strengthening the link to potassium channel function; a few terms related to immune signaling or pain perception appear as peripheral noise rather than core themes. Overall, the group seems best characterized by potassium-channel\u2013driven control of membrane potential in cardiac and neuronal systems.","confidence":"High","size":9,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1990573","count":3},{"id":"GO:0097623","count":3},{"id":"GO:0098910","count":2},{"id":"GO:0019228","count":2},{"id":"GO:0043029","count":2}]},{"hash":"2061795124819838325","title":"Ion Transport and Homeostasis","description":"The top GO terms point to ion transport/export across the plasma membrane (Na+, K+, Cu, Mn) and cell volume homeostasis, indicating a cluster of proteins primarily involved in maintaining ionic balance and membrane potential. Additional terms related to dephosphorylation and steroid hormone signaling, plus skeletal muscle relaxation, suggest secondary connections to signaling and muscle physiology that can accompany ion homeostasis.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036376","count":2},{"id":"GO:0030007","count":2},{"id":"GO:0097623","count":2},{"id":"GO:0006884","count":2},{"id":"GO:0006825","count":1}]},{"hash":"726086347252985434","title":"Mitochondrial Transport and Metabolism","description":"Dominated by transport-related GO terms focused on mitochondrial energy carriers (mitochondrial ATP transmembrane transport, ADP transport) and other membrane transport of small metabolites (thiamine pyrophosphate, glycine, thiosulfate). The presence of related metabolic processes (mannosyl-inositol phosphorylceramide metabolic process) and oxidative stress response (response to superoxide) supports a broad theme around mitochondrial energy metabolism and metabolite exchange. Some terms relate to physiological states (liver regeneration, female pregnancy, insulin stimulus) that can reflect systemic metabolic status, but the core signal is mitochondrial transport/metabolism.","confidence":"Medium","size":9,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006675","count":3},{"id":"GO:1990544","count":3},{"id":"GO:0097421","count":3},{"id":"GO:0032869","count":3},{"id":"GO:0007565","count":3}]},{"hash":"359966602464414041","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010019","count":9},{"id":"GO:0031426","count":9},{"id":"GO:0016554","count":9},{"id":"GO:0090615","count":9},{"id":"GO:0070129","count":9}]},{"hash":"1903383994666302999","title":"Epithelial ion transport and osmoregulation","description":"The Top Terms show ion transport across membranes (potassium, nitrate, chloride, monoatomic anions, protons) and transepithelial water transport, along with a link to pH response and cell volume regulation. This pattern indicates proteins functioning in epithelial ion transport and water/volume homeostasis, potentially in salivary gland contexts. ","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006813","count":4},{"id":"GO:0034756","count":3},{"id":"GO:1902600","count":3},{"id":"GO:0060689","count":3},{"id":"GO:1903959","count":3}]},{"hash":"1499200017344923157","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"renal system process","top_go_terms":[{"id":"GO:0046704","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0003014","count":3},{"id":"GO:1902254","count":3},{"id":"GO:0006240","count":3}]},{"hash":"599597665976644357","title":"Translation regulation and ribosome biogenesis","description":"Dominant terms are translation and ribosome-related processes (translation; ribosome assembly; preribosome large subunit assembly), with some regulation of translation and biogenesis, suggesting a cluster focused on coordinating protein synthesis and ribosome production.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0006351","count":1},{"id":"GO:0042255","count":1},{"id":"GO:0017148","count":1},{"id":"GO:0006353","count":1}]},{"hash":"891970756402023369","title":"Unknown","description":"The top GO terms span unrelated biological contexts (aerobic respiration, protein tetramerization, development of kidney tissue, lens, and brain structures, excretion/secretory processes, fungal spore formation, and cAMP signaling), suggesting no single, coherent function binding these proteins. The diversity implies either a mixed set of annotations or proteins with unrelated roles, so a concise, shared label isn\u2019t discernible.","confidence":"","size":8,"edges":14,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009060","count":3},{"id":"GO:0051289","count":3},{"id":"GO:0072014","count":3},{"id":"GO:0002088","count":3},{"id":"GO:0021670","count":3}]},{"hash":"68947209810999192","title":"Xenobiotic Detox and ROS Response","description":"This cluster shows enrichment for xenobiotic metabolic processes (xenobiotic metabolic process and 4-nitrophenol catabolic process) and detoxification (removal of superoxide radicals), with accompanying hints of nutrient response and ERK signaling, suggesting a theme of detoxification coupled to stress signaling.","confidence":"Medium","size":8,"edges":26,"triangles":44,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":1},{"id":"GO:0032355","count":1},{"id":"GO:0043525","count":1},{"id":"GO:0046196","count":1},{"id":"GO:0032414","count":1}]},{"hash":"2175072142563363823","title":"mRNA processing and splicing regulation","description":"The GO terms cluster around post-transcriptional RNA processing: mRNA modification, export, stabilization, and splicing regulation (including alternative splicing via the spliceosome), plus ncRNA-guided gene silencing. Some terms appear ancillary (blastocyst formation, viral translation), but the core signal is RNA metabolism and regulation after transcription.","confidence":"High","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016556","count":1},{"id":"GO:0006406","count":1},{"id":"GO:0031047","count":1},{"id":"GO:0048026","count":1},{"id":"GO:0000381","count":1}]},{"hash":"1671914691234242485","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006777","count":2},{"id":"GO:0050428","count":1},{"id":"GO:0019344","count":1},{"id":"GO:0019379","count":1},{"id":"GO:0009086","count":1}]},{"hash":"1478660110243119229","title":"Plant Development and Metabolic Regulation","description":"The cluster highlights terms tied to multicellular organism development, herbicide response, and hormone biosynthesis, suggesting roles in plant growth signaling and regulation. Additional metabolism-related terms (heme biosynthesis, tRNA wobble modification) indicate a broader metabolic regulatory context. Some terms are obsolete and the term set is mixed, so the label is plausible but not definitive.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0006783","count":3},{"id":"GO:0006782","count":3},{"id":"GO:0002097","count":2}]},{"hash":"1870080218641870614","title":"Ribosome Biogenesis and Translation Regulation","description":"This cluster centers on ribosome-related processes: translation, ribosome biogenesis, and rRNA maturation, with supporting RNA processing activities (RNA folding, splicing). The inclusion of responses to translation inhibitors (antibiotics, cycloheximide) reinforces a theme around regulation of protein synthesis.","confidence":"High","size":8,"edges":27,"triangles":50,"max_degree":7,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0042254","count":3},{"id":"GO:0006450","count":2},{"id":"GO:0006407","count":2},{"id":"GO:0046677","count":2}]},{"hash":"1138223501915393244","title":"Unknown","description":"The GO terms span immune regulation (T cell proliferation, tolerance induction), apoptotic cell clearance, viral response, and broad developmental/cellular processes (placental differentiation, organ regeneration, ER polarization, nuclear export, meiosis), with no clear single functional theme tying them together. Therefore no concise, specific label fits all terms.","confidence":"","size":8,"edges":9,"triangles":2,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043277","count":7},{"id":"GO:0046641","count":7},{"id":"GO:0060709","count":7},{"id":"GO:0006611","count":7},{"id":"GO:0061167","count":7}]},{"hash":"1916613352396656767","title":"Mitotic progression and microtubule dynamics","description":"This cluster is driven by mitosis and cytoskeleton-related functions: mitotic cell cycle, G2/M transition, spindle pole body duplication, and microtubule nucleation, along with regulation of protein serine/threonine kinases. Together these terms suggest a cohesive role in cell division and microtubule organization, with some developmental signals that may reflect broader growth-related roles.","confidence":"High","size":8,"edges":12,"triangles":8,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0009738","count":4},{"id":"GO:0014850","count":4},{"id":"GO:0043547","count":4}]},{"hash":"97670899066473904","title":"Unknown","description":"Top GO terms span several distinct biological areas\u2014cell division and APC-dependent catabolic process; antiviral/immune responses (cellular response to type I interferon and exogenous dsRNA); metabolic regulation (gluconeogenesis and fatty acid biosynthesis), protein interactions/modification, and plant-specific chlorophyll regulation\u2014with multiple obsolete terms. There is no single unifying function that coherently ties these 8 proteins together, so a specific, representative label cannot be assigned.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0071357","count":4},{"id":"GO:0090526","count":4},{"id":"GO:0031145","count":4},{"id":"GO:0051291","count":4}]},{"hash":"1517861255417731043","title":"Redox Homeostasis and Prostaglandin Signaling in Spermatogenesis","description":"The cluster shows enrichment for redox-related terms (cellular oxidant detoxification, removal of superoxide radicals) alongside lipid signaling (prostaglandin biosynthetic process) and reproductive development (spermatogenesis, male gonad development), with triglyceride metabolism and selenium ion response supporting a metabolic/redox context. This suggests a cohesive theme of redox balance regulating lipid-derived signaling in male reproductive biology.","confidence":"Medium","size":8,"edges":16,"triangles":20,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":4},{"id":"GO:0045454","count":4},{"id":"GO:0006641","count":4},{"id":"GO:0010269","count":3},{"id":"GO:0055114","count":3}]},{"hash":"1553132014102943869","title":"Biosynthesis and modification of biomolecules","description":"This cluster groups proteins involved in diverse biosynthetic pathways (long-chain fatty-acyl-CoA metabolism, PHB and sporopollenin biosynthesis, folate/THF biosynthesis) and modified biomolecules (methylation, phosphorylation), plus tRNA amidotransferase activity and a node for protein quality control. The common thread is synthesis and processing of biomolecules, spanning lipids, cofactors, nucleic acids, and polymers, with auxiliary quality-control activities.","confidence":"Medium","size":8,"edges":12,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0035336","count":2},{"id":"GO:0080110","count":2},{"id":"GO:0042619","count":2},{"id":"GO:0006515","count":1}]},{"hash":"118156715426240540","title":"Redox Homeostasis and Calcium Signaling","description":"This cluster centers on glutathione-dependent redox balance and detoxification (glutathione metabolism, protein glutathionylation, cellular oxidant detoxification, toxin/ar\u00adsenic response) and on calcium handling linked to mitochondria and the sarcoplasmic reticulum (mitochondrial membrane potential regulation, SR calcium release). The combination of redox-focused processes with calcium signaling suggests a coordinated stress-response module for maintaining cellular homeostasis under toxin or oxidative stress.","confidence":"High","size":8,"edges":26,"triangles":45,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0009407","count":7},{"id":"GO:0019852","count":7},{"id":"GO:0051881","count":7},{"id":"GO:0098869","count":7},{"id":"GO:0010731","count":7}]},{"hash":"970818967997767880","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019344","count":2},{"id":"GO:0070814","count":2},{"id":"GO:0032332","count":1},{"id":"GO:0006814","count":1},{"id":"GO:1901300","count":1}]},{"hash":"2267655912519730688","title":"Unknown","description":"The cluster shows a highly varied mix of GO terms with no single shared function, including epithelial\u2013mesenchymal transition regulation, SMAD signaling regulation, epithelium maintenance, tRNA modification, translational fidelity, phenazine biosynthesis, pollen tube growth, and protein carbamoylation; with no edges connecting proteins, suggesting annotation noise or diverse, unrelated roles.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010719","count":1},{"id":"GO:0060394","count":1},{"id":"GO:0009405","count":1},{"id":"GO:0030277","count":1},{"id":"GO:0002047","count":1}]},{"hash":"1639818949189167780","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015969","count":1},{"id":"GO:0001680","count":1},{"id":"GO:0006808","count":1},{"id":"GO:0006203","count":1},{"id":"GO:0042245","count":1}]},{"hash":"1827850825468761360","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0015979","count":1},{"id":"GO:0010833","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0006296","count":1}]},{"hash":"1209346535925001334","title":"Nuclear RNA Processing & RNP Import","description":"The cluster shows strong representation of GO terms for mRNA export from the nucleus, ribosomal protein import, tRNA transport, and import of hnRNP/splicing factors, all pointing to a functional module centered on nuclear RNA processing and ribonucleoprotein trafficking. A few terms related to transcription regulation and protein desumoylation suggest broader regulatory connections, but the dominant pattern is import/export and processing of RNA-associated RNPs in the nucleus.","confidence":"High","size":8,"edges":8,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006406","count":4},{"id":"GO:0006610","count":4},{"id":"GO:0051031","count":4},{"id":"GO:0000122","count":4},{"id":"GO:0042176","count":4}]},{"hash":"1300306740393591489","title":"Unknown","description":"The GO terms are scattered across transcription, immune response, metabolism, lipid signaling, and microtubule organization, with no single shared function. The cluster shows very weak connectivity (one edge, no triangles, max degree 1), supporting a lack of coherent functional theme. ","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0097755","count":3},{"id":"GO:0046272","count":3},{"id":"GO:0046839","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0098869","count":2}]},{"hash":"927435331901486926","title":"Ribosome biogenesis and translation","description":"The top GO terms center on translation and ribosome assembly/biogenesis (including mitochondrial translation), indicating the proteins likely function in protein synthesis machinery. Some terms about protein stability and targeting appear, but the dominant signal is ribosome-associated translation.","confidence":"High","size":8,"edges":14,"triangles":8,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:2000435","count":1},{"id":"GO:1904667","count":1},{"id":"GO:0050821","count":1},{"id":"GO:0006605","count":1}]},{"hash":"891103836772693337","title":"Central metabolism and quinone biosynthesis","description":"The cluster shows strong signals for core energy metabolism (glycolysis, TCA cycle, beta-oxidation) and quinone biosynthesis (menaquinone, phylloquinone) plus related biosynthesis processes, suggesting a metabolism-focused cluster. Some terms like cellular response to type I interferon and microtubule anchoring are less representative.","confidence":"Medium","size":8,"edges":23,"triangles":30,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":2},{"id":"GO:0006096","count":2},{"id":"GO:0009234","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0010124","count":2}]},{"hash":"775997455198538903","title":"mRNA Processing and Splicing Regulation","description":"The cluster is dominated by post-transcriptional processes: mRNA modification, export, stabilization, and especially spliceosome-regulated splicing (including alternative splicing). While there are a few broader expression terms (transcription elongation, translation) they are less central, so the core theme points to mRNA maturation and splicing control.","confidence":"High","size":8,"edges":15,"triangles":13,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006368","count":2},{"id":"GO:0016556","count":2},{"id":"GO:0006406","count":2},{"id":"GO:0031047","count":2}]},{"hash":"21296435880999990","title":"Unknown","description":"The GO terms span DNA repair, diverse plant and animal signaling and development processes (anthocyanin biosynthesis, auxin signaling, estradiol response, endothelial morphogenesis, organ regeneration) as well as general stress-related categories. This broad mix suggests no single cohesive function tying the cluster, so a specific label is not justifiable.","confidence":"","size":8,"edges":5,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006289","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009718","count":2},{"id":"GO:0032355","count":1},{"id":"GO:0009734","count":1}]},{"hash":"1386297812033105434","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":27,"triangles":50,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006825","count":2},{"id":"GO:0016311","count":2},{"id":"GO:0046295","count":2},{"id":"GO:0097171","count":2},{"id":"GO:0009244","count":2}]},{"hash":"1989929487583902038","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006424","count":1},{"id":"GO:0006450","count":1},{"id":"GO:0070681","count":1},{"id":"GO:0032543","count":1},{"id":"GO:0019354","count":1}]},{"hash":"790860363179339449","title":"Transcriptional regulation and ubiquitin-mediated proteolysis","description":"This cluster centers on DNA-templated transcription and chromatin organization, with supporting terms for RNA methylation and transcriptional regulation, plus protein ubiquitination and SCF-dependent proteasomal degradation, indicating coordinated gene expression control with post-translational turnover; developmental signals like TGF-beta and spinal cord development further tie these processes to growth and differentiation.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0070208","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0036265","count":4},{"id":"GO:0070262","count":3}]},{"hash":"484206440927952826","title":"Unknown","description":"Top terms span phylloquinone catabolic process, several biosynthetic processes (phenylpropanoid, very long-chain fatty acid, LPS O antigen/core, ADP-L-glycero-beta-D-manno-heptose) and various catabolic reactions. This mix across plant and bacterial metabolism provides no single unifying function for the cluster, so a cohesive, specific label is not apparent.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042376","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0045150","count":1},{"id":"GO:0009699","count":1},{"id":"GO:1902123","count":1}]},{"hash":"1252370651827647693","title":"Unknown","description":"The top GO terms show a scattered mix of energy metabolism, genome replication and transcription regulation, protein processing, cell cycle (centriole) dynamics, viral replication, and even a plant-specific photosystem II process. There is no clear, cohesive theme uniting these proteins, so a specific functional label isn\u2019t justifiable. ","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046034","count":1},{"id":"GO:0006406","count":1},{"id":"GO:2001171","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0019079","count":1}]},{"hash":"1547788550732283067","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":2},{"id":"GO:0015979","count":1},{"id":"GO:0042549","count":1},{"id":"GO:0090615","count":1},{"id":"GO:0090617","count":1}]},{"hash":"454378629813276404","title":"Membrane transporters for ions and nutrients","description":"These proteins are linked to transmembrane transport across membranes for a variety of ions and metabolites (e.g., nitrite, nitrate, sodium, potassium, galactose, phosphate, sialic acid, fucose), with an additional related role in neurotransmitter loading into synaptic vesicles. The shared GO terms center on transport activity, suggesting a cohesive theme of membrane transport rather than a single substrate type.","confidence":"High","size":8,"edges":10,"triangles":4,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":7},{"id":"GO:0042891","count":7},{"id":"GO:0015757","count":7},{"id":"GO:0035725","count":7},{"id":"GO:0098700","count":7}]},{"hash":"659269978633072688","title":"Ribosome Biogenesis and Translation","description":"The cluster\u2019s strongest signals are translation and ribosome biogenesis (translation, cytoplasmic translation, ribosome biogenesis, ribosomal small subunit biogenesis), indicating a core role in making and using ribosomes. The presence of cell division-related terms (cell cycle, cell division, cell septum assembly) suggests these proteins may also participate in growth-linked division processes, common for ribosome-associated factors in bacteria. Overall, the cluster centers on ribosome assembly and protein synthesis with an ancillary link to cytokinesis.","confidence":"High","size":8,"edges":7,"triangles":1,"max_degree":3,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0002181","count":3},{"id":"GO:0090529","count":2},{"id":"GO:0042274","count":2},{"id":"GO:1903833","count":2}]},{"hash":"1266400971724338934","title":"Cell cycle regulation and RNA processing cluster","description":"Top GO terms indicate strong signals for cell cycle control (positive regulation of cell cycle, DNA replication) and RNA processing (mRNA polyadenylation, snoRNA splicing), with additional involvement in translation regulation and apoptosis, plus responses to estradiol and hydrogen peroxide. This points to a cohesive function in coordinating gene expression during cell cycle progression and cellular stress/hormonal signaling, hence the label. ","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045787","count":2},{"id":"GO:0098789","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0034247","count":2},{"id":"GO:0032355","count":2}]},{"hash":"1246991082287697512","title":"Neuronal dendrite morphogenesis and branching","description":"The top GO terms are dominated by neuronal development and dendrite-related processes (dendrite morphogenesis, dendrite development, neuronal stem cell maintenance, ephrin signaling, and nerve branching regulation), suggesting the proteins cluster around neural differentiation and dendritic patterning. A few plant-related terms appear but are outliers compared to the neurally focused terms.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009955","count":1},{"id":"GO:1900170","count":1},{"id":"GO:0097150","count":1},{"id":"GO:0050775","count":1},{"id":"GO:1902213","count":1}]},{"hash":"980599554363733400","title":"Unknown","description":"The top GO terms are highly heterogeneous, spanning sulfur-related metabolism and RNA/tRNA modification, plus various development and signaling processes. With no edges and only singleton terms, there is no clear, shared function binding this protein set, so a single interpretable label cannot be confidently assigned.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019346","count":1},{"id":"GO:0018192","count":1},{"id":"GO:0070329","count":1},{"id":"GO:0002143","count":1},{"id":"GO:0006071","count":1}]},{"hash":"1794668768224462125","title":"Nucleobase Transporters","description":"The top GO terms are dominated by transport of purine and pyrimidine compounds (hypoxanthine, guanine, adenine, urate, uracil, xanthine), indicating a shared role in membrane transport of nucleobases and related metabolites. An overall lack of protein-interaction edges suggests these proteins may be a dispersed transporter family. The salicylic acid-related terms are less central and may reflect broader signaling context or annotation noise. Based on the prominent transport terms, the cluster best labeled as nucleobase/nucleoside transporters.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035344","count":1},{"id":"GO:0098710","count":1},{"id":"GO:1903825","count":1},{"id":"GO:0098702","count":1},{"id":"GO:0015747","count":1}]},{"hash":"1326532609451818200","title":"Unknown","description":"The GO terms in this cluster span plant signaling, multiple unrelated catabolic and biosynthetic processes, mitochondrial respiration, and even vertebrate reproductive functions, showing no single cohesive function. This breadth prevents a meaningful, specific label.","confidence":"","size":8,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009736","count":2},{"id":"GO:0006103","count":2},{"id":"GO:0006552","count":2},{"id":"GO:0006120","count":2},{"id":"GO:0043448","count":2}]},{"hash":"412724899926866333","title":"Oocyte maturation and meiotic spindle assembly","description":"Dominant GO terms are about oocyte maturation, spindle assembly in female meiosis I, and ubiquitin-proteasome\u2013related protein degradation during the cell cycle, suggesting a cohesive theme of oocyte meiosis and spindle dynamics. A couple of neural development terms appear but are less central to the cluster\u2019s core function.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":2},{"id":"GO:0070544","count":2},{"id":"GO:0046785","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0021993","count":2}]},{"hash":"1577182092950118190","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0000398","count":5},{"id":"GO:0000464","count":5},{"id":"GO:0000393","count":4},{"id":"GO:0071035","count":4},{"id":"GO:0000467","count":4}]},{"hash":"2201132883933474608","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0000472","count":2}]},{"hash":"1568595870460239823","title":"Splicing and mRNA Export Regulators","description":"The cluster centers on RNA processing and nuclear-cytoplasmic mRNA handling, with GO terms for spliceosome-mediated splicing and regulation (positive/alternative splicing) and mRNA export and modification. Additional trafficking terms (ER-Golgi and endosome-Golgi transport) and developmental terms (dendrite development, blastocyst formation) suggest broader roles in gene expression regulation and development, possibly linked to nuclear-cytoplasmic transport and RNA maturation.","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0034498","count":2},{"id":"GO:0016358","count":2},{"id":"GO:0016556","count":1},{"id":"GO:0006406","count":1}]},{"hash":"677448127106846131","title":"Microtubule dynamics and mitotic processes","description":"Based on GO terms dominated by microtubule depolymerization (axonal and cytoplasmic), mitotic spindle events (metaphase chromosome alignment, spindle orientation), and cytokinesis, the cluster centers on regulation and remodeling of microtubules during cell division. Additional terms about neuron projection maintenance, cerebellar structure, and stem cell homeostasis suggest a broader role for microtubule dynamics in neuronal and epithelial tissue maintenance, consistent with the core theme of cytoskeletal control during division and neural maintenance.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000742","count":7},{"id":"GO:1990535","count":6},{"id":"GO:1990942","count":6},{"id":"GO:0021685","count":6},{"id":"GO:0036334","count":6}]},{"hash":"122541311329582621","title":"Spliceosome-driven mRNA splicing and RNA processing","description":"Based on the dominance of GO terms related to mRNA splicing via the spliceosome, plus positive regulation of splicing and regulatory ncRNA-mediated gene silencing, the cluster appears to center on RNA processing by the spliceosome. Additional terms about polyadenylation and spliceosomal conformational changes support a focus on pre-mRNA processing, while some DNA replication/repair annotations may reflect broader nuclear RNA metabolism or pleiotropic roles of involved proteins.","confidence":"High","size":8,"edges":26,"triangles":44,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000398","count":6},{"id":"GO:0031047","count":6},{"id":"GO:0048026","count":6},{"id":"GO:0045292","count":4},{"id":"GO:0006378","count":4}]},{"hash":"36570937389388443","title":"Brain development and neural injury response","description":"Top GO terms point to a brain-centric theme, including brain development, axon injury response, and circadian sleep/wake cycle regulation, with estradiol response suggesting hormonal signaling in neural contexts. While a few terms relate to bone mineralization or integrin regulation, the strongest, most coherent signal centers on neural development and neural stress/hormonal signaling. Medium","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032355","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0031667","count":1},{"id":"GO:0007420","count":1},{"id":"GO:0008284","count":1}]},{"hash":"174913782708308230","title":"Nutrient and Ion Transporters","description":"The cluster shows multiple transmembrane transport terms across diverse substrates: nitrate/nitrite, sodium and phosphate ions, sugars (galactose, fucose), and xenobiotics, plus a related neurotransmitter loading term. This pattern points to membrane transporter proteins handling various nutrients and ions, rather than a single specific metabolic pathway.","confidence":"Medium","size":8,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":6},{"id":"GO:0006004","count":4},{"id":"GO:0098700","count":4},{"id":"GO:0015757","count":4},{"id":"GO:1900754","count":4}]},{"hash":"32020140132765649","title":"Epidermal development and pigmentation","description":"The top GO terms include multicellular organism development, skin development, and pigmentation, indicating a theme around epidermal differentiation and pigment-related processes. Additional terms like cellular response to calcium, regulation of GTPase and kinase activity suggest signaling pathways governing keratinocyte proliferation, differentiation, and pigment cell function. Together, these points support labeling the cluster as related to epidermal development and pigmentation signaling.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0071277","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0008284","count":2},{"id":"GO:0071902","count":2}]},{"hash":"1964530415759249021","title":"Cerebellar Development and Glial Differentiation","description":"This cluster is dominated by cerebellum-related terms, notably cerebellar cortex formation and Bergmann glial cell differentiation, with axon regeneration as a complementary neural-development signal. While insulin and T cell signaling terms appear, the strongest and most representative theme centers on cerebellar development and glial maturation, supported by cell-cycle regulation motifs typical of developmental processes.","confidence":"High","size":8,"edges":22,"triangles":31,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0048679","count":8},{"id":"GO:0008286","count":8},{"id":"GO:0021697","count":8},{"id":"GO:0050852","count":8},{"id":"GO:0060020","count":8}]},{"hash":"1481213647057122028","title":"Oocyte Meiosis and Spindle Assembly Regulation","description":"This cluster\u2019s terms repeatedly point to oocyte maturation, spindle assembly in female meiosis I, and SCF-dependent proteasomal ubiquitin-dependent protein catabolic processes, indicating coordinated control of meiosis via ubiquitin-proteasome\u2013mediated protein turnover and microtubule dynamics. Some terms about neural development appear but the dominant signal is meiosis/spindle progression and proteolysis in oocytes.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051436","count":1},{"id":"GO:0001556","count":1},{"id":"GO:0070544","count":1},{"id":"GO:0046785","count":1},{"id":"GO:0006516","count":1}]},{"hash":"1217239334557230227","title":"Nucleotide metabolism and salvage","description":"The cluster shows GO terms focused on nucleotide metabolism and related RNA processing: UMP salvage, uridine and cytidine metabolism, deoxycytidine catabolism, guanine catabolic process, and tRNA wobble editing. A riboflavin biosynthesis term and a few ancillary annotations appear, but the dominant signal is nucleotide metabolism and its related RNA processes.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044206","count":1},{"id":"GO:0046109","count":1},{"id":"GO:0006147","count":1},{"id":"GO:0009231","count":1},{"id":"GO:0046677","count":1}]},{"hash":"1258285999298553100","title":"Spermatid flagellum assembly","description":"The top GO signals center on spermatid development and inner dynein arm assembly, pointing to a role in sperm flagellum formation and motility; other terms suggest broader spermatogenesis and cellular transport, but the strongest theme is flagellar axoneme assembly.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007286","count":2},{"id":"GO:1902064","count":1},{"id":"GO:0032147","count":1},{"id":"GO:0006351","count":1},{"id":"GO:2000574","count":1}]},{"hash":"1616796515487869810","title":"Antibiotic biosynthesis and response","description":"The top GO terms are dominated by antibiotic-related activity, with antibiotic biosynthetic process and response to antibiotic each appearing twice, suggesting a central theme around antibiotic production or defense. Additional terms include related metabolic processes (phosphinothricin biosynthesis, purine/ureide/allantoin catabolism, oxalate metabolism) and plasmodesmata-mediated transport, which together point to a broader plant-associated defense/metabolic context rather than a single narrow pathway. Overall, the cluster seems best described by antibiotic-related functions, with supporting metabolism and intercellular coordination considerations.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0055114","count":2},{"id":"GO:1901766","count":1},{"id":"GO:0010136","count":1}]},{"hash":"585534089640202803","title":"RNA Polymerase II Transcription Regulation","description":"The top GO terms are dominated by regulation and initiation of transcription by RNA polymerase II (GO:0006355, GO:0006351, GO:0006357, GO:0011123), indicating the cluster centers on transcriptional control. Some mitochondrial-related terms appear (membrane potential, permeability, ATP synthesis) and a transport term, which may reflect broader cellular energy context or secondary associations, but do not override the transcription-focused signal. Therefore, a label emphasizing RNA Pol II transcription regulation best represents the cluster\u2019s core function.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0010940","count":1},{"id":"GO:0010917","count":1},{"id":"GO:0035794","count":1},{"id":"GO:0099132","count":1}]},{"hash":"2258589096862583026","title":"Unknown","description":"These proteins collectively show a mixture of metabolism (redox, ethanol/furaldehyde, retinoic acid, lignin) and stress/immune signaling (copper, lipopolysaccharide, extracellular signaling regulation), with no single unifying function evident.","confidence":"","size":8,"edges":22,"triangles":28,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0042573","count":2},{"id":"GO:0045777","count":2},{"id":"GO:0043458","count":2},{"id":"GO:0046688","count":2}]},{"hash":"972048444717266888","title":"Flower and inflorescence development","description":"Based on the GO terms, this cluster centers on plant reproductive development, with multiple terms for flower development, inflorescence development, and the timing of transitioning from vegetative to reproductive growth. The presence of general development terms (cell differentiation, multicellular organism development) supports a cohesive theme of floral morphogenesis, while a few unrelated terms likely reflect noise. Confidence: High","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030154","count":2},{"id":"GO:0007275","count":1},{"id":"GO:0009911","count":1},{"id":"GO:0048510","count":1},{"id":"GO:0010229","count":1}]},{"hash":"2289226420636364085","title":"Bacterial metabolism and division with metal transport","description":"The top GO terms point to diverse bacterial processes: antibiotic biosynthesis, nitrate assimilation, lignin degradation, and copper/iron transport, alongside FtsZ-dependent cytokinesis and transcription. This mix suggests a prokaryotic cluster characterized by metabolic versatility (including secondary metabolism and nutrient processing) and essential cell division, with metal ion transport supporting these activities. Thus, the label reflects a broad prokaryotic functional theme rather than a single pathway.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0042128","count":3},{"id":"GO:0035023","count":2},{"id":"GO:0006351","count":2}]},{"hash":"295710853429793337","title":"Transcription and DNA Recombination Proteins","description":"The prominent GO terms are DNA recombination and transcription by RNA polymerase II (plus RNA-templated transcription), pointing to nuclear transcription/DNA-processing roles. The brain development and axon guidance terms are less represented and may reflect multifunctional or less-specific annotations. Overall, the cluster centers on transcription and DNA processing activities.","confidence":"Medium","size":8,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006310","count":2},{"id":"GO:0006366","count":2},{"id":"GO:0001172","count":2},{"id":"GO:0007420","count":1},{"id":"GO:1905050","count":1}]},{"hash":"1707599483829595815","title":"Unknown","description":"The top GO terms are fragmented across methylation/dna methylation (and a DNA restriction-modification system) and various catabolic and signaling processes from plants and animals, with several obsolete terms. There is no clear, shared function tying these eight proteins together, so a cohesive label cannot be assigned.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090124","count":3},{"id":"GO:0006479","count":3},{"id":"GO:0032775","count":3},{"id":"GO:0009307","count":3},{"id":"GO:0019762","count":1}]},{"hash":"2053855137515905955","title":"Membrane Solute Transporters","description":"This cluster is dominated by transmembrane transporter GO terms covering a wide range of substrates, including xenobiotics, vitamins, sugars (glucose, fructose, trehalose), nitrite, and organic anions, plus related stress responses. The coherence around transporting diverse solutes across membranes suggests a group of membrane transport proteins with broad substrate specificity. Confidence: High","confidence":"","size":8,"edges":16,"triangles":11,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":8},{"id":"GO:0035461","count":8},{"id":"GO:0042149","count":6},{"id":"GO:1990539","count":6},{"id":"GO:0043252","count":6}]},{"hash":"1874359068066785004","title":"Unknown","description":"The GO terms are varied across organisms and processes (lipid catabolism, heterocyst development, transcription regulation, sensing of hypoxia and visible light, chlorophyll regulation, ethylene signaling, and iron transport regulation), with no single cohesive function tying them together, so there is no clear thematic cluster.","confidence":"","size":8,"edges":8,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0016042","count":1},{"id":"GO:0043158","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0070483","count":1},{"id":"GO:1903660","count":1}]},{"hash":"643736734851383812","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0007399","count":2},{"id":"GO:0006543","count":1},{"id":"GO:0009236","count":1}]},{"hash":"1354119993530137536","title":"Unknown","description":"There are no top GO terms provided for this cluster, so there is no identifiable shared function or theme to connect the eight proteins. Without enrichment or thematic terms, the cluster cannot be confidently characterized beyond being a set of interacting or co-listed proteins.","confidence":"","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[]},{"hash":"318926373031002251","title":"Unknown","description":"The top GO terms include aging (obsolete), response to xenobiotic stimulus, glycosylation, cell wall organization, DNA catabolic process, cellular response to cAMP, redox homeostasis, transcription regulation and mRNA stability. The terms point to disparate processes (aging, stress response, post-translational modification, structural biology, nucleic acid metabolism, and gene regulation), with no clear, unifying function for the cluster. Therefore a specific label cannot be confidently assigned.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":3},{"id":"GO:0042493","count":3},{"id":"GO:0016266","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0006308","count":2}]},{"hash":"1139642830000029388","title":"Unknown","description":"The top GO terms are a mix of diverse metabolic and signaling processes (prostaglandin catabolic, strigolactone biosynthesis, endocannabinoid signaling regulation, various catabolic and biosynthetic processes), with no clear, cohesive function linking the proteins. This suggests heterogeneous roles rather than a single shared pathway.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1905344","count":4},{"id":"GO:0009086","count":4},{"id":"GO:1901601","count":4},{"id":"GO:2000124","count":4},{"id":"GO:0019380","count":4}]},{"hash":"1754005266707996938","title":"Triglyceride and phospholipid catabolism","description":"Based on the GO terms, the cluster centers on lipid degradation and membrane lipid remodeling, including triglyceride catabolic process, triglyceride mobilization, triglyceride acyl-chain remodeling, and phosphatidylcholine/phosphatidylethanolamine catabolic processes. A couple of terms about cell shape and peptidoglycan processes are present but appear peripheral to the main lipid-catabolic theme, so the label reflects the dominant function.","confidence":"High","size":8,"edges":7,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0010898","count":1},{"id":"GO:0034638","count":1},{"id":"GO:0006642","count":1},{"id":"GO:0019433","count":1},{"id":"GO:0046338","count":1}]},{"hash":"1182684682736579517","title":"Sterol and ether lipid biosynthesis","description":"This cluster shows a cohesive theme around lipid metabolism, with GO terms pointing to cholesterol biosynthesis via lathosterol, ergosterol biosynthesis, and ether lipid metabolism, plus related sphingolipid pathways. Despite a couple obsolete terms and peripheral annotations (e.g., sebaceous gland differentiation, B cell chemotaxis), the dominant signal is sterol/ether lipid biosynthetic processes, suggesting a lipid biosynthesis module. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006627","count":2},{"id":"GO:0000746","count":2},{"id":"GO:0033490","count":1},{"id":"GO:0080065","count":1},{"id":"GO:0001949","count":1}]},{"hash":"1690546347867724872","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":7},{"id":"GO:0090617","count":7},{"id":"GO:0042793","count":7},{"id":"GO:1905639","count":7},{"id":"GO:1900865","count":7}]},{"hash":"2230852925166955086","title":"Unknown","description":"The GO terms are highly heterogeneous, ranging from metal transport and lipid/lipoprotein metabolism to pollination, endothelial activation, and glutamatergic synaptic activity, with no clear single biological theme binding the cluster. This lack of a cohesive function makes a confident, specific label inappropriate.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015690","count":1},{"id":"GO:0009856","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0006869","count":1},{"id":"GO:0042157","count":1}]},{"hash":"2058016316708839608","title":"Plant lipid signaling and defense responses","description":"The terms center on lipid metabolism and lipid signaling (lipid catabolic processes and regulation of endocannabinoid signaling) intertwined with plant defense pathways (salicylic acid signaling, camalexin biosynthesis) and stress-related plant processes (aerenchyma formation, pectin remodeling). This suggests a theme where lipid signaling modulates plant defense and stress responses, justifying the label.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000124","count":4},{"id":"GO:0019433","count":4},{"id":"GO:0034727","count":3},{"id":"GO:0010618","count":3},{"id":"GO:0006624","count":3}]},{"hash":"591677507606968929","title":"Photosynthesis Light Harvesting and Light Response","description":"The top GO terms cluster around photosynthesis and light harvesting in photosystems I and II, with multiple light-regulated responses (far-red, UV-A, high/low light) and nonphotochemical quenching, plus a link to phytol biosynthesis; together they point to chloroplast light capture and protective/light-adjustment processes.","confidence":"High","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0009768","count":3},{"id":"GO:1904964","count":3},{"id":"GO:0010218","count":3},{"id":"GO:0071486","count":3},{"id":"GO:0071492","count":3}]},{"hash":"760111422386137617","title":"Protein and RNA methylation enzymes","description":"The top GO terms are methylation-related: N-terminal peptidyl-glycine methylation, rRNA methylation, and peptidyl-lysine dimethylation, indicating a set of methyltransferases targeting proteins and RNA. Additional terms reflect oxidative stress response and various metabolic processes, but the methylation theme dominates, supporting a label for methyltransferase-containing cluster.","confidence":"High","size":7,"edges":17,"triangles":21,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0018013","count":2},{"id":"GO:0031167","count":2},{"id":"GO:0018027","count":2},{"id":"GO:0006979","count":2},{"id":"GO:0006099","count":2}]},{"hash":"1653313465544290087","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by GO terms related to ribosome production and function: translation, ribosomal large subunit export from the nucleus, and ribosome biogenesis. These suggest the proteins primarily participate in ribosome assembly and protein synthesis. A few regulatory or transcription-related terms are present, but they are less central to the core theme. Overall, the hub appears to be ribosome biogenesis and translation.","confidence":"High","size":7,"edges":16,"triangles":17,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0000055","count":1},{"id":"GO:0042273","count":1},{"id":"GO:0042254","count":1},{"id":"GO:1901724","count":1}]},{"hash":"1123708132430853763","title":"Ribosome Biogenesis and Translation","description":"The top terms cluster around ribosome biology: rRNA processing (ITS1 cleavage), ribosome biogenesis, and both cytoplasmic and mitochondrial translation. The presence of transcription-related terms likely reflects regulation of ribosomal gene expression rather than a separate pathway. Together, these suggest a function group dedicated to ribosome assembly and protein synthesis.","confidence":"High","size":7,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0006355","count":1}]},{"hash":"352749242616115321","title":"Photosynthesis Light Harvesting and Light-Response Proteins","description":"The cluster is dominated by GO terms tied to photosynthesis and light-related responses, including light harvesting in photosystems I and II, responses to various light intensities and wavelengths (far red, UV-A), and nonphotochemical quenching, plus phytol biosynthesis. This combination points to chloroplast-associated proteins involved in capturing light for photosynthesis and protecting against light stress, justifying a label focused on photosynthesis and light response.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":3},{"id":"GO:0009768","count":2},{"id":"GO:1904964","count":2},{"id":"GO:0010218","count":2},{"id":"GO:0071486","count":2}]},{"hash":"743064896465396893","title":"Photosystem I Electron Transport and Light Harvesting","description":"The terms show a clear PSI-centered theme: nonphotochemical quenching, photosynthesis, and several PSI-specific processes such as electron transport, light harvesting in photosystem I, and responses to light quality/intensity (far-red, high light). Additional terms about phytol biosynthesis and N-terminal acetylation support chloroplast-associated functions that underpin photosystem stability and membrane composition. Together, they point to proteins involved in PSI-driven photosynthetic light reactions and related chloroplast maintenance, justifying a PSI-focused label.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010196","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0017196","count":1},{"id":"GO:0009780","count":1},{"id":"GO:0009773","count":1}]},{"hash":"2075956423855797539","title":"Unknown","description":"The top GO terms are highly heterogeneous, spanning plant-specific processes (strigolactone biosynthesis/response, chlorophyll catabolism) and unrelated metabolic or signaling processes (prostaglandin catabolism, endocannabinoid signaling, nitrogen utilization, methionine biosynthesis, C-terminal demethylation). With zero edges and no coherent shared function across terms, there is no clear common theme tying these proteins together.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902348","count":1},{"id":"GO:1905344","count":1},{"id":"GO:0009086","count":1},{"id":"GO:1901601","count":1},{"id":"GO:0015996","count":1}]},{"hash":"1860769431705095659","title":"Chloroplast Protein Synthesis and PSII Repair","description":"This cluster centers on chloroplast-associated processes: ribosome biogenesis and translation alongside photosystem II repair/assembly and light-response terms. The co-occurrence of translation-related terms with PSII maintenance strongly suggests a chloroplast protein synthesis and photosystem II repair theme, with a few other organelle-related terms likely incidental noise.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0006412","count":1},{"id":"GO:0010206","count":1},{"id":"GO:0071484","count":1}]},{"hash":"2286021542332351500","title":"Hormone signaling and redox metabolism","description":"This cluster includes GO terms for prostaglandin biosynthesis, estradiol response, and auxin-activated signaling, suggesting involvement in hormone signaling. It also contains terms for glutathione derivative and ascorbate metabolism, toxin catabolic processes, and regulation of ERK cascades, pointing to redox/metabolic regulation and signaling control. Together, these terms imply proteins that mediate hormonal signaling coupled with redox and metabolic processes.","confidence":"Medium","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":7},{"id":"GO:0032355","count":5},{"id":"GO:0009734","count":5},{"id":"GO:0031100","count":5},{"id":"GO:0042994","count":5}]},{"hash":"1548294621654271572","title":"Unknown","description":"The cluster includes diverse GO terms spanning amino acid and lipid metabolism, transcription, insulin signaling, and plant development (fruit ripening), with no single dominant theme. Therefore no clear common function can be assigned.","confidence":"","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019878","count":5},{"id":"GO:0019441","count":4},{"id":"GO:0032869","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0006107","count":4}]},{"hash":"1568696272129239189","title":"Redox Homeostasis and Oxidative Stress Response","description":"The proteins show strong enrichment for redox-related processes: cellular oxidant detoxification, redox homeostasis, oxidative stress response, and protein deglutathionylation, suggesting a shared function in maintaining cellular redox balance. Additional terms (ion transporter regulation, development) appear ancillary or context-specific, but do not outweigh the redox-dominant theme.","confidence":"Medium","size":7,"edges":17,"triangles":21,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1903026","count":6},{"id":"GO:0034599","count":6},{"id":"GO:0055114","count":6},{"id":"GO:2000651","count":6},{"id":"GO:0080058","count":6}]},{"hash":"1103271268697394047","title":"Redox Regulation and Oxidative Stress Response","description":"Driven by strong representation of redox-related GO terms (cellular redox homeostasis, cellular oxidant detoxification, cellular response to oxidative stress, and protein deglutathionylation), this cluster appears enriched for redox balance and detoxification functions. Some other terms (methylamine metabolism, prostaglandin biosynthesis, etc.) may reflect additional roles or annotation noise, but the dominant theme is redox regulation.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":4},{"id":"GO:0098869","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0030416","count":3},{"id":"GO:0001516","count":3}]},{"hash":"63461687913303070","title":"Dendritic spine development and actin remodeling","description":"The top terms center on actin cytoskeleton dynamics and neuronal development, including Rac/Rho signaling, lamellipodium and ruffle formation, dendritic spine development, and hippocampus development, which together point to neuronal synaptic remodeling. Immune-related terms appear but are less representative of the main theme. ","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042088","count":2},{"id":"GO:0046330","count":2},{"id":"GO:0032707","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0007266","count":2}]},{"hash":"1462566306627782900","title":"Mixed Metabolic Catabolism","description":"Proteins in this cluster map to a variety of catabolic processes across different substrates, with no single pathway dominating. The shared theme is broad metabolism and breakdown rather than a specific function, making a general \u201cmixed metabolic catabolism\u201d label appropriate. ","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015914","count":1},{"id":"GO:0019470","count":1},{"id":"GO:0019877","count":1},{"id":"GO:0009089","count":1},{"id":"GO:0046176","count":1}]},{"hash":"1122393595871712557","title":"Unknown","description":"The term set includes responses to estradiol, auxin signaling, herbicide response, endothelial and retina vasculature morphogenesis, organ regeneration, transcription factor sequestration, toxin catabolic process, ascorbic acid metabolism, and MAPK pathway regulation. The terms span diverse biological areas (hormone signaling, development, detoxification, metabolism) with no clear, singular theme linking them, so a cohesive label is not apparent.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032355","count":1},{"id":"GO:0009734","count":1},{"id":"GO:0009635","count":1},{"id":"GO:0001886","count":1},{"id":"GO:0031100","count":1}]},{"hash":"1861144073113642905","title":"Neuronal proteostasis and autophagy regulation","description":"This cluster is dominated by ubiquitin-dependent quality control (protein autoubiquitination, ERAD) and autophagy-related processes (mitophagy, aggrephagy, autophagosome maturation), with connections to neuronal development and neurotransmitter regulation, suggesting a cohesive theme of proteostasis maintenance in neurons; a ribosomal subunit assembly term may be a secondary association.","confidence":"Medium","size":7,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":7},{"id":"GO:1903265","count":7},{"id":"GO:0030433","count":7},{"id":"GO:1902236","count":6},{"id":"GO:0021888","count":6}]},{"hash":"1672417120338649552","title":"Redox homeostasis and NF-kB signaling","description":"This cluster centers on oxidative stress management (redox homeostasis, hydrogen peroxide catabolic processes, removal of superoxide radicals) and stress-responsive signaling pathways (regulation of non-canonical NF-kB signaling, I-kappaB phosphorylation, MAPK cascade regulation). Contextual terms like erythrocyte homeostasis and spermatogenesis are likely tissue-specific associations rather than defining features, so the core theme remains redox regulation linked to NF-kB/MAPK signaling.","confidence":"Medium","size":7,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:0042744","count":1},{"id":"GO:0019430","count":1},{"id":"GO:0042345","count":1},{"id":"GO:0034101","count":1}]},{"hash":"613772763709749649","title":"Ribosome biogenesis and translation initiation","description":"The top GO terms cluster tightly around ribosome production (rRNA processing; ribosomal subunit biogenesis) and translation initiation/early translation steps (preinitiation complex formation; translation reinitiation), with a minor context of cell division and hypoxia response. This supports a cohesive theme of ribosome assembly and translation control within the cluster.","confidence":"Medium","size":7,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1901407","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0000747","count":2},{"id":"GO:0006364","count":2},{"id":"GO:0051301","count":2}]},{"hash":"1429182738494646373","title":"RNA processing and ribosome biogenesis","description":"The top GO terms cluster around RNA maturation and ribosome assembly, with multiple splicing-related (spliceosome) terms and ribosome biogenesis highlighted, suggesting a shared role in nucleic acid processing. Other terms in the list relate to plant development or general cell growth, which may reflect broader cellular housekeeping roles among these proteins. Overall, the strongest signal is RNA processing and ribosome biogenesis. ","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0010102","count":1},{"id":"GO:0000373","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0000278","count":1}]},{"hash":"947004932702034502","title":"Plant defense and hormone signaling","description":"The top GO terms cluster around plant immune responses (antifungal innate immunity, chitin response) and hormone-related signaling (ethylene precursor ACC, gibberellin, salicylic acid), suggesting a cohesive theme of plant defense integrated with hormonal regulation. A few terms like peroxisome import and atrichoblast differentiation are more peripheral but can relate to broader stress and development pathways in plants.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009961","count":3},{"id":"GO:1905034","count":3},{"id":"GO:0009739","count":3},{"id":"GO:0010200","count":3},{"id":"GO:1904369","count":3}]},{"hash":"1061516020071811057","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090617","count":2},{"id":"GO:1905639","count":2},{"id":"GO:1900865","count":2},{"id":"GO:0042793","count":2},{"id":"GO:0031426","count":2}]},{"hash":"1839235824387009907","title":"Unknown","description":"The top terms span differentiation, transport, mitochondrial inheritance, redox- and hormone-related processes, and even fungal lipid metabolism, with no single unifying function tying them together. The diverse, and sometimes species-specific, annotations suggest noise rather than a coherent cluster theme, so a specific label cannot be confidently assigned.","confidence":"","size":7,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032332","count":2},{"id":"GO:0006814","count":2},{"id":"GO:0000001","count":2},{"id":"GO:1901300","count":2},{"id":"GO:0090031","count":2}]},{"hash":"1567387570181164153","title":"Chromosome Maintenance and Cell-Cycle Control","description":"The top GO terms cluster around cell-cycle regulation and nuclear/chromosome processes: negative regulation of CDK activity, kinetochore localization, nuclear export, and meiotic double-strand break processing. These collectively point to a module focused on chromosome maintenance and cell-cycle control. Some terms (immune response, placental development) are broader or less directly connected to the core theme, suggesting the primary function centers on nuclear division and chromosome integrity rather than immune or developmental roles.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045736","count":5},{"id":"GO:0034501","count":5},{"id":"GO:0006611","count":5},{"id":"GO:0043277","count":4},{"id":"GO:0046641","count":4}]},{"hash":"836830401047048556","title":"Ribosome and Translation Machinery","description":"Top terms are dominated by translation-related processes (cytoplasmic and mitochondrial translation, general translation), ribosomal subunit biogenesis, and mRNA turnover linked to translation, indicating a cluster centered on protein synthesis machinery; the elongation regulation term further supports a translation-focused function.","confidence":"High","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0006407","count":3},{"id":"GO:0002181","count":2},{"id":"GO:0046677","count":2},{"id":"GO:1990090","count":1}]},{"hash":"1575525246283708698","title":"Bacterial cell wall biosynthesis and division","description":"This cluster consolidates signals for peptidoglycan biosynthesis and turnover, cell wall organization, and cell division, paired with related folate and one-carbon metabolism that supply building blocks for nucleotide synthesis needed in cell wall precursor production. The presence of GO terms like peptidoglycan biosynthesis, turnover, cell shape regulation, and cell division points to a cohesive bacterial cell wall and division module; the macrophage activation term may reflect host-pathogen interaction rather than core function. Confidence is High.","confidence":"","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042116","count":2},{"id":"GO:0046901","count":1},{"id":"GO:0006761","count":1},{"id":"GO:0009252","count":1},{"id":"GO:0006730","count":1}]},{"hash":"1925360153525789497","title":"SNARE-Mediated Vesicle Trafficking","description":"The GO terms cluster around membrane insertion, SNARE complex assembly, endosomal-to-Golgi transport, vacuole fusion, and secretion-related processes (neutrophil degranulation, synaptic vesicle release), indicating a common role in vesicle trafficking and exocytosis.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051205","count":2},{"id":"GO:0043165","count":2},{"id":"GO:0042147","count":2},{"id":"GO:0060291","count":2},{"id":"GO:0032869","count":2}]},{"hash":"33082936623794418","title":"Membrane Transporters and Vesicular Loading","description":"The top GO terms cluster around transmembrane transport of diverse substrates (ions like Na+, K+, phosphate; nitrite/nitrate; sugars such as galactose and fucose; sialic acid) and a specific vesicular transport process for neurotransmitter loading, pointing to a theme of membrane transport proteins with vesicle-related roles.","confidence":"High","size":7,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":4},{"id":"GO:0042891","count":4},{"id":"GO:0015757","count":4},{"id":"GO:0035725","count":4},{"id":"GO:0098700","count":4}]},{"hash":"1338568968368821207","title":"Translation machinery and ribosome biogenesis","description":"This cluster is dominated by GO terms for translation, ribosome biogenesis, tRNA modification, and regulation of translational steps, indicating a core group involved in protein synthesis machinery. There is a single outlier term for glial cell proliferation, but the predominant theme centers on translation-related processes.","confidence":"High","size":7,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0042254","count":2},{"id":"GO:0006400","count":2},{"id":"GO:0006417","count":2},{"id":"GO:0002184","count":1}]},{"hash":"1089303413787358610","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0008033","count":4},{"id":"GO:0010610","count":3},{"id":"GO:0045292","count":3},{"id":"GO:1901254","count":2}]},{"hash":"1287866626146634939","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0042273","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0006283","count":2},{"id":"GO:0000462","count":2}]},{"hash":"2048313475585434297","title":"Chromatin regulation and ubiquitin/neddylation","description":"The top GO terms cluster around chromatin organization, heterochromatin maintenance, and regulation of silent mating-type cassette heterochromatin, together with DNA repair (homologous recombination) and ubiquitin/neddylation pathways (SCF-dependent proteasomal degradation and free ubiquitin chain polymerization). This suggests a coherent module linking chromatin state and gene silencing with protein turnover and post-translational modification via ubiquitin/neddylation, potentially impacting DNA repair and chromatin dynamics.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1903955","count":7},{"id":"GO:0031497","count":7},{"id":"GO:0016032","count":7},{"id":"GO:0031146","count":7},{"id":"GO:0000724","count":7}]},{"hash":"416550729654049805","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031126","count":1},{"id":"GO:0030420","count":1},{"id":"GO:0090503","count":1},{"id":"GO:0034247","count":1},{"id":"GO:0098789","count":1}]},{"hash":"1393724917391197413","title":"Nuclear RNA Splicing and Processing","description":"The cluster is dominated by terms related to nuclear RNA maturation, especially spliceosome assembly and mRNA/tRNA processing, splicing, and transcription termination, suggesting a cohesive role in nuclear RNA processing rather than cytosolic functions. Some plant-stress terms appear incidental to this core theme.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0009414","count":7},{"id":"GO:0051170","count":7},{"id":"GO:0000290","count":7},{"id":"GO:0000387","count":7},{"id":"GO:0000245","count":7}]},{"hash":"1830610668758155816","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":10,"triangles":4,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009432","count":3},{"id":"GO:0006289","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0017038","count":3},{"id":"GO:0006605","count":3}]},{"hash":"1743445157455781089","title":"Diverse secondary metabolite biosynthesis and metal ion transport","description":"Proteins in this cluster are linked to multiple biosynthetic processes (chalcone, flavonoid, fatty acid, sporopollenin, lignin, cell wall-related assembly) as well as transport of metal ions (copper, iron). The common thread is a focus on biosynthesis and deposition of diverse metabolites and cell-wall components, with accompanying metal transport, rather than a single specific pathway.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009715","count":1},{"id":"GO:0009813","count":1},{"id":"GO:0071770","count":1},{"id":"GO:0031148","count":1},{"id":"GO:0080110","count":1}]},{"hash":"177172328941303864","title":"RNA and protein methylation","description":"This cluster is dominated by GO terms relating to methylation across proteins (N-terminal, histone, arginine) and RNAs (RNA methylation, mRNA capping, tRNA methylation, guanine-N7 methylation), indicating a core theme of methylation-based regulation, with a few ancillary biosynthetic processes.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018012","count":4},{"id":"GO:0030961","count":3},{"id":"GO:0016126","count":3},{"id":"GO:0043985","count":3},{"id":"GO:0001300","count":3}]},{"hash":"1151327657563408432","title":"Post-transcriptional mRNA processing and silencing","description":"The terms cluster around RNA maturation and post-transcriptional regulation: mRNA modification and export, spliceosome-mediated and alternative splicing regulation, mRNA stabilization, and miRNA/regulatory ncRNA\u2013mediated gene silencing. This indicates a cohesive theme of RNA processing and gene expression control at the post-transcriptional level, despite a couple outliers. ","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016556","count":1},{"id":"GO:0006406","count":1},{"id":"GO:0031047","count":1},{"id":"GO:0048026","count":1},{"id":"GO:0000381","count":1}]},{"hash":"2133816173799044511","title":"Epidermal development and keratinization","description":"This cluster is strongly enriched for epidermal and skin differentiation terms (keratinization, regulation of epidermal cell division, skin development), indicating proteins likely involved in epidermal maturation and keratinocyte biology. Some trafficking-related GO terms (Golgi localization, protein export from nucleus) are present but secondary to the skin-related signals.","confidence":"High","size":7,"edges":11,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051291","count":3},{"id":"GO:0030307","count":3},{"id":"GO:0032869","count":3},{"id":"GO:0043154","count":3},{"id":"GO:0031424","count":3}]},{"hash":"2252163781676628158","title":"mRNA Processing and Splicing Regulation","description":"Enrichment centers on post-transcriptional mRNA processing: export from the nucleus, splicing regulation (canonical and alternative), mRNA modification and stabilization, and polyadenylation. This ensemble points to a cohesive role in mRNA maturation rather than transcription or translation.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":3},{"id":"GO:1901407","count":3},{"id":"GO:0016556","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0048026","count":2}]},{"hash":"1730631556230548797","title":"DNA Repair and Xenobiotic Stress Response","description":"This cluster centers on genome maintenance with base-excision repair and DNA recombination, complemented by DNA catabolic processes. It also includes cellular responses to chemical stress (xenobiotics and ethanol) and redox homeostasis, suggesting a cohesive role in protecting genome integrity under chemical stress conditions.","confidence":"Medium","size":7,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":3},{"id":"GO:0006284","count":3},{"id":"GO:0006310","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0045471","count":2}]},{"hash":"2281367894663783343","title":"Nuclear RNA Splicing and Processing","description":"Proteins in this cluster are enriched for spliceosome-related GO terms (mRNA cis splicing via spliceosome; spliceosomal snRNP/complex/assembly) and other nuclear RNA processing steps (deadenylation-dependent decapping of nuclear-transcribed mRNA; tRNA processing; termination of RNA polymerase II transcription) plus nuclear import, indicating a cohesive function in nuclear RNA maturation and transcription termination. Plant stress terms (abscisic acid response, water deprivation) may reflect context rather than core function.","confidence":"High","size":7,"edges":13,"triangles":13,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":4},{"id":"GO:0009414","count":3},{"id":"GO:0051170","count":3},{"id":"GO:0000290","count":3},{"id":"GO:0000387","count":3}]},{"hash":"408948366959359648","title":"Unknown","description":"The GO terms are highly diverse (Rho signaling, TNF regulation, neural axis specification, insulin secretion, aging, calcium response, mismatch repair, sphingolipid biosynthesis, vesicle transport/fusion), with no single cohesive function dominating and no interactions evident (Edges 0). This prevents a specific shared theme from emerging, so Unknown is appropriate.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":1},{"id":"GO:1904468","count":1},{"id":"GO:0021997","count":1},{"id":"GO:0035773","count":1},{"id":"GO:0001302","count":1}]},{"hash":"1983905356312908468","title":"Chromatin regulation and transcription control in development","description":"This cluster centers on chromatin-related processes\u2014sister chromatid cohesion maintenance, protein localization to chromatin, and heterochromatin formation\u2014paired with transcriptional regulation. The inclusion of development-related terms (brain development, cardiac atrium morphogenesis, oogenesis, spermatid development) suggests a common theme where chromatin state governs developmental gene expression. A secondary signal from Rho signaling is present but less central. Overall, the label captures the core shared function of chromatin regulation underlying development.","confidence":"High","size":7,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0034184","count":5},{"id":"GO:0071169","count":5},{"id":"GO:0035023","count":4},{"id":"GO:0007420","count":4},{"id":"GO:2000973","count":4}]},{"hash":"1523701084348345401","title":"Meiosis and DNA Repair Signaling","description":"The cluster centers on meiotic cell cycle and meiotic recombination checkpoint signaling, plus DNA double-strand break processing involved in repair via synthesis-dependent strand annealing, which together point to meiotic DNA repair and checkpoint control. Regulatory phosphatase activity hints at control of phosphorylation events in these processes (peptidyl-serine dephosphorylation). A few terms relate to T cell regulation, which may be peripheral to the core meiotic/DNA repair theme.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070262","count":7},{"id":"GO:0072462","count":7},{"id":"GO:0032516","count":7},{"id":"GO:0043029","count":7},{"id":"GO:0005981","count":7}]},{"hash":"402357293546140713","title":"Gene Expression Machinery","description":"The top GO terms cover transcription initiation by RNA polymerase II (including snRNA transcription) and regulation of transcription, alongside several tRNA aminoacylation activities and general translation, as well as translational fidelity and group I intron splicing. This mix points to a cluster centered on gene expression processes spanning transcription to translation, rather than a single specific pathway.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006367","count":1},{"id":"GO:0042795","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0006429","count":1},{"id":"GO:0006431","count":1}]},{"hash":"466761924651352119","title":"Ubiquitin-Proteasome-Mediated Protein Degradation","description":"The top GO terms strongly point to ubiquitin-dependent proteolysis and proteasomal degradation (including autoubiquitination and specific ubiquitin linkages like K48 and K6), which defines protein turnover and proteostasis. While a few terms touch on DNA repair or chromatin turnover, the dominant signal is ubiquitin-proteasome\u2013driven degradation.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032436","count":3},{"id":"GO:0000715","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0051865","count":2}]},{"hash":"306259245606937725","title":"Unknown","description":"No GO terms are listed for this cluster (Top Terms are empty), so there is no clear shared function to base a label on. The small network (3 edges, max degree 2) and the note that 20 proteins were re-added by ReCIPE do not reveal a dominant biological theme. Therefore, Unknown.","confidence":"","size":7,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[]},{"hash":"2165288450144380674","title":"RNA Splicing and Post-Transcriptional Regulation","description":"This cluster is dominated by GO terms related to RNA processing and post-transcriptional control\u2014for example, regulation and promotion of mRNA splicing via the spliceosome, mRNA export and stability, mRNA modification, and miRNA- or ncRNA-mediated gene silencing. These together point to a coherent theme of processing and regulating mRNA after transcription rather than transcription initiation, with some related developmental notes (e.g., blastocyst formation) that may reflect broader developmental expression patterns.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000381","count":7},{"id":"GO:0016556","count":6},{"id":"GO:0006406","count":6},{"id":"GO:0031047","count":6},{"id":"GO:0048026","count":6}]},{"hash":"973648804069418629","title":"mRNA processing and splicing regulation","description":"The cluster's GO terms center on mRNA modification, nuclear export, spliceosome-dependent and alternative splicing regulation, mRNA stabilization, and miRNA-mediated gene silencing, indicating a coherent theme of post-transcriptional control of mRNA maturation, localization, and translation; a couple of peripheral terms are less central but do not override the overall signal.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0016556","count":6},{"id":"GO:0006406","count":6},{"id":"GO:0031047","count":6},{"id":"GO:0048026","count":6},{"id":"GO:0000381","count":6}]},{"hash":"2280954038326033970","title":"Immune Activation and Tolerance Regulation","description":"The proteins cluster around immune processes: apoptotic cell clearance, positive regulation of T cell proliferation, cellular response to virus, and positive regulation of tolerance induction to self antigen. Although there are some diverse developmental or cellular terms, the immune-related GO terms dominate the top terms, suggesting the cluster reflects immune activation and tolerance regulation.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043277","count":7},{"id":"GO:0046641","count":7},{"id":"GO:0060709","count":7},{"id":"GO:0006611","count":7},{"id":"GO:0061167","count":7}]},{"hash":"703643054715046666","title":"Transmembrane Ion and Metabolite Transport","description":"This cluster is dominated by GO terms for transmembrane transport, including specific ion transport (potassium and sodium) and metabolite transport (citrate, succinate, monoatomic anions), plus a general transmembrane transport term. These recurring themes suggest the proteins broadly participate in moving ions and small molecules across membranes. A few other terms (retina vasculature development, sperm capacitation, antibiotic response) may reflect broader transport-related roles in specific tissues or contexts but do not outweigh the shared transport focus.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006813","count":2},{"id":"GO:0061298","count":2},{"id":"GO:0048240","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0006814","count":1}]},{"hash":"617097381654432006","title":"Ventricular Calcium Signaling and Morphogenesis","description":"The cluster\u2019s top GO terms center on ventricular cardiac muscle morphogenesis and sarcoplasmic reticulum\u2013mediated calcium signaling (Ca2+ release, and regulation of ryanodine-sensitive channels), which strongly points to proteins involved in cardiac Ca2+ handling and ventricular development. Additional terms like response to cAMP and stress-related processes further support a cardiac signaling and stress-response theme, while other terms may reflect shared membrane trafficking or housekeeping roles. Overall, the set coalesces around cardiac calcium signaling in the ventricle and its regulation under stress.","confidence":"High","size":7,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055010","count":2},{"id":"GO:0014808","count":2},{"id":"GO:0060315","count":2},{"id":"GO:0035023","count":1},{"id":"GO:0033555","count":1}]},{"hash":"1114413144579299385","title":"Receptor Internalization and Lysosomal Trafficking","description":"These 7 proteins feature GO terms centered on receptor internalization, cell surface receptor signaling, and protein localization to the lysosome, pointing to a shared function in endocytic trafficking and downregulation of signaling. While a couple terms refer to neural/sensory contexts (paranodal junction assembly, photoreceptor differentiation) or growth factor pathways (VEGF signaling), the strongest recurring theme is membrane receptor turnover via internalization and lysosomal targeting.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2000145","count":1},{"id":"GO:0043128","count":1},{"id":"GO:1901223","count":1},{"id":"GO:0031623","count":1},{"id":"GO:0007166","count":1}]},{"hash":"999959979889093886","title":"Mitosis and Chromosome Segregation","description":"The strongest signals are CENP-A\u2013containing chromatin assembly, DNA-templated transcription, and cell division, with microtubule severing reinforcing mitotic activity. While ER-related terms appear, the core cluster centers on chromosome maintenance and mitotic progression; other terms may reflect auxiliary processes or broader protein properties.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051260","count":5},{"id":"GO:0061641","count":5},{"id":"GO:0006888","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0051013","count":5}]},{"hash":"1525659728012806955","title":"Multi-tissue development","description":"The proteins in this cluster show GO terms tied to development across multiple tissues and organs (retinal cone cells, Schwann cells, heart tissue, kidney ureteric bud, and nurse cell/oocyte development). While there are some additional terms (calcium response, sensory detection, digestion), the dominant theme is tissue/organ development across different lineages, suggesting a broad developmental role rather than a single functional niche.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019749","count":2},{"id":"GO:0046549","count":2},{"id":"GO:0071277","count":2},{"id":"GO:0032516","count":2},{"id":"GO:0008016","count":2}]},{"hash":"2042186144485739605","title":"DNA Repair and Xenobiotic Response with Lipid Metabolism","description":"This cluster centers on DNA maintenance (base-excision repair and DNA recombination) and detox response (response to xenobiotic stimulus), with several lipid metabolism themes (fatty-acyl-CoA metabolism, lipid hydroperoxide transport, and cholesterol transport). The co-occurrence suggests a coordinated emphasis on genome maintenance alongside metabolic stress responses, including lipid handling. Some terms are obsolete, but the core pattern remains DNA repair/detox coupled with lipid metabolism.","confidence":"Medium","size":7,"edges":6,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":2},{"id":"GO:0006310","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0006284","count":2},{"id":"GO:1901373","count":1}]},{"hash":"2185722485362419426","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":7,"triangles":1,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070869","count":6},{"id":"GO:0000393","count":6},{"id":"GO:0000209","count":6},{"id":"GO:0071035","count":6},{"id":"GO:0000467","count":6}]},{"hash":"1152322882198606408","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032869","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0006168","count":5},{"id":"GO:0032264","count":5},{"id":"GO:0006178","count":5}]},{"hash":"1629371237940560744","title":"Unknown","description":"The set shows a heterogeneous mix of processes: DNA replication and meiotic DNA processing, nuclear transport, ER polarization, immune signaling (T cell proliferation, tolerance to self), viral response, placenta-related development, and organ regeneration. No single unifying theme dominates these terms, suggesting the cluster may be multi-functional or an artifact of clustering, so there isn\u2019t a cohesive label beyond Unknown.","confidence":"","size":7,"edges":4,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0043277","count":5},{"id":"GO:0046641","count":5},{"id":"GO:0060709","count":5},{"id":"GO:0006611","count":5}]},{"hash":"5731299512870539","title":"Cell proliferation and energy metabolism","description":"The cluster shows strong signals for DNA replication and cell division, pointing to proliferation. Energy-related terms (ATP metabolic process and positive regulation of ATP biosynthesis) suggest a focus on energy supply to support growth. Additional terms cover RNA processing, mRNA export, membrane trafficking (SNARE/stress granule disassembly), and mitochondrial inheritance, all of which accompany cell growth and division. Viral genome replication is present but does not define the core function of the cluster. Overall, the dominant theme is proliferation with accompanying energy and cellular housekeeping processes.","confidence":"Medium","size":7,"edges":12,"triangles":8,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0035494","count":3},{"id":"GO:0035617","count":3},{"id":"GO:0000001","count":3}]},{"hash":"2015663376521830861","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":6},{"id":"GO:0090617","count":6},{"id":"GO:0042793","count":6},{"id":"GO:1905639","count":6},{"id":"GO:1900865","count":6}]},{"hash":"773142623863308554","title":"Unknown","description":"The GO terms span immune regulation (positive regulation of T cell proliferation, tolerance to self antigen), apoptotic cell clearance, viral response, placental development, organ regeneration, and several core cellular processes (nuclear export, ER polarization, meiotic DSB processing, hormone secretion). This breadth suggests no single cohesive function unites the cluster, so a specific label is not justifiable.","confidence":"","size":7,"edges":19,"triangles":26,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043277","count":7},{"id":"GO:0046641","count":7},{"id":"GO:0060709","count":7},{"id":"GO:0006611","count":7},{"id":"GO:0061167","count":7}]},{"hash":"803224387075352345","title":"Unknown","description":"The top GO terms span chloroplast movement, chromatin regulation, transcription, cell death, nuclear migration, spindle checkpoint, ethanol response, and ubiquitin signaling, with no single dominant process tying them together. Because of this heterogeneity, there isn't a clear functional theme to label.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009904","count":1},{"id":"GO:0009903","count":1},{"id":"GO:0034729","count":1},{"id":"GO:0006351","count":1},{"id":"GO:1901300","count":1}]},{"hash":"1971292739704239978","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0048701","count":4},{"id":"GO:0033129","count":4},{"id":"GO:0070935","count":4},{"id":"GO:0043277","count":3}]},{"hash":"988523161128707551","title":"MVB sorting and lysosome-mediated degradation","description":"The dominant GO terms are the multivesicular body sorting pathway and both ubiquitin-dependent and -independent protein catabolic processes via the MVB sorting pathway, along with MVB-lysosome fusion. This strongly points to proteins involved in MVB-mediated trafficking to lysosomes and subsequent degradation. Additional terms related to cell cycle and lens maintenance are present but appear secondary to the core MVB/lysosomal turnover theme.","confidence":"High","size":7,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071985","count":4},{"id":"GO:0030713","count":4},{"id":"GO:0090611","count":4},{"id":"GO:0036438","count":4},{"id":"GO:0043162","count":4}]},{"hash":"2300882195538678909","title":"Mitochondrial respiratory chain (Complex I/II)","description":"Two top GO terms point to mitochondrial energy metabolism (mitochondrial electron transport NADH to ubiquinone and respiratory chain complex II assembly), suggesting the proteins cluster around mitochondrial respiration. A single outlier term for globoside biosynthesis is not enough to redefine the group toward lipid metabolism, so the mitochondria-energetics theme is likely representative.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001576","count":1},{"id":"GO:0034553","count":1},{"id":"GO:0006120","count":1}]},{"hash":"1836365623283282417","title":"TLR Signaling and Innate Immunity","description":"This cluster shows a clear enrichment for toll-like receptor signaling (TLR4 and TLR10), LPS detection, and NF-kB-related processes (I-kappaB phosphorylation), plus a Th1-type immune response, pointing to an innate immune signaling theme. Some neural development terms appear but do not define the main functional grouping.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000172","count":1},{"id":"GO:0002730","count":1},{"id":"GO:0007413","count":1},{"id":"GO:0034142","count":1},{"id":"GO:0051965","count":1}]},{"hash":"1201298161613645580","title":"Ubiquitin-Proteasome Mediated Proteolysis","description":"The top GO terms center on ubiquitin-dependent protein catabolism (including SCF complex\u2013driven proteasomal degradation and K48-linked ubiquitination) and autoubiquitination, with NF-\u03baB\u2013activating kinase activity suggesting signaling roles; a few developmental terms appear as context. Taken together, the core theme is ubiquitin-proteasome\u2013mediated proteolysis.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0070544","count":3},{"id":"GO:0031146","count":3},{"id":"GO:0021993","count":3},{"id":"GO:0021678","count":3}]},{"hash":"1917898317610881295","title":"ER-Golgi Trafficking and ER Stress Response","description":"This cluster is dominated by terms for ER-to-Golgi vesicle transport and ER stress response, with two proteins linked to each, indicating a core theme of intracellular trafficking coupled to stress signaling. Additional terms touch on related trafficking and regulatory processes (endosome-lysosome transport, amino acid starvation response, polarity), but the strongest connections revolve around ER-to-Golgi transport and ER stress, justifying a label centered on these functions.","confidence":"Medium","size":7,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0034198","count":2},{"id":"GO:0034976","count":2},{"id":"GO:1903206","count":2},{"id":"GO:0051301","count":2}]},{"hash":"1879220911276954998","title":"Regulators of signaling and genome maintenance","description":"Top GO terms indicate regulatory roles across signaling (notably Wnt), apoptosis, mRNA processing, proteostasis, differentiation, migration, and telomere maintenance. This suggests a broad module of regulators coordinating growth, survival, differentiation, and genome integrity rather than a single pathway. Confidence: Medium","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043065","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0032435","count":2},{"id":"GO:0045444","count":2}]},{"hash":"1924024396244844777","title":"Meiosis and Oocyte Maturation Regulation","description":"The top GO terms are dominated by meiotic processes (meiotic sister chromatid cohesion centromeric; regulation of meiotic cell cycle involved in oocyte maturation; female meiotic nuclear division), pointing to regulation of meiosis and meiotic nuclear events during oocyte development. Additional terms reference related cell-cycle processes, DNA replication regulation, and nuclear transport, which support a broader but still meiosis-centered regulatory theme. Overall, the cluster seems best described by meiosis/oocyte maturation regulation rather than general metabolism or signaling. ","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051754","count":1},{"id":"GO:0070262","count":1},{"id":"GO:0006275","count":1},{"id":"GO:0006610","count":1},{"id":"GO:1903538","count":1}]},{"hash":"627121819077789334","title":"Unknown","description":"There are no GO terms or connections provided for this cluster (no edges, no terms), so there is no clear shared function to define. With no unifying theme among the proteins, the label Unknown is appropriate.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2010510883363975123","title":"Sulfur amino acid metabolism","description":"Top terms center on transsulfuration, homocysteine catabolism, and cysteine biosynthesis, which together point to processing of sulfur-containing amino acids. While a few other terms appear (growth hormone response, chromatin organization, collagen catabolic), the strongest and most consistent signal is sulfur amino acid metabolism, suggesting the cluster represents enzymes or proteins involved in cysteine/homocysteine pathways. ","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0060416","count":2},{"id":"GO:0006465","count":1},{"id":"GO:0034724","count":1},{"id":"GO:0035551","count":1},{"id":"GO:0034396","count":1}]},{"hash":"1559644375988736567","title":"Organelle protein import and translation (mitochondria/chloroplast)","description":"This cluster is driven by GO terms related to mitochondrial translation and protein import into both mitochondrial and chloroplast compartments, as well as membrane insertion events. Despite a couple of unrelated terms, the dominant theme is organelle biogenesis\u2014protein import and translation within mitochondria and chloroplasts\u2014so the label reflects a cohesive function for the group.","confidence":"High","size":6,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0070126","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0045037","count":1},{"id":"GO:0045039","count":1},{"id":"GO:0000002","count":1}]},{"hash":"1037729715105519436","title":"Oxidative Stress Response and Energy Metabolism","description":"This cluster's top GO terms are dominated by oxidative stress response and energy-related processes (ATP synthesis coupled electron transport, ferredoxin metabolism, various catabolic processes), suggesting a module centered on redox management and energy production. A few vascular development terms appear but are represented only once, implying possible multifunctionality or annotation noise. Therefore, the label Oxidative Stress Response and Energy Metabolism is the best representative for this group.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006979","count":2},{"id":"GO:0006814","count":1},{"id":"GO:0009115","count":1},{"id":"GO:0045602","count":1},{"id":"GO:0006124","count":1}]},{"hash":"1976648474448431935","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":2},{"id":"GO:0090617","count":2},{"id":"GO:0042793","count":2},{"id":"GO:1905639","count":2},{"id":"GO:1900865","count":2}]},{"hash":"734159453386813362","title":"Lung development and tissue remodeling","description":"This cluster's terms cluster around lung-specific development (surfactant homeostasis, branching morphogenesis) and extracellular matrix remodeling (basement membrane disassembly), with additional hints from developmental hormone response and macrophage-associated processes. Although bone-related terms appear, the prominent theme centers on organ development and remodeling, especially of lung tissue.","confidence":"Medium","size":6,"edges":7,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1903955","count":2},{"id":"GO:0097067","count":2},{"id":"GO:0043129","count":2},{"id":"GO:0051603","count":2},{"id":"GO:0010815","count":2}]},{"hash":"991924079669957669","title":"Glycolysis and glycogen catabolism","description":"The cluster is dominated by GO terms related to glycolytic processes and carbohydrate metabolism (canonical glycolysis, glycolysis from storage polysaccharides, fructose-6-phosphate metabolism, glycogen catabolic process), suggesting a core function in energy production from glucose and glycogen. The presence of a hypoxia response term aligns with glycolytic upregulation under low oxygen, while a few terms about angiogenesis and epithelial differentiation may reflect broader cellular states or secondary functions. Overall, the group appears to reflect glycolytic metabolism with glycogenolysis as a key component.","confidence":"High","size":6,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006096","count":2},{"id":"GO:0046835","count":2},{"id":"GO:0016525","count":1},{"id":"GO:0030855","count":1},{"id":"GO:0031639","count":1}]},{"hash":"605973805938738658","title":"Nuclear Gene Expression and Metabolism","description":"The terms point to core nuclear processes (mRNA export, transcription preinitiation assembly, DNA replication) and general energy metabolism (ATP metabolism, aerobic respiration), suggesting a cluster centered on fundamental gene expression and metabolic activities. Some terms like autophagosome maturation and centriole elongation are related but less central, making the overall theme somewhat broad.","confidence":"Low","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046034","count":2},{"id":"GO:0006406","count":2},{"id":"GO:2001171","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0019079","count":2}]},{"hash":"582231391967391503","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":7,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019878","count":2},{"id":"GO:0006552","count":1},{"id":"GO:0006094","count":1},{"id":"GO:0044205","count":1},{"id":"GO:0006090","count":1}]},{"hash":"542090726408603152","title":"Unknown","description":"The top GO terms describe a wide range of organismal and regulatory processes (behavior, hormonal response, lens development, muscle contraction, light response, intracellular transport) with no clear shared function or pathway, and there are no edges tying them together. Therefore there isn't a coherent, specific label that confidently represents this cluster.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035641","count":2},{"id":"GO:0032355","count":1},{"id":"GO:0050821","count":1},{"id":"GO:0070309","count":1},{"id":"GO:0007568","count":1}]},{"hash":"1846524018401470318","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006740","count":2},{"id":"GO:0039694","count":1},{"id":"GO:0000453","count":1},{"id":"GO:0002128","count":1},{"id":"GO:0039520","count":1}]},{"hash":"1562569925195461201","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":3},{"id":"GO:0090617","count":3},{"id":"GO:0042793","count":3},{"id":"GO:1905639","count":3},{"id":"GO:1900865","count":3}]},{"hash":"1726946143809199097","title":"Mitochondrial Energy Metabolism","description":"Based on the top GO terms, the proteins cluster around mitochondrial metabolism and redox-related processes, including NADH to ubiquinone electron transport, 2-oxoglutarate and L-glutamate metabolism, and lipoate metabolism, which together point to mitochondrial energy production. Some terms (chromatin binding, granulocyte differentiation) are less aligned and may reflect broader or incidental annotations.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0046886","count":3},{"id":"GO:0009106","count":3},{"id":"GO:0060992","count":3},{"id":"GO:0030851","count":3}]},{"hash":"989392821781707234","title":"Chaperone-mediated folding and stabilization","description":"The GO terms converge on chaperone activity (folding, refolding, stabilization, and complex assembly) and associated protein localization, especially mitochondrial targeting, suggesting a folding/quality-control cluster. The immune signaling terms (IL-6 and B cell cytokine production) appear as peripheral associations rather than core functions.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:2000778","count":6},{"id":"GO:0050821","count":6},{"id":"GO:0051973","count":6},{"id":"GO:0051086","count":6},{"id":"GO:0051085","count":6}]},{"hash":"63727312481237967","title":"Cofactor and Fatty Acid Biosynthesis","description":"The top GO terms are dominated by biosynthetic processes for vitamins/cofactors (biotin, cobalamin, phylloquinone, protoporphyrinogen IX) and fatty acids (methyl-branched and very long-chain), indicating a functional theme centered on biosynthesis of cofactors and lipids; a few antibiotic-related terms and tRNA methylation are present but do not override the main signal.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":2},{"id":"GO:1902321","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0009102","count":2},{"id":"GO:0006782","count":2}]},{"hash":"1228368565395576252","title":"Metabolic Regulation and Tissue Homeostasis","description":"This cluster combines diverse metabolic biosynthetic and catabolic processes (bile acid, glucuronate, retinoic acid, and ascorbate; steroid hormone biosynthesis) with regulatory processes affecting tissue homeostasis and growth signaling (PI3K/AKT pathway and smooth muscle proliferation). The common thread appears to be broad metabolic regulation coupled with mechanisms that maintain tissue integrity and cell signaling, rather than a single, cohesive pathway.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009414","count":6},{"id":"GO:0006699","count":6},{"id":"GO:0042840","count":6},{"id":"GO:1900053","count":6},{"id":"GO:0019853","count":6}]},{"hash":"922178152417805086","title":"Unknown","description":"The GO terms span diverse processes (fructose and other sugar biosynthesis, retinol and sialic acid biosynthesis, copper transport, dephosphorylation, lipopolysaccharide biosynthesis, testosterone response, and calcium homeostasis), with no single coherent function uniting all six proteins.","confidence":"","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0046370","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0042572","count":3},{"id":"GO:0006825","count":2},{"id":"GO:0016311","count":2}]},{"hash":"41567922145430036","title":"Alkaloid and lipid metabolism","description":"The GO terms show multiple catabolic and biosynthetic processes for small organic molecules, especially alkaloids (alkaloid catabolic process, isoquinoline alkaloid metabolic process, camphor catabolic process), triglycerides, and bile acids, plus retinoic acid catabolism. This points to a metabolic cluster focused on the processing of organic compounds, particularly alkaloids and lipids. Some terms about ion responses and chronic inflammation appear peripheral and not central to the cluster\u2019s core function. ","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009822","count":3},{"id":"GO:0006641","count":3},{"id":"GO:0071615","count":3},{"id":"GO:0034653","count":3},{"id":"GO:0033076","count":3}]},{"hash":"296607377105859267","title":"Xenobiotic and lipid catabolism","description":"The cluster is dominated by catabolic/metabolic GO terms for small molecules, including alkaloids (isoquinoline, camphor), retinoic acid, triglycerides, and bile acids, suggesting a shared function in xenobiotic and lipid breakdown. A few ion-response terms are present but do not define the core theme.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009822","count":6},{"id":"GO:0006641","count":6},{"id":"GO:0071615","count":6},{"id":"GO:0034653","count":6},{"id":"GO:0033076","count":6}]},{"hash":"168735359231069537","title":"ER-Golgi trafficking and glycosylation","description":"Most terms point to membrane transport and the secretory pathway: ER-to-Golgi vesicle transport and dolichol-linked oligosaccharide biosynthesis (glycosylation) along with various amino acid and glucose transport processes. Although a couple terms (lens development, grooming behavior) are unrelated, the dominant signals describe a coherent functional module around protein processing and trafficking in the secretory pathway and intracellular nutrient transport.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0002088","count":1},{"id":"GO:0060905","count":1},{"id":"GO:0006488","count":1},{"id":"GO:0015811","count":1},{"id":"GO:0034488","count":1}]},{"hash":"1597122336899878632","title":"Alkaloid and lipid metabolism","description":"The top GO terms are dominated by catabolic and metabolic processes for alkaloids and other small organic molecules (alkaloid catabolic, isoquinoline alkaloid metabolism, camphor catabolic, retinoic acid catabolic) plus lipid-related pathways (triglyceride metabolism, bile acid biosynthesis). This suggests the cluster centers on small-molecule xenobiotic and lipid catabolic functions. Some terms about ion response and inflammation are present but appear less central to the main theme. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009822","count":6},{"id":"GO:0006641","count":6},{"id":"GO:0071615","count":6},{"id":"GO:0034653","count":6},{"id":"GO:0033076","count":6}]},{"hash":"1790404444612211717","title":"Developmental transcriptional regulators","description":"Based on the GO terms, the cluster centers on regulation of transcription during development, with multiple entries for regulation of DNA-templated transcription and several lineage- or tissue-specific differentiation processes (T cell, EMT, neural, cardiac, ureter, endocardial cushion). This pattern suggests proteins acting as transcriptional regulators that guide diverse developmental programs across tissues; the plant-specific shoot formation term appears as an outlier but does not negate the overarching theme. ","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:2000032","count":5},{"id":"GO:0006355","count":5},{"id":"GO:0045582","count":1},{"id":"GO:0035799","count":1},{"id":"GO:0071442","count":1}]},{"hash":"13959918197019365","title":"Neuronal proteostasis and autophagy regulation","description":"This cluster centers on neuronal development and axonogenesis, and is dominated by terms for ubiquitin-mediated protein degradation, autophagy including mitophagy/aggrephagy, and ER-stress\u2013related apoptosis control, indicating a coordinated neuronal proteostasis/autophagy program.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1902236","count":6},{"id":"GO:0021888","count":6},{"id":"GO:0032436","count":6},{"id":"GO:1904049","count":6},{"id":"GO:0007023","count":6}]},{"hash":"84643838980018659","title":"Unknown","description":"The GO terms are highly diverse, covering sensory perception, various differentiation and developmental processes, spindle assembly, signaling pathways, telomere maintenance, and tissue regeneration. With no clear shared function or pathway linking the proteins, there isn\u2019t a cohesive theme to name a specific cluster.","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048549","count":1},{"id":"GO:0021707","count":1},{"id":"GO:0051225","count":1},{"id":"GO:0050968","count":1},{"id":"GO:0044707","count":1}]},{"hash":"642788280341834211","title":"Flavonoid and lignin biosynthesis","description":"The cluster shows strong representation of GO terms for biosynthesis of kaempferol, quercetin, and cyanidin glucosides, plus lignin metabolic process, which together reflect phenylpropanoid-derived secondary metabolism common in plants. While there are some xenobiotic or unrelated terms present, the flavonoid glucoside biosynthesis and lignin pathways provide a cohesive function for the cluster.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016999","count":5},{"id":"GO:0030259","count":5},{"id":"GO:0006711","count":4},{"id":"GO:0052696","count":4},{"id":"GO:0070980","count":4}]},{"hash":"1204837024888634409","title":"Regulation of secondary shoot formation","description":"Dominated by GO:2000032 (regulation of secondary shoot formation) and GO:0006355 (regulation of DNA-templated transcription), both with 5 proteins, indicating a core transcriptional control program tied to shoot development in plants; other signals (nutrient response, lignin biosynthesis) suggest adjunct metabolic and stress-linked roles but do not override the developmental theme.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:2000032","count":5},{"id":"GO:0006355","count":5},{"id":"GO:0031667","count":1},{"id":"GO:0042573","count":1},{"id":"GO:0045777","count":1}]},{"hash":"1623305263187925313","title":"Unknown","description":"The top terms are highly diverse, spanning freezing response, plant development, mitochondrial metabolism, NAD biosynthesis, and reproductive processes, with only a single edge connecting the proteins. There is no clear, cohesive function or pathway tying these terms together, so a specific label isn\u2019t justifiable. ","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0050826","count":3},{"id":"GO:0010227","count":3},{"id":"GO:0006103","count":1},{"id":"GO:0006120","count":1},{"id":"GO:0045654","count":1}]},{"hash":"539625735541595625","title":"Nucleotide and Cofactor Biosynthesis","description":"The top GO terms point to nucleotide biosynthesis and salvage (CDP, ADP, AMP salvage, ITP), phosphorylation steps, and key cofactors (NAD+, CoA). This suggests the proteins function together in nucleotide and energy-cofactor metabolism, with organismal development terms likely reflecting broader annotations rather than a shared function of the cluster.","confidence":"High","size":6,"edges":10,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0046705","count":1},{"id":"GO:0007420","count":1},{"id":"GO:0001889","count":1},{"id":"GO:0046939","count":1},{"id":"GO:0046940","count":1}]},{"hash":"1869228886972253038","title":"Amino acid and cofactor biosynthesis","description":"The GO terms show multiple biosynthetic processes, including protoporphyrinogen IX (heme precursor) biosynthesis, biotin biosynthesis, and several amino acid biosyntheses (lysine, arginine, alanine, beta-alanine), plus antibiotic biosynthesis. This pattern indicates a cluster centered on production of amino acids and cofactors (and related metabolites), so a concise label focusing on biosynthesis of amino acids and cofactors fits well.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006782","count":4},{"id":"GO:0009102","count":4},{"id":"GO:0019878","count":4},{"id":"GO:0010121","count":2},{"id":"GO:0006593","count":2}]},{"hash":"584936239240603144","title":"Plant immune and hormone signaling","description":"The GO terms cluster around plant defense responses (response to chitin, antifungal innate immune response) and a suite of hormone-related processes (response to 1-aminocyclopropane-1-carboxylic acid/ethylene, response to gibberellin, response to salicylic acid, and regulation of gibberellin signaling). There are also developmental terms (atrichoblast differentiation, sclerenchyma differentiation) that are often hormonally regulated, reinforcing the theme of defense intertwined with growth signaling in plants. This cohesive pattern supports labeling the cluster as plant immune and hormone signaling.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009961","count":2},{"id":"GO:1905034","count":2},{"id":"GO:0009739","count":2},{"id":"GO:0010200","count":2},{"id":"GO:1904369","count":2}]},{"hash":"1164039097221921702","title":"Unknown","description":"The terms mix membrane transport (arsenite/antimonite/organic anion transport) with several post-translational modification terms (multiple methylations and arginine hydroxylation) and sterol biosynthesis, giving no single cohesive biological theme; the cluster has no edges, so a unified label isn\u2019t supported.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015700","count":1},{"id":"GO:0006849","count":1},{"id":"GO:0015699","count":1},{"id":"GO:0043251","count":1},{"id":"GO:0030961","count":1}]},{"hash":"555339008282476442","title":"Translation Initiation and RNA Processing Regulation","description":"The cluster is dominated by translation-related terms (formation of translation preinitiation complex, translation reinitiation, IRES-dependent initiation, ribosome disassembly, regulation of translation) and RNA processing terms (spliceosome-mediated splicing, regulatory ncRNA-mediated gene silencing, maintenance of translational fidelity), suggesting coordinated roles in initiating/controlling translation and RNA processing.","confidence":"High","size":6,"edges":7,"triangles":2,"max_degree":4,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0001731","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0048026","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0000398","count":2}]},{"hash":"1673968900966188334","title":"Peptidyl methylation","description":"The cluster is dominated by GO terms for methylation of peptide residues (lysine, arginine, serine, glycine, glutamine) and N-terminal modifications, suggesting proteins involved in peptide/protein methyltransferase activity and related post-translational modifications. Some terms related to sterol/selenium metabolism and tumor cell response appear, but the core theme is peptide methylation.","confidence":"High","size":6,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030961","count":2},{"id":"GO:0016126","count":2},{"id":"GO:0035572","count":2},{"id":"GO:0018026","count":2},{"id":"GO:0001887","count":2}]},{"hash":"1941184059731219126","title":"Phospholipid Biosynthesis and Remodeling","description":"Cluster appears enriched for lipid metabolism terms related to phospholipid biosynthesis and remodeling, including cardiolipin remodeling, phosphatidylcholine remodeling, and CDP-diacylglycerol biosynthesis, as well as platelet activating factor biosynthesis. Although translation-related terms appear, the lipid-related GO terms dominate, suggesting a coherent theme around membrane lipid synthesis and remodeling.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0000027","count":1},{"id":"GO:0046898","count":1},{"id":"GO:0019432","count":1}]},{"hash":"118165669861024514","title":"RNA processing and translation regulation","description":"The top GO terms converge on RNA metabolism and protein synthesis, including translation (and mitochondrial termination), tRNA and rRNA processing, miRNA processing, and RISC complex assembly, indicating a cohesive module for RNA processing and translational control; additional terms point to regulatory aspects of viral replication, cell proliferation, and phosphorylation, but the dominant theme is RNA-based regulation of translation.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0070126","count":2},{"id":"GO:0045071","count":2},{"id":"GO:0097049","count":2},{"id":"GO:0008033","count":2}]},{"hash":"1690565430204974678","title":"Nuclear DNA Replication and Centrosome/Microtubule Processes","description":"The top terms cluster around nuclear DNA replication and regulation, the centrosome cycle, and protein localization to microtubules, with supporting signals for nuclear export and RNA processing. These suggest a cohesive theme of nuclear/cell-cycle machinery and cytoskeletal organization, despite a few development and innate-immune annotations that are less central to the core function.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048701","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0035372","count":3},{"id":"GO:0010571","count":3},{"id":"GO:0051092","count":3}]},{"hash":"2199257260830393052","title":"Cardiac and Neuronal Action Potentials","description":"This cluster centers on electrical signaling: atrial/AV node/ventricular membrane depolarization and action potential terms, plus neuronal action potential and pain sensation, pointing to shared mechanisms of excitability in heart and nervous system. Other terms like cerebellum maturation, T cell homeostasis, multicellular development, and protein homooligomerization appear less central; given no edges, the core theme still matches cardiac/neuronal electrical activity.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0098910","count":1},{"id":"GO:0019228","count":1},{"id":"GO:0043029","count":1},{"id":"GO:0050968","count":1}]},{"hash":"1789600203139437338","title":"Gluconeogenesis and Carbohydrate Metabolism","description":"The top GO terms cluster around glucose-related processes\u2014gluconeogenesis, its regulation, and fructose-6-phosphate metabolism, plus a glucose starvation response\u2014pointing to a carbohydrate metabolism and energy balance theme. Some terms are tangential (dephosphorylation, Ras signaling regulation, xenobiotic response), but the dominant signal supports a sugar metabolism cluster.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006111","count":1},{"id":"GO:0042149","count":1},{"id":"GO:0005986","count":1},{"id":"GO:0016311","count":1},{"id":"GO:0046580","count":1}]},{"hash":"1496348634605053308","title":"Quinone and pigment biosynthesis","description":"A cluster appears enriched for biosynthetic processes of electron carriers and pigments: menaquinone, ubiquinone, phylloquinone, and heme O biosynthesis, as well as chlorophyll biosynthesis. These shared functions suggest a cohesive theme around production of quinones and related pigments/cofactors, despite some unrelated terms in the list.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001890","count":3},{"id":"GO:0034198","count":3},{"id":"GO:2000114","count":3},{"id":"GO:0009636","count":3},{"id":"GO:0009234","count":2}]},{"hash":"880174722433485885","title":"Autophagy and Organelle Quality Control","description":"The set centers on autophagy-related processes (mitophagy, aggrephagy, autophagosome maturation) and related regulation (negative regulation of ER-stress\u2013induced apoptosis, ubiquitination), suggesting a cluster focused on cellular quality control via autophagy and protein turnover, including organelle turnover under stress. A single outlier term about hypothalamic neuron development is present but does not define the cluster\u2019s core function.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1902236","count":1},{"id":"GO:2000134","count":1},{"id":"GO:0021888","count":1},{"id":"GO:1904049","count":1},{"id":"GO:1901097","count":1}]},{"hash":"2096939872977607245","title":"Stress-Responsive Signaling Regulation","description":"Most terms point to regulation of signaling pathways (kinase activity, Rho signaling, cAMP response) and stress-related processes (multicellular stress response, abscisic acid signaling, hydrogen peroxide biosynthesis). Some terms like endocytic recycling and surfactant homeostasis may reflect broader membrane trafficking roles connected to signaling. Overall, the cluster appears to represent modulation of signaling networks underlying stress responses in multicellular contexts.","confidence":"Medium","size":6,"edges":4,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":4},{"id":"GO:0009738","count":4},{"id":"GO:0006469","count":4},{"id":"GO:0035023","count":3},{"id":"GO:0033555","count":3}]},{"hash":"882664274363465911","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":2},{"id":"GO:0090617","count":2},{"id":"GO:1905639","count":2},{"id":"GO:1900865","count":2},{"id":"GO:0042793","count":2}]},{"hash":"1702043223768602413","title":"GTPase-regulated cytoskeleton and trafficking","description":"The GO terms cluster around small GTPase signaling driving cytoskeletal rearrangements (podosome and dendritic spine regulation, cell migration) and vesicle trafficking (exocytosis, endosome-to-lysosome transport). While some terms touch on liver lipid processes, the dominant signal ties to cytoskeleton dynamics and membrane trafficking regulated by GTPases.","confidence":"High","size":6,"edges":7,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0097284","count":1},{"id":"GO:0045956","count":1},{"id":"GO:1902824","count":1},{"id":"GO:0007264","count":1},{"id":"GO:1902307","count":1}]},{"hash":"121175598850716139","title":"Vesicle trafficking and organelle dynamics","description":"The top GO terms cluster around intracellular transport and organelle maturation (endosome to lysosome transport, phagosome acidification, regulation of the secretory pathway), with mitochondrial inheritance and budding growth suggesting organelle dynamics during cell division. Some terms (mRNA decay, methylation, neuromuscular balance) are peripheral, but the core theme of vesicle trafficking and organelle maintenance is present. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000001","count":1},{"id":"GO:0051291","count":1},{"id":"GO:1903307","count":1},{"id":"GO:0008333","count":1},{"id":"GO:1900026","count":1}]},{"hash":"2020919567615431585","title":"ER-Golgi trafficking and cell cycle regulation","description":"This cluster\u2019s top GO terms center on ER-to-Golgi vesicle transport and SNARE complex disassembly, together with cell cycle-related processes such as cell division and DNA replication. While a few terms (estradiol response, lens morphogenesis, aging) are more tangential, the strongest signals point to membrane trafficking machinery coupled with fundamental cell cycle functions, suggesting proteins that participate in the coordination of intracellular transport with cell proliferation. Confidence: Medium","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0035494","count":2},{"id":"GO:0032355","count":1}]},{"hash":"348044953672869541","title":"Immune signaling and endosomal transport","description":"The cluster shows enrichment for TH1-type immune signaling and regulation of JNK cascades, plus negative regulation of IL-23 production, indicating signaling roles in immunity. It also includes endosomal/lysosomal trafficking terms (endosome to lysosome transport, late endosome transport), apical protein localization, and gene expression regulation, suggesting accompanying roles in intracellular transport and protein localization. This combination points to a cohesive theme of immune signaling intertwined with vesicle trafficking and cellular localization.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042088","count":3},{"id":"GO:0046330","count":3},{"id":"GO:0032707","count":3},{"id":"GO:0000055","count":3},{"id":"GO:0071260","count":3}]},{"hash":"1504475418082639892","title":"Endosome-lysosome trafficking","description":"Proteins in this cluster are enriched for GO terms related to endosome-to-lysosome transport, phagosome acidification, and regulation of the secretory pathway, pointing to a common role in intracellular cargo routing and lysosomal function. While there are a few outliers touching mitochondrial inheritance or neural development, the prevailing theme centers on vesicle trafficking and organelle maturation.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000001","count":2},{"id":"GO:0051291","count":2},{"id":"GO:1903307","count":2},{"id":"GO:0008333","count":2},{"id":"GO:1900026","count":2}]},{"hash":"562508094587960114","title":"Mitochondrial respiration and ROS detoxification","description":"The top GO terms center on mitochondrial electron transport, cytochrome c to oxygen, ATP synthesis, and assembly of complex IV, with additional terms related to removal of superoxide radicals and ROS-related aging. While a few odd or obsolete terms appear, the prevailing signal is mitochondrial energy metabolism and oxidative stress management, suggesting a cohesive cluster of mitochondria-focused proteins.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006123","count":1},{"id":"GO:0042776","count":1},{"id":"GO:0033617","count":1},{"id":"GO:0048773","count":1},{"id":"GO:0001320","count":1}]},{"hash":"58007870087985522","title":"Unfolded Protein Response and ER Translation Regulation","description":"The top GO terms cluster around ER stress and protein homeostasis, including response to unfolded protein, chaperone-assisted refolding, ERAD, and positive regulation of translation initiation in response to ER stress. There are also signals for transcription elongation regulation and metabolic control, suggesting broader stress-responsive regulation. Overall, the dominant theme is ER stress\u2013related protein folding and translation control.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032968","count":2},{"id":"GO:0090526","count":2},{"id":"GO:0006986","count":2},{"id":"GO:0036494","count":2},{"id":"GO:0051301","count":2}]},{"hash":"220558144317538816","title":"Glycolysis and nucleotide biosynthesis","description":"This cluster\u2019s top GO terms are dominated by glycolytic (glucose catabolic, glycolytic) processes and 5-phosphoribose 1-diphosphate biosynthesis, pointing to central carbon metabolism feeding nucleotide production (PRPP) and related salvage/degradation of nucleotides. There are some sporulation and transcription terms present, but the strongest signal ties energy metabolism to nucleotide metabolism, making this a metabolism-centered cluster.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006015","count":2},{"id":"GO:0006007","count":2},{"id":"GO:0006096","count":2},{"id":"GO:0009264","count":2},{"id":"GO:0043937","count":2}]},{"hash":"157666893255248052","title":"Unknown","description":"This cluster's top GO terms span transcription and translation machinery, signaling pathway regulation, and unrelated metabolic/light-response processes, with no clear shared function or interaction pattern among the proteins. The absence of edges supports a heterogeneous or non-cohesive cluster.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0006413","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0001732","count":1}]},{"hash":"1210486926894044941","title":"Cross-species developmental processes","description":"The top GO terms are dominated by developmental themes across organisms and tissues (neural crest formation, heart development, leaf formation, multicellular organism development, visual perception), suggesting a broad developmental regulation motif. There are some outliers (viral process, specific enzymatic regulations) that dilute coherence, and the lack of edge connectivity among proteins adds ambiguity. Overall, the common thread points to developmental roles across species, justifying this label with moderate confidence.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014029","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0007507","count":2},{"id":"GO:1903770","count":2}]},{"hash":"1257333398708582648","title":"Calcium- and sphingolipid-mediated signaling regulators","description":"The cluster shows enrichment for signaling regulation across multiple pathways, notably calcium-mediated signaling and sphingolipid metabolism (phytosphingosine/dihydrosphingosine-1-P), with additional hints from cytokine signaling and hormonal biosynthesis regulation, which together point to a theme of regulators coordinating neural/endocrine signaling processes.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":1},{"id":"GO:0030307","count":1},{"id":"GO:0019722","count":1},{"id":"GO:2000064","count":1},{"id":"GO:0010803","count":1}]},{"hash":"293174000833431866","title":"Ubiquitin-regulated transcription control","description":"The GO terms point to ubiquitin-dependent protein catabolic processes coupled with transcriptional regulation (including RNA polymerase II and I\u2013related regulatory processes) and responses related to DNA damage, suggesting a theme where protein turnover intersects with transcriptional control. Although several terms are obsolete and there are no evident interactions among the six proteins, the core pattern centers on regulation of proteostasis in the context of transcriptional activity.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903071","count":2},{"id":"GO:0036369","count":1},{"id":"GO:0071318","count":1},{"id":"GO:1903026","count":1},{"id":"GO:0010767","count":1}]},{"hash":"2102838561022111478","title":"Mitotic cell cycle regulation","description":"The proteins show enrichment for DNA replication, G1/S transition, meiotic and nuclear cell cycle regulation, and centrosome/kinetochore processes, suggesting a core theme of mitotic progression and chromosome segregation. A few terms relate to neuronal development or signaling, but the dominant pattern aligns with cell-cycle control and centrosome/kinetochore dynamics.","confidence":"Medium","size":6,"edges":5,"triangles":1,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046827","count":4},{"id":"GO:0014044","count":3},{"id":"GO:0034501","count":3},{"id":"GO:0060079","count":3},{"id":"GO:0006260","count":3}]},{"hash":"601607004204619602","title":"Organ Development and Energy Metabolism","description":"The cluster shows strong representation of developmental terms across brain, liver, and kidney (brain development, liver development, metanephric proximal convoluted tubule development) alongside metabolic pathways such as fatty acid beta-oxidation, ketone body biosynthesis/catabolism, and amino acid catabolism (L-isoleucine). This suggests a link between organ development programs and energy metabolism, rather than a single, narrow function.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":6},{"id":"GO:0019619","count":6},{"id":"GO:0006635","count":6},{"id":"GO:0046951","count":6},{"id":"GO:0072229","count":6}]},{"hash":"551867458079593704","title":"Developmental Transcription Regulators","description":"The cluster is enriched for terms linked to development (placenta, thymus, multicellular organism development) and DNA-templated transcription, implying these proteins likely function as transcriptional regulators guiding developmental processes. Some stress-response terms appear but are less central to the core theme, so the developmentally focused transcriptional regulation interpretation fits best.","confidence":"Medium","size":6,"edges":5,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000187","count":3},{"id":"GO:0001890","count":3},{"id":"GO:0048538","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0019233","count":3}]},{"hash":"1765446760615162898","title":"Unknown","description":"The top terms are highly diverse, spanning embryonic development and cell fate specification to transcription initiation and RNA processing, plus DNA metabolism and SOS response. There are no shared pathways or direct functional connections, and the cluster has no edges or interactions, making a single coherent label inappropriate. ","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048568","count":2},{"id":"GO:0072674","count":1},{"id":"GO:0072327","count":1},{"id":"GO:0001113","count":1},{"id":"GO:0000184","count":1}]},{"hash":"1222324461254220690","title":"Chaperone-Mediated Protein Folding and Localization","description":"The cluster shows strong enrichment for chaperone-related terms (protein folding/refolding, stabilization, chaperone complexes) and protein localization processes (mitochondrial intermembrane space import, telomere localization), with a few immune-related terms likely reflecting broader annotations. This suggests a cohesive theme around protein quality control and trafficking rather than a single signaling pathway.","confidence":"High","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:2000778","count":5},{"id":"GO:0050821","count":5},{"id":"GO:0051973","count":5},{"id":"GO:0051086","count":5},{"id":"GO:0051085","count":5}]},{"hash":"1057144199462877917","title":"Unknown","description":"This cluster shows a mix of GO terms: potassium ion transport, dendrite morphogenesis, immune defense, transcription, and ER organization. There is no clear shared function or pathway that ties all six proteins together, suggesting either heterogeneous roles or annotation noise rather than a cohesive module.","confidence":"","size":6,"edges":9,"triangles":4,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006813","count":4},{"id":"GO:0048813","count":4},{"id":"GO:0050830","count":4},{"id":"GO:0043552","count":4},{"id":"GO:0006351","count":4}]},{"hash":"1886517077728390674","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":7,"triangles":4,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060271","count":6},{"id":"GO:1905869","count":6},{"id":"GO:0042068","count":6},{"id":"GO:0051036","count":6},{"id":"GO:0010224","count":6}]},{"hash":"1858449205860101588","title":"Ribosome biogenesis and RNA processing","description":"The cluster shows strong representation of rRNA maturation (SSU/LSU, 5.8S) and ribosomal subunit biogenesis terms, indicating a core theme around ribosome assembly and RNA processing. Additional terms related to ubiquitin-mediated processes, transcription regulation, and a retina development term are present but appear secondary to the primary ribosome/RNA maturation signal. Therefore, the label reflects the dominant function of the group with medium confidence due to some functional noise. ","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0060041","count":2},{"id":"GO:0000209","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0006283","count":2}]},{"hash":"12062384578357520","title":"Ribosome biogenesis and cell cycle regulation","description":"The cluster centers on ribosome biogenesis, especially large subunit biogenesis and its nuclear export, together with cell cycle control terms (mitotic start point and general cell cycle). Actin cytoskeleton organization ties to mitosis/cytokinesis, reinforcing a growth and division theme. The remaining terms, like lipid A/LPS and cell wall mannoprotein biosynthesis, appear more peripheral or noisy, but do not override the dominant ribosome/cell cycle signal.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007089","count":1},{"id":"GO:0030036","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0007049","count":1},{"id":"GO:0000055","count":1}]},{"hash":"1991731722755228790","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":13,"triangles":13,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032869","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006168","count":3},{"id":"GO:0032264","count":3},{"id":"GO:0006178","count":3}]},{"hash":"1516600169590879397","title":"Nutrient-Stress Metabolism and Transcription","description":"The terms point to metabolic processes (amino acid catabolism, gluconeogenesis, GMP biosynthesis, transport) and transcriptional activity (DNA-templated transcription), plus a glucose-starvation response and nuclear import, suggesting a cluster related to coordinating metabolism and gene expression under nutrient stress rather than a single pathway.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0042149","count":2},{"id":"GO:0006565","count":2},{"id":"GO:0019343","count":2},{"id":"GO:0030071","count":2}]},{"hash":"1306600409365630147","title":"Mitochondrial electron transport and respiration","description":"The selected GO terms center on mitochondrial oxidative phosphorylation\u2014electron transport (ubiquinol to cytochrome c), assembly of respiratory complex III, and proton translocation, covering aerobic respiration. Some non-core terms exist (pollen sperm differentiation, brown fat differentiation), but the dominant theme is energy production by mitochondria.","confidence":"Medium","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006122","count":1},{"id":"GO:0034551","count":1},{"id":"GO:1902600","count":1},{"id":"GO:0009060","count":1},{"id":"GO:0048235","count":1}]},{"hash":"1830528684060370093","title":"Unknown","description":"The top GO terms span immune regulation (T cell proliferation, tolerance), development (placental differentiation, organ regeneration), and general cellular processes (nuclear export, ER polarization, virus response), with no clear single function tying them together. This heterogeneity makes a precise label inappropriate.","confidence":"","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043277","count":3},{"id":"GO:0046641","count":3},{"id":"GO:0060709","count":3},{"id":"GO:0006611","count":3},{"id":"GO:0061167","count":3}]},{"hash":"605972036737969588","title":"Chromatin regulation and ubiquitin-proteasome pathway","description":"The cluster is enriched for chromatin-related terms (chromatin organization, heterochromatin maintenance, DNA repair) and for ubiquitin/neddylation\u2013dependent processes (SCF-dependent proteasomal degradation, free ubiquitin chain formation, protein neddylation). These together suggest a functional group centered on controlling chromatin state and protein turnover via ubiquitin/neddylation pathways. Some terms like viral process or synapse assembly appear incidental, but the dominant theme ties chromatin regulation to ubiquitin-mediated degradation. ","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1903955","count":6},{"id":"GO:0031497","count":6},{"id":"GO:0016032","count":6},{"id":"GO:0031146","count":6},{"id":"GO:0000724","count":6}]},{"hash":"376714243689898355","title":"Neural development with immune signaling","description":"This cluster contains neural development-related terms (axonal fasciculation, branching morphogenesis of a nerve, regulation of synapse assembly) alongside innate immune signaling terms (TLR4 signaling, I-kappaB phosphorylation, regulation of dendritic cell cytokine production, IL-1\u03b2 production). The mix suggests proteins involved in neurodevelopment that also participate in neuroimmune communication or inflammatory signaling. Some terms like cornea development and proteasomal processes are less central but can be linked to broader developmental or regulatory roles. Confidence: Medium","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061303","count":2},{"id":"GO:0050718","count":2},{"id":"GO:2000172","count":1},{"id":"GO:0031146","count":1},{"id":"GO:0006409","count":1}]},{"hash":"894314571435339247","title":"Ribosome Biogenesis and Translation Regulation","description":"The terms cluster around translation and ribosome biogenesis, including translation, positive regulation of translation, ribosome biogenesis, and maturation of LSU/5.8S rRNA, indicating a ribosome assembly/translation regulatory theme.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0045727","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0042273","count":2}]},{"hash":"1869288834143621621","title":"Plant Hormone Metabolism and Fruit Ripening","description":"GO terms indicate auxin, ethylene, and gibberellin biosynthesis and catabolism, together with fruit ripening and related oxidation-reduction processes, suggesting a cluster centered on hormonal regulation of ripening and associated secondary metabolism in plants.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009852","count":5},{"id":"GO:0009835","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0009693","count":5},{"id":"GO:0045487","count":5}]},{"hash":"867689819727377670","title":"BMP signaling in embryonic development","description":"The top GO terms point to BMP signaling and multiple embryonic morphogenesis processes (pectoral fin, olfactory bulb, skeletal joint development), suggesting a cohesive theme around developmental signaling during embryogenesis. Supportive terms like endomembrane organization and various glycan biosynthesis processes may reflect cellular and extracellular remodeling that accompanies development, but the central thread appears to be BMP-associated developmental signaling.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008101","count":2},{"id":"GO:0035118","count":2},{"id":"GO:0035884","count":2},{"id":"GO:0021772","count":2},{"id":"GO:0072498","count":2}]},{"hash":"2046318834605685321","title":"Fungal cell wall biogenesis and glycosylation","description":"The terms converge on constructing and modifying fungal cell walls and glycoproteins: septum assembly and budding reflect cell division in fungi, while several GO terms describe mannoprotein and galactomannan biosynthesis, fungal-type cell wall biogenesis, and N-linked glycosylation, plus related polysaccharide biosynthesis (xyloglucan, mucilage). This points to a coherent role in fungal cell wall biosynthesis and glycosylation.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000917","count":1},{"id":"GO:0007114","count":1},{"id":"GO:0000032","count":1},{"id":"GO:0009272","count":1},{"id":"GO:0010392","count":1}]},{"hash":"316389169105387045","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046444","count":1},{"id":"GO:0006747","count":1},{"id":"GO:0019350","count":1},{"id":"GO:1990966","count":1},{"id":"GO:0015937","count":1}]},{"hash":"1666775507937051859","title":"Unknown","description":"GO terms span signaling and development across diverse processes and species, including GPCR signaling, Rho signaling, taste perception, neural remodeling, and even fungal sporulation, with no single cohesive function tying them together. Because there is no clear common theme, this cluster is best labeled Unknown.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043950","count":1},{"id":"GO:0007266","count":1},{"id":"GO:0007213","count":1},{"id":"GO:0001501","count":1},{"id":"GO:0016322","count":1}]},{"hash":"807644618828828305","title":"Seed development and mitochondrial respiration","description":"This cluster includes GO terms related to seed development (embryo ending in dormancy and endosperm development) alongside mitochondrial energy metabolism (complex IV assembly, proton transport, and ATP synthesis-coupled electron transport), suggesting a link between seed development and mitochondrial function.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009793","count":1},{"id":"GO:0009960","count":1},{"id":"GO:0033617","count":1},{"id":"GO:1902600","count":1},{"id":"GO:0042774","count":1}]},{"hash":"1943346613683167331","title":"Xenobiotic and metabolic stress response","description":"The proteins show enrichment for responses to chemical stimuli (xenobiotic stimulus, herbicide, lipopolysaccharide) and include related metabolic and regulatory processes (malate metabolism, thiamine biosynthesis, chromatin binding regulation, and cAMP signaling), suggesting a cohesive theme of chemical-stress response coupled with metabolic regulation.","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0006108","count":2},{"id":"GO:0045654","count":2},{"id":"GO:0035563","count":2}]},{"hash":"447539267202213532","title":"DNA Replication and Transcription with ATP Metabolism","description":"The cluster groups core cellular processes tied to genome maintenance and gene expression (DNA replication; mRNA export; transcription initiation) with energy metabolism (ATP metabolism; regulation of ATP biosynthesis; aerobic respiration). Additional terms around centriole elongation and autophagosome maturation hint at broader cell-cycle and autophagy connections, but the dominant theme centers on energy-dependent DNA replication and transcription activities.","confidence":"Medium","size":5,"edges":8,"triangles":5,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046034","count":3},{"id":"GO:0006406","count":3},{"id":"GO:2001171","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0019079","count":3}]},{"hash":"444987353073275612","title":"Neurovascular development signaling","description":"This cluster is enriched for brain development and vascular development terms, plus signaling pathways and receptor internalization, indicating a neurovascular development signaling module.","confidence":"Medium","size":5,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":5},{"id":"GO:0007213","count":3},{"id":"GO:0032835","count":3},{"id":"GO:0002092","count":3},{"id":"GO:0035723","count":3}]},{"hash":"1013226604540232371","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0090615","count":1},{"id":"GO:0090617","count":1},{"id":"GO:0042793","count":1},{"id":"GO:1905639","count":1}]},{"hash":"860549480854675346","title":"Mitochondrial dynamics and vesicle trafficking in immunity","description":"The dominant GO terms center on mitochondria (inheritance, cytochrome c release, fission-related activity) and vesicle trafficking/processing (phagocytic vesicles, endocytic recycling), with innate immune response involvement, suggesting a cluster of proteins coordinating mitochondrial regulation of apoptosis and vesicle trafficking in immune cells.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0045087","count":2},{"id":"GO:1900063","count":2},{"id":"GO:0000001","count":2},{"id":"GO:0070584","count":2}]},{"hash":"522874001139883685","title":"Ribosome Biogenesis and Translation","description":"The top terms cluster around translation and ribosome biogenesis (with rRNA processing) and include related transcription-related processes, suggesting the proteins mainly relate to gene expression machinery and ribosome assembly rather than signaling or metabolism.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0000447","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0016032","count":1}]},{"hash":"861365224974806663","title":"Valine/Isoleucine biosynthesis cluster","description":"Dominant theme is amino acid biosynthesis, esp. valine and, to a lesser extent, isoleucine biosynthesis (GO:0009099, GO:0009097). A few terms point to NAD+ biosynthesis and basic metabolism, with some development-related terms likely due to broad annotation. Therefore, labeling as Valine/Isoleucine biosynthesis cluster captures the main shared function among the proteins.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009097","count":2},{"id":"GO:0009099","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0021987","count":2},{"id":"GO:0009255","count":1}]},{"hash":"1177147064006357514","title":"Organogenesis and lineage differentiation","description":"This cluster's GO terms cluster around developmental and differentiation processes across multiple tissues, including heart structure formation (endocardial cushion, ventricular septum, vascular smooth muscle), ureter maturation, mesenchymal-to-epithelial transition, and neuronal differentiation (GABAergic), as well as immune differentiation (T cell and TH2 cytokine production). The common thread is cellular differentiation during embryogenesis and organogenesis across multiple lineages rather than a single pathway. ","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045582","count":4},{"id":"GO:0035799","count":4},{"id":"GO:0071442","count":4},{"id":"GO:0003197","count":4},{"id":"GO:2000553","count":4}]},{"hash":"1665808174244170289","title":"Spliceosome-mediated mRNA processing","description":"The top GO terms center on spliceosome-driven mRNA splicing and its positive regulation, with related RNA regulatory activities (ncRNA-mediated silencing, stress-responsive mRNA stability), indicating a cluster aligned with RNA processing and splicing control.","confidence":"High","size":5,"edges":4,"triangles":1,"max_degree":2,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0010610","count":3},{"id":"GO:1901254","count":2}]},{"hash":"1146482470398954543","title":"Oxidative Stress Response","description":"The GO terms cluster around redox balance and detoxification (redox homeostasis, oxidant detoxification, hydrogen peroxide catabolic process, removal of superoxide radicals). While there are additional terms related to signaling and metabolism, the dominant theme is management of reactive oxygen species.","confidence":"High","size":5,"edges":8,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006641","count":4},{"id":"GO:0045454","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0033599","count":2},{"id":"GO:0042744","count":2}]},{"hash":"937944339705623892","title":"Mitochondrial protein import and folding","description":"The top GO terms point to mitochondrial processes, including protein insertion into the mitochondrial inner membrane, protein unfolding, and chaperone-mediated protein complex assembly, as well as positive regulation of ATP biosynthesis. This combo suggests a cluster centered on mitochondrial protein maturation and energy production, with some terms being more peripheral or obsolete but not contradicting the core theme. Confidence is tempered by a few outliers, hence a Medium label.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006808","count":2},{"id":"GO:0006406","count":1},{"id":"GO:2001171","count":1},{"id":"GO:1903724","count":1},{"id":"GO:0039546","count":1}]},{"hash":"490006076261574911","title":"Alkaloid and lipid metabolism","description":"This cluster shows strong representation of alkaloid catabolic processes (isoquinoline, camphor, and other alkaloid catabolism), retinoic acid catabolism, as well as lipid-related metabolism (triglyceride metabolism, bile acid biosynthesis). The common theme is metabolism/catabolism of diverse small organic molecules, rather than a single specific pathway, suggesting a general organic-molecule processing function. Confidence: High","confidence":"","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009822","count":3},{"id":"GO:0006641","count":3},{"id":"GO:0071615","count":3},{"id":"GO:0034653","count":3},{"id":"GO:0033076","count":3}]},{"hash":"2143037380547407655","title":"Redox and hormone signaling","description":"The proteins show enrichment for redox homeostasis and detoxification, along with prostaglandin biosynthesis and responses to hormones like estradiol and insulin, plus related cardiovascular and growth signaling. This points to a theme of redox-regulated, hormone-responsive signaling across different tissues. ","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0001516","count":2},{"id":"GO:0010043","count":1},{"id":"GO:0032355","count":1}]},{"hash":"259705775515764027","title":"Lipopolysaccharide biosynthesis","description":"Most top GO terms point to the synthesis of lipopolysaccharide and related sugars (UDP-L-arabinose, UDP-rhamnose, ADP-L-glycero-manno-heptose) and LPS components (O antigen, core region). This pattern suggests proteins in a module for assembling the bacterial outer membrane glycan. Some outlier terms (sporopollenin biosynthesis, cytolysis) appear noise relative to the dominant LPS theme, but the overall signal supports LPS biosynthesis.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033358","count":2},{"id":"GO:0009699","count":2},{"id":"GO:0097171","count":2},{"id":"GO:0010253","count":2},{"id":"GO:0009243","count":2}]},{"hash":"930408078928416959","title":"Plant osmotic stress signaling and lipid metabolism","description":"This cluster\u2019s top terms strongly emphasize plant-like responses to osmotic/solute stress (hyperosmotic salinity response) and abscisic acid\u2013activated signaling, complemented by terms for inositol and phosphatidylinositol biosynthesis and related lipid signaling pathways. While other metabolism/development terms appear, the dominant theme ties stress signaling to lipid-related metabolism in plants. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042538","count":1},{"id":"GO:0006661","count":1},{"id":"GO:0000103","count":1},{"id":"GO:0006094","count":1},{"id":"GO:0009738","count":1}]},{"hash":"2111179630930589648","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":3},{"id":"GO:0006508","count":3},{"id":"GO:0010043","count":2},{"id":"GO:0046900","count":2},{"id":"GO:0044205","count":2}]},{"hash":"192586608371786537","title":"Unknown","description":"The terms show a mix of protein degradation (proteolysis, peptide catabolic) and various, often unrelated, metabolic pathways (purine, lysine/arginine biosynthesis, allantoin assimilation, fatty acid biosynthesis) with some obsolete annotations, yielding no clear, cohesive function for the cluster. Therefore no representative label beyond Unknown can be confidently assigned.","confidence":"","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006144","count":1},{"id":"GO:0006508","count":1},{"id":"GO:0043171","count":1},{"id":"GO:0019877","count":1},{"id":"GO:0009089","count":1}]},{"hash":"30277498945677960","title":"Glycan biosynthesis and metabolism","description":"The top GO terms are dominated by sugar- and glycan-related biosynthetic and catabolic processes (e.g., GDP-mannose, galactose, glucose-1-phosphate, glycogen, lipopolysaccharide/O antigen biosynthesis) and related cell wall organization, suggesting a cohesive theme around glycan production and sugar metabolism in bacteria. A minority of terms (like thiamine biosynthesis) are peripheral but do not override the main glycan/metabolism signal.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009228","count":2},{"id":"GO:0019388","count":1},{"id":"GO:0019255","count":1},{"id":"GO:0009298","count":1},{"id":"GO:0006148","count":1}]},{"hash":"512233858437636757","title":"Chloroplast Translation and Photosynthesis Light Response","description":"The cluster centers on chloroplast-associated processes: translation (plastid ribosomes) alongside photosynthesis in PSI and PSII, and a suite of light-responsive terms (far-red, UV-A, high/low light) plus nonphotochemical quenching and chlorophyll-related phytol biosynthesis. This combination points to proteins involved in chloroplast gene expression and light-harvesting/photoprotection during photosynthesis.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0009768","count":1},{"id":"GO:1904964","count":1},{"id":"GO:0010218","count":1},{"id":"GO:0071486","count":1}]},{"hash":"2025569052890426707","title":"RNA Pol II Regulation and Chromatin Modification","description":"The top terms cluster around transcriptional control by RNA polymerase II, including negative/positive regulation and preinitiation complex assembly, as well as histone H3 acetylation indicating chromatin remodeling. While a few terms touch on other processes, the dominant theme is transcription regulation and chromatin state.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0043966","count":3},{"id":"GO:0045898","count":2},{"id":"GO:1900446","count":2},{"id":"GO:0061408","count":2}]},{"hash":"1352716866454411920","title":"Phosphorylation Regulation","description":"The top terms cluster around negative regulation of kinase activity and dephosphorylation, i.e., control of phosphorylation states (GO:0006469, GO:0006470, GO:0032516). While there are some photoreceptor and calcium signaling terms, the common theme is modulation of signaling through phosphorylation state control. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0033555","count":1},{"id":"GO:0051591","count":1},{"id":"GO:0050665","count":1},{"id":"GO:0019749","count":1}]},{"hash":"843201031877554966","title":"Unknown","description":"The annotated terms span DNA replication, immune modulation, placental development, protein trafficking, and antiviral responses, with no dominant shared function across the proteins. The absence of edges and the heterogeneous GO signals suggest this cluster lacks a coherent single-function 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:0043277","count":3},{"id":"GO:0046641","count":3},{"id":"GO:0060709","count":3},{"id":"GO:0006611","count":3}]},{"hash":"2271992811852623105","title":"Sugar and small-molecule transporters","description":"Proteins here cluster around membrane transporter activities, with GO terms for transmembrane transport of glucose (D-glucose transport), fructose import, trehalose transport, nitrite transport, and sodium-independent organic anion transport. A translation term is present but much less representative. Overall, the group seems focused on carbohydrate and related small-molecule transport across membranes.","confidence":"Medium","size":5,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0042149","count":1},{"id":"GO:1990539","count":1},{"id":"GO:0043252","count":1},{"id":"GO:0015771","count":1}]},{"hash":"1340860227002313212","title":"Bacterial metabolism and antibiotic biosynthesis","description":"Glycolysis and multiple catabolic processes point to central metabolism, while antibiotic biosynthesis and menaquinone biosynthesis indicate secondary metabolite production; some xenobiotic response terms suggest environmental sensing. Together, this cluster reflects bacterial metabolic versatility with secondary metabolite capabilities.","confidence":"Medium","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":4},{"id":"GO:0009234","count":3},{"id":"GO:0042493","count":3},{"id":"GO:0006096","count":3},{"id":"GO:0032868","count":3}]},{"hash":"2185190955711614328","title":"Multi-polymerase transcription initiation","description":"The cluster is dominated by GO terms for transcription initiation and regulation across RNA polymerases I, II, and III (including Pol I\u2013specific rRNA transcription, Pol II and Pol III initiation, and preinitiation complex assembly), indicating a shared function in assembling and regulating transcription machinery. The presence of Pol I, II, and III\u2013related terms (and Pol I regulation) supports a cohesive theme around transcription initiation, with occasional linkage to spermatogenesis noted in the terms.","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042790","count":3},{"id":"GO:0070893","count":2},{"id":"GO:0045893","count":2},{"id":"GO:0006352","count":2},{"id":"GO:0006359","count":2}]},{"hash":"1701696668458020299","title":"Fatty acid oxidation and leucine catabolism","description":"This cluster's terms cluster around energy-yielding catabolic processes, especially fatty acid beta-oxidation and medium-chain fatty acid catabolism, plus leucine (branched-chain amino acid) catabolism. Carnitine biosynthesis ties to transporting fatty acids into mitochondria, supporting a lipid- and amino acid\u2013driven energy metabolism theme. A few terms (AMP salvage, development, steroid biosynthesis) are peripheral, but the dominant signal is lipid and BCAA catabolism.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044209","count":2},{"id":"GO:0046835","count":2},{"id":"GO:0045329","count":1},{"id":"GO:0006111","count":1},{"id":"GO:0006552","count":1}]},{"hash":"230792730184255362","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":1},{"id":"GO:0001172","count":1},{"id":"GO:0031990","count":1},{"id":"GO:0000288","count":1},{"id":"GO:0006397","count":1}]},{"hash":"283742506947699734","title":"Redox Homeostasis and Oxidative Stress Signaling","description":"The top GO terms cluster around redox balance and detoxification of reactive oxygen species (cell redox homeostasis, hydrogen peroxide and superoxide removal, cellular response to hydrogen peroxide), with supporting signals in ROS-responsive pathways (I-kappaB phosphorylation, non-canonical NF-kappaB and stress-activated MAPK regulation). Copper transport also ties to metal-associated redox biology. While erythrocyte homeostasis and spermatogenesis are present, the dominant theme is redox regulation and oxidative stress signaling.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006825","count":1},{"id":"GO:0042744","count":1},{"id":"GO:0045454","count":1},{"id":"GO:0019430","count":1},{"id":"GO:0042345","count":1}]},{"hash":"1922414738415549638","title":"Chromatin Regulation and Development","description":"The top terms point to chromatin state and transcriptional control (DNA repair, heterochromatin formation, transcription preinitiation complex assembly) with several development-related processes (epithalamus, myoblast, ureter development) and signaling responses (steroid hormone, TGF-beta). This suggests a theme of gene regulation via chromatin dynamics during development, rather than a single specific pathway. Confidence: Medium","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0045899","count":2},{"id":"GO:0070869","count":1},{"id":"GO:0021538","count":1},{"id":"GO:0048545","count":1}]},{"hash":"1335511028543547377","title":"Mitotic spindle assembly and cytokinesis","description":"Top GO terms point to microtubule organization and division processes, including cytoplasmic microtubule organization, microtubule nucleation, mitotic spindle midzone assembly, spindle pole body duplication, FtsZ-dependent cytokinesis, and the cell cycle. While there are some outlier terms (interleukin-4 response, neuron migration, cell septum assembly) the dominant signal is cytoskeletal machinery governing mitosis and cytokinesis. ","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071353","count":5},{"id":"GO:0090529","count":5},{"id":"GO:0031122","count":5},{"id":"GO:0001764","count":5},{"id":"GO:0051258","count":5}]},{"hash":"1558864511234450484","title":"Unknown","description":"The GO terms span mitochondrial inheritance and membrane potential regulation, lipid metabolism regulation (SREBP signaling and cholesterol biosynthesis), excretion, and cell adhesion-related processes, which don\u2019t converge on a single clear function or pathway for this cluster. This diversity suggests no coherent, specific function characterizes the group.","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0000001","count":1},{"id":"GO:0010918","count":1},{"id":"GO:0052547","count":1},{"id":"GO:2000049","count":1}]},{"hash":"1622507321949838865","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1901621","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0097428","count":4},{"id":"GO:0045454","count":4},{"id":"GO:0006458","count":4}]},{"hash":"433285564350522231","title":"Fatty acid biosynthesis and catabolism","description":"The Top Terms show a clear enrichment in fatty-acyl-CoA metabolism, including long- and medium-chain fatty acid biosynthetic and catabolic processes, plus a negative regulation of fatty acid biosynthesis. This cohesive pattern supports a fatty acid metabolism theme for the cluster, while a few outlier terms likely reflect annotation noise in a small set of proteins.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036116","count":1},{"id":"GO:0035338","count":1},{"id":"GO:0045717","count":1},{"id":"GO:1900535","count":1},{"id":"GO:0010124","count":1}]},{"hash":"1382663706777265654","title":"Ubiquitin-Dependent TNF-NF-kB-JNK Signaling","description":"The proteins show strong representation of ubiquitination processes (K48- and K6-linked) and core inflammatory signaling pathways (TNF-mediated NF-kB activation, I-kB phosphorylation, JNK regulation, NIK activity), suggesting a module of ubiquitin-regulated inflammatory signaling.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903762","count":4},{"id":"GO:0042787","count":4},{"id":"GO:0051865","count":4},{"id":"GO:0007250","count":4},{"id":"GO:0070936","count":4}]},{"hash":"569532761930529852","title":"Chloroplast Photosynthesis Electron Transport","description":"This cluster is dominated by photosynthesis-related terms (photosynthesis, light reaction, photosynthetic electron transport in photosystem II), suggesting chloroplast components involved in electron transport. A few low-count terms touch on stress responses and organelle regulation, but they are much less represented, so the core function is photosynthesis.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":2},{"id":"GO:0019684","count":2},{"id":"GO:0009772","count":2},{"id":"GO:0018298","count":2},{"id":"GO:0006950","count":1}]},{"hash":"1319135347190025084","title":"mRNA processing and splicing regulation","description":"The top terms are dominated by post-transcriptional RNA processing activities, especially ncRNA-mediated gene silencing, regulation of mRNA splicing via the spliceosome (including alternative splicing), mRNA export, modification, stabilization, and polyadenylation. Together these indicate a cluster of proteins involved in RNA maturation and control of transcript fate rather than transcriptional initiation.","confidence":"High","size":5,"edges":8,"triangles":5,"max_degree":4,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":4},{"id":"GO:0048026","count":4},{"id":"GO:1901407","count":4},{"id":"GO:0016556","count":3},{"id":"GO:0006406","count":3}]},{"hash":"2003314080132445787","title":"Nuclear import and mitosis","description":"The cluster shows enrichment for GO terms tied to nuclear processes: import of NLS-bearing proteins into the nucleus, spindle organization, and G1/S transition, with karyogamy pointing to nuclear fusion. This pattern suggests the proteins function in nuclear transport and mitotic regulation, despite a few broader terms like skin development and extracellular matrix organization that may reflect annotation noise. ","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006607","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0032516","count":2},{"id":"GO:0043588","count":2},{"id":"GO:0007613","count":2}]},{"hash":"187271280460304392","title":"mRNA processing and splicing regulation","description":"The terms cluster around post-transcriptional control: mRNA modification, export from the nucleus, splicing (including alternative splicing and spliceosome regulation), mRNA stabilization, and miRNA-mediated silencing. This points to a cohesive group of proteins involved in RNA maturation and regulation after transcription, rather than DNA-level processes. ","confidence":"High","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0016556","count":3},{"id":"GO:0006406","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0000381","count":3}]},{"hash":"525380618722576164","title":"Ubiquitin-Dependent Protein Degradation","description":"The top GO terms are dominated by ubiquitin-related processes such as protein polyubiquitination, ubiquitin-dependent protein catabolic processes, autoubiquitination, and K48-linked ubiquitination, all hallmark steps in targeting proteins for proteasomal degradation. Other terms point to ubiquitin\u2019s role in turnover and trafficking (e.g., peroxisomal import, receptor catabolic processes), supporting a cohesive theme of ubiquitin-tagged protein degradation. Confidence: High","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0000209","count":2},{"id":"GO:0016558","count":2},{"id":"GO:0038018","count":2},{"id":"GO:0060816","count":2}]},{"hash":"1308356872295817431","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0000393","count":5},{"id":"GO:0000716","count":5},{"id":"GO:1990417","count":5},{"id":"GO:0071035","count":5},{"id":"GO:0006260","count":5}]},{"hash":"327633815066745295","title":"Pol I/II/III Transcription Initiation and Regulation","description":"The top GO terms cluster around transcription initiation and regulation across RNA polymerases I, II, and III, including preinitiation complex assembly, DNA-templated transcription initiation, and Pol I\u2013mediated nucleolar rRNA transcription, suggesting a common theme of transcription initiation machinery across all three polymerases. A spermatogenesis term appears but does not define the cluster\u2019s core function.","confidence":"High","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007283","count":2},{"id":"GO:0051123","count":2},{"id":"GO:0043966","count":2},{"id":"GO:0070893","count":1},{"id":"GO:0045893","count":1}]},{"hash":"459574323061422465","title":"Unknown","description":"The GO terms span chromatin organization, proteostasis (ubiquitination and SCF-dependent degradation), DNA repair, signaling (TGF-beta and glucose-mediated), development (spinal cord), and cytoskeletal regulation. This broad mix lacks a single cohesive function or pathway, making it unclear to assign a specific, concise label to the cluster.","confidence":"","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070262","count":1},{"id":"GO:0031497","count":1},{"id":"GO:0000209","count":1},{"id":"GO:0071560","count":1},{"id":"GO:0031146","count":1}]},{"hash":"1951555230101507196","title":"Calcium-regulated synaptic vesicle exocytosis","description":"The top GO terms are dominated by regulation of synaptic vesicle exocytosis and cellular response to calcium, suggesting a focus on calcium-dependent neurotransmitter release at synapses. Supporting terms involving Rho signaling, neural plate axis specification, and vesicle-associated lipid transport imply broader neuronal signaling and membrane trafficking roles that underpin vesicle docking and release. Overall, the cluster centers on calcium-controlled presynaptic exocytosis, with ancillary links to cytoskeletal dynamics and membrane biology.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:2000300","count":5},{"id":"GO:0035023","count":4},{"id":"GO:1904468","count":4},{"id":"GO:0021997","count":4},{"id":"GO:0035773","count":4}]},{"hash":"1497610641314849861","title":"Phosphatase-regulated meiosis and T cell signaling","description":"This cluster centers on serine dephosphorylation and regulation of phosphatase activity, pointing to a shared role for phosphatases in controlling signaling. The presence of meiotic cell cycle and meiotic recombination checkpoint terms, along with DNA double-strand break repair, suggests involvement in meiosis and genome maintenance. Immune-related terms like T cell homeostasis and negative regulation of T cell cytotoxicity indicate a tie to T cell signaling. Taken together, the proteins appear linked by phosphatase-mediated signaling regulation spanning meiosis/DNA repair and T cell biology.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070262","count":5},{"id":"GO:0072462","count":5},{"id":"GO:0032516","count":5},{"id":"GO:0043029","count":5},{"id":"GO:0005981","count":5}]},{"hash":"728824271549538016","title":"Plant secondary metabolite and fatty-acid biosynthesis","description":"These proteins are linked to several related biosynthetic processes, notably flavonoid/chalcone biosynthesis, sporopollenin formation, and fatty acid/lipid biosynthesis, suggesting a role in plant secondary metabolite and lipid production rather than a single dedicated pathway.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009715","count":3},{"id":"GO:0009813","count":3},{"id":"GO:0071770","count":3},{"id":"GO:0031148","count":3},{"id":"GO:0035336","count":3}]},{"hash":"2120244039342980051","title":"Metabolic adaptation to glucose starvation","description":"This cluster centers on responses to glucose deprivation and metabolic reprogramming, highlighted by cellular response to glucose starvation, gluconeogenesis, and amino-acid catabolic/nucleotide biosynthesis processes (serine, cysteine/homocysteine, and GMP), suggesting coordinated adaptation to energy/nutrient stress; a nuclear import term may reflect ancillary transport aspects. ","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0042149","count":4},{"id":"GO:0006565","count":4},{"id":"GO:0019343","count":4},{"id":"GO:0030071","count":4},{"id":"GO:0043418","count":4}]},{"hash":"2131479556248970329","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060271","count":5},{"id":"GO:1905869","count":5},{"id":"GO:0042068","count":5},{"id":"GO:0051036","count":5},{"id":"GO:0010224","count":5}]},{"hash":"524112929264007474","title":"Flavonoid and pollen-wall biosynthesis","description":"This cluster is characterized by strong representation of chalcone and flavonoid biosynthesis terms, plus sporopollenin biosynthesis and DIM/DIP cell wall layer assembly, all pointing to plant secondary metabolism and pollen-wall formation. Fatty-acid and long-chain acyl-CoA metabolic processes further support lipid-derived components of the pollen coat, making the overall theme flavonoid production linked with pollen-wall biosynthesis. Some related terms (e.g., DIF-1 biosynthesis, chromatin organization) may reflect broader regulatory connections but do not override the core biosynthetic signal.","confidence":"Medium","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009715","count":2},{"id":"GO:0009813","count":2},{"id":"GO:0071770","count":2},{"id":"GO:0031148","count":2},{"id":"GO:0035336","count":2}]},{"hash":"387545901136160441","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":3},{"id":"GO:0090617","count":3},{"id":"GO:1905639","count":3},{"id":"GO:1900865","count":3},{"id":"GO:0042793","count":3}]},{"hash":"2223474723729173967","title":"Transcriptional Stress Response and Apoptosis","description":"This cluster is dominated by terms for transcription by RNA polymerase II and intrinsic apoptotic signaling triggered by nitrosative and ER stress, pointing to a shared stress-response program that can drive apoptosis and transcriptional reprogramming. The presence of terms related to liver regeneration and hepatocyte proliferation fits with tissue-repair contexts where such stress signaling influences cell fate and growth. Some terms (e.g., eyelid development) appear incidental or historical, but do not negate the central theme. ","confidence":"Medium","size":5,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":3},{"id":"GO:1990442","count":2},{"id":"GO:0097421","count":2},{"id":"GO:0070059","count":2},{"id":"GO:0061029","count":2}]},{"hash":"1489693908227758348","title":"Bacterial catabolic metabolism and sporulation","description":"The cluster\u2019s top GO terms include cellulose and lignin catabolic processes, nitrate and iron assimilation, copper transport, antibiotic biosynthesis, and sporulation with FtsZ-dependent cytokinesis. This mix points to diverse bacterial metabolic and reproduction-related activities (nutrient acquisition, metal handling, and sporulation/division), making a label focused on bacterial catabolic metabolism and sporulation representative of the set. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0017000","count":3},{"id":"GO:0030245","count":3},{"id":"GO:0030435","count":3},{"id":"GO:0046274","count":2}]},{"hash":"2229881218005332387","title":"TLR signaling and innate immune activation","description":"This cluster is dominated by terms for Toll-like receptor signaling (TLR4/TLR10), NF-kB pathway activity (I-kappaB phosphorylation), and innate immune sensing, including detection of lipopolysaccharide and downstream dendritic cell cytokine production and T-helper 1 responses, pointing to a coherent theme of innate immune activation and adaptive cytokine responses. A few terms (L-methionine cycle, plant-type hypersensitive response, sperm individualization) appear less connected and may reflect cross-annotation noise, but the core themes strongly support TLR-mediated immune signaling.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0033353","count":3},{"id":"GO:0071560","count":3},{"id":"GO:0002730","count":3},{"id":"GO:0034142","count":3},{"id":"GO:0009626","count":3}]},{"hash":"1331031563125506591","title":"mRNA processing and splicing regulation","description":"These proteins cluster around multiple aspects of the mRNA lifecycle: regulation of mRNA stability, mRNA export from the nucleus, mRNA modification and stabilization, and control of splicing (including alternative splicing) via the spliceosome, with some involvement in ncRNA-mediated silencing. The dominant signal is mRNA maturation/regulation rather than a single downstream function, suggesting a coordinated role in mRNA processing and gene expression control, possibly under stress conditions.","confidence":"High","size":5,"edges":7,"triangles":3,"max_degree":4,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":5},{"id":"GO:0016556","count":3},{"id":"GO:0006406","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0048026","count":3}]},{"hash":"874669942840249100","title":"Chloroplast Thylakoid Organization and NPQ","description":"The top GO terms cluster around chloroplast processes: nonphotochemical quenching, thylakoid membrane organization, and granum assembly, indicating a focus on photosynthetic membrane architecture and energy dissipation. While there are also terms related to vesicle sorting and protein turnover, these likely reflect general membrane trafficking associated with chloroplasts and the broader cell, rather than a separate function. ","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010196","count":1},{"id":"GO:0010027","count":1},{"id":"GO:0090391","count":1},{"id":"GO:0080167","count":1},{"id":"GO:0071985","count":1}]},{"hash":"464571731359180684","title":"Plasma membrane ion transport and osmoregulation","description":"The cluster is dominated by GO terms describing transport across the plasma membrane for ions (sodium, potassium) and amino acids (D-serine, L-lysine), as well as cell volume homeostasis and hypotonic salinity response. This points to a coherent theme of membrane transport and osmotic regulation, with some additional, less central terms (e.g., macrophage activation regulation) that may represent ancillary roles or annotations. ","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006884","count":2},{"id":"GO:0098719","count":2},{"id":"GO:0097623","count":2},{"id":"GO:0042942","count":1},{"id":"GO:0071477","count":1}]},{"hash":"309554683406444811","title":"Vacuolar amino acid transport","description":"This cluster is dominated by GO terms describing transmembrane import of various amino acids (lysine, glutamate, proline, histidine, asparagine, arginine export from vacuole) into the vacuole, with an additional glutamine transport regulation term. The common theme is proteins involved in vacuolar amino acid transport, so this name captures the shared function. The small size and presence of one less-related term (potassium starvation response) do not override the amino acid transport focus.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015824","count":4},{"id":"GO:0090517","count":4},{"id":"GO:0090515","count":4},{"id":"GO:0061402","count":4},{"id":"GO:0006867","count":4}]},{"hash":"834737905067305464","title":"Protein turnover and chromatin regulation","description":"The cluster combines ubiquitin-proteasome\u2013mediated protein degradation (SCF-dependent degradation and polyubiquitination) with chromatin organization and DNA repair, suggesting a link between proteostasis and gene/genome regulation. It also touches signaling and development pathways, indicating broader regulation of cellular state, but the strongest shared theme centers on protein turnover influencing chromatin and genome maintenance.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0070262","count":1},{"id":"GO:0031497","count":1},{"id":"GO:0000209","count":1},{"id":"GO:0071560","count":1},{"id":"GO:0031146","count":1}]},{"hash":"1170949033123740360","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035975","count":1},{"id":"GO:0046939","count":1},{"id":"GO:0019877","count":1},{"id":"GO:0009089","count":1},{"id":"GO:0006526","count":1}]},{"hash":"2139683210771204656","title":"Gram-positive bacterial membrane transporters (nutrients and bacteriocins)","description":"This cluster is dominated by GO terms for transmembrane transport of diverse substrates (glycerophosphodiesters, molybdate, teichoic acids, methionine, thiamine, phospholipids) and bacteriocin transport/immunity, pointing to membrane transport proteins in Gram-positive bacteria involved in nutrient uptake and defense. Some terms like SOS response or intestinal cholesterol absorption appear as noise but do not override the primary transport theme.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045796","count":5},{"id":"GO:0001407","count":5},{"id":"GO:0015689","count":5},{"id":"GO:0043213","count":5},{"id":"GO:0015777","count":5}]},{"hash":"261787835096741600","title":"Fungal sporulation and polarity regulation","description":"Reasoning: The strongest terms point to fungal development, including a sporulation-specific spindle pole body remodeling term and regulation of cell polarity and filamentous growth, which together reflect fungal morphogenesis and sporulation processes. Related terms about responding to nutrients and toxins align with environmental stress responses typical in fungi. Some terms like placenta development appear noisy or misannotated, but the core signal suggests a fungal sporulation/polarity theme.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046909","count":1},{"id":"GO:0007584","count":1},{"id":"GO:2000114","count":1},{"id":"GO:0031322","count":1},{"id":"GO:0051452","count":1}]},{"hash":"1732881949858674629","title":"Lung development and surfactant homeostasis","description":"This cluster\u2019s top GO terms concentrate on lung-related biology: surfactant homeostasis, branching morphogenesis in the lung, and macrophage activity within the pulmonary environment, with related inflammatory and remodeling processes. Although a few terms touch on bone-related processes, the dominant signals point to lung structure and function, particularly surfactant regulation and airway development. ","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1903955","count":4},{"id":"GO:0097067","count":4},{"id":"GO:0043129","count":4},{"id":"GO:0051603","count":4},{"id":"GO:0010815","count":4}]},{"hash":"1553925139742254926","title":"Bacterial cell wall and lipid biosynthesis","description":"The proteins in this cluster are tied to biosynthesis of cell wall components and membrane lipids, as evidenced by GO terms for lipid A biosynthesis, teichoic acid biosynthesis and D-alanylation, and fatty acid biosynthesis, along with cell wall organization. The presence of antibiotic and nonribosomal peptide biosynthesis terms also suggests bacterial secondary metabolite pathways that often accompany cell envelope biosynthesis, supporting a cohesive theme around bacterial cell envelope construction and modification.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006515","count":1},{"id":"GO:0009245","count":1},{"id":"GO:0070395","count":1},{"id":"GO:0009258","count":1},{"id":"GO:0043041","count":1}]},{"hash":"1985687655499703801","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031426","count":2},{"id":"GO:0016554","count":2},{"id":"GO:0031425","count":2},{"id":"GO:0042793","count":2},{"id":"GO:1905639","count":2}]},{"hash":"151858960369669429","title":"Methylation-Driven Transcription Regulation","description":"The cluster is dominated by GO terms for various methylation activities (peptidyl-lysine/peptidyl-glutamine/histone methylation, RNA methylation, and mRNA capping) along with negative regulation of transcription by RNA polymerase II, indicating a cohesive theme of methylation-based regulation of transcription and RNA processing. A nodulation term is present but appears as a minor, possible annotation artifact relative to the core methylation/transcription theme.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006310","count":2},{"id":"GO:0018026","count":1},{"id":"GO:0018364","count":1},{"id":"GO:0043985","count":1},{"id":"GO:0000122","count":1}]},{"hash":"1091971110323916041","title":"Mitochondrial Energy and Lipid Biosynthesis","description":"The top terms are dominated by mitochondrial functions (electron transport, ATP synthesis, inheritance) and several lipid/membrane biosynthesis processes (ergosterol, sphingolipid, unsaturated fatty acids), suggesting a theme around mitochondrial energy production linked to membrane lipid metabolism. Some terms appear less connected (nerve/myelin, sebaceous differentiation), likely reflecting annotation noise or cross-species annotations, but the core pattern supports a mitochondrial-energy\u2013lipid biosynthesis link.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006122","count":2},{"id":"GO:0000001","count":2},{"id":"GO:0032443","count":2},{"id":"GO:0001949","count":2},{"id":"GO:0042128","count":2}]},{"hash":"658340426753178674","title":"Redox-Responsive NF-\u03baB Signaling","description":"The cluster is dominated by oxidative stress and redox homeostasis terms (hydrogen peroxide catabolic process, removal of superoxide radicals, cellular response to hydrogen peroxide, redox homeostasis), with supporting links to NF-\u03baB pathway regulation (I-\u03baB phosphorylation, regulation of non-canonical NF-kappaB signaling) and stress-activated MAPK cascade. While a couple of terms touch on tissue-specific processes (erythrocyte homeostasis, spermatogenesis), the core pattern ties redox balance to NF-\u03baB signaling.","confidence":"Medium","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042744","count":1},{"id":"GO:0045454","count":1},{"id":"GO:0019430","count":1},{"id":"GO:0042345","count":1},{"id":"GO:0034101","count":1}]},{"hash":"972118936183031215","title":"Unknown","description":"The terms span redox processes, protein modification, stress response, several biosynthetic pathways (bile acids, ascorbate, retinoic and steroid hormones), and a proliferative signal, with no clear common function tying all four proteins together. Therefore, there isn\u2019t a cohesive theme to name the cluster.","confidence":"","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006470","count":1},{"id":"GO:0009414","count":1},{"id":"GO:0006699","count":1},{"id":"GO:0042840","count":1}]},{"hash":"2292332021368041567","title":"Redox Homeostasis and Oxidative Stress Response","description":"The top GO terms cluster tightly around detoxifying oxidants, maintaining cellular redox balance, and responding to oxidative stress, with protein deglutathionylation reflecting redox regulation. Prostaglandin biosynthesis can intersect with redox/inflammatory signaling, supporting the overall theme, while a few outliers (RNA polymerase regulation, neural crest migration) are less central to redox biology. Overall, the dominant signal points to redox balance and oxidative stress pathways.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0001516","count":2},{"id":"GO:1903026","count":1},{"id":"GO:0034599","count":1}]},{"hash":"1752876770859129633","title":"Unknown","description":"The top GO terms span diverse processes (oxidation-reduction, phylloquinone and steroid/retinoic acid biosynthesis, very long-chain fatty acid biosynthesis, sporulation, lung development, transcription regulation). There is no single coherent function or pathway linking all four proteins, so a unified label cannot be assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0042376","count":2},{"id":"GO:0045150","count":2},{"id":"GO:0042761","count":2},{"id":"GO:0030324","count":2}]},{"hash":"1018270938642038389","title":"Cell division and microtubule organization","description":"This cluster centers on cytoskeletal dynamics essential for division and spindle formation, as shown by GO terms like division septum assembly, FtsZ-dependent cytokinesis, mitotic spindle midzone assembly, cytoplasmic microtubule organization, microtubule nucleation, and cell cycle. Although a few terms touch on broader roles such as neuron migration and cytokinesis-related polymerization, the dominant signal is microtubule- and division-related processes across contexts. Therefore, a name emphasizing cell division and microtubule organization best represents the cluster\u2019s function.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000917","count":2},{"id":"GO:0071353","count":2},{"id":"GO:0090529","count":2},{"id":"GO:0031122","count":2},{"id":"GO:0001764","count":2}]},{"hash":"490802468359827188","title":"Neuronal Development and Signaling","description":"The top GO terms are dominated by neural development: spinal cord motor neuron cell fate specification, motor neuron axon guidance, and midbrain dopaminergic neuron differentiation. While there are also endocrine and organogenesis terms, the strongest shared theme is neuronal differentiation and signaling pathways.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0035331","count":3},{"id":"GO:0097067","count":3},{"id":"GO:0072283","count":3},{"id":"GO:0021520","count":3},{"id":"GO:0008045","count":3}]},{"hash":"744691575211240143","title":"Purine Nucleotide Biosynthesis and Salvage","description":"The cluster is dominated by GO terms for purine metabolism and nucleotide biosynthesis\u2014ADP and nucleotide biosynthesis, ITP metabolism, AMP salvage, CDP biosynthesis, and purine ribonucleotide interconversion\u2014with NAD+ biosynthesis also aligning with purine metabolism. Brain and liver development terms appear but seem secondary annotations, suggesting these proteins primarily participate in nucleotide production and turnover.","confidence":"High","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046705","count":4},{"id":"GO:0007420","count":4},{"id":"GO:0001889","count":4},{"id":"GO:0046939","count":4},{"id":"GO:0046940","count":4}]},{"hash":"1188805687052311915","title":"Vascular redox signaling and morphogenesis","description":"The cluster centers on redox-related processes (glutathione metabolism, redox homeostasis) and endothelial/retina vasculature morphogenesis, with supporting signals from prostaglandin biosynthesis and hormone responses. This points to a cohesive theme of redox-regulated vascular development and signaling in endothelial tissues, especially the eye. ","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006749","count":3},{"id":"GO:0001516","count":3},{"id":"GO:0045454","count":2},{"id":"GO:0032355","count":2},{"id":"GO:0009734","count":2}]},{"hash":"1144084353759621630","title":"Unknown","description":"The listed GO terms cover very diverse processes (sucrose response, nitrogen signaling, circadian rhythm, pollen hydration, protein heterooligomerization, transcriptional regulation, and basic metabolism) with no clear, common function tying them together. There isn\u2019t a cohesive theme to give a specific, accurate label, so Unknown is appropriate here.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009744","count":1},{"id":"GO:0043562","count":1},{"id":"GO:0051291","count":1},{"id":"GO:0009859","count":1},{"id":"GO:0045859","count":1}]},{"hash":"700161554421576418","title":"Organelle Gene Expression (Mitochondria and Chloroplasts)","description":"The top GO terms center on transcription and RNA processing in mitochondrial and plastid genomes, plus plastid organization and ribosome assembly, indicating a cluster of proteins involved in organelle gene expression and ribosome biogenesis.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006390","count":1},{"id":"GO:0006393","count":1},{"id":"GO:0009658","count":1},{"id":"GO:1903108","count":1},{"id":"GO:0061668","count":1}]},{"hash":"118995743983795113","title":"Alkaloid catabolism and lipid metabolism","description":"The top GO terms show a clear enrichment for alkaloid catabolic processes (alkaloid, isoquinoline alkaloid, camphor catabolism) along with lipid-related metabolism (triglyceride metabolism, bile acid biosynthesis). This pattern points to a cluster involved in detoxification and transformation of small organic molecules, spanning alkaloids and lipids. Some ion-response and inflammatory terms appear but are less central to the main shared function. Therefore, the label Alkaloid catabolism and lipid metabolism best captures the cluster\u2019s primary theme.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009822","count":3},{"id":"GO:0006641","count":3},{"id":"GO:0071615","count":3},{"id":"GO:0034653","count":3},{"id":"GO:0033076","count":3}]},{"hash":"1621123700099639860","title":"Ribosome biogenesis and translation","description":"The dominant GO terms cluster around rRNA maturation and the process of translation, with supporting RNA processing activities such as intron splicing and RNA folding. This suggests the proteins participate in ribosome assembly and broader RNA metabolism tied to protein synthesis. A few peripheral terms (antibiotic response, sterol biosynthesis, histone methylation) may reflect multifunctionality or noise rather than a core function of the cluster.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006450","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0000372","count":1}]},{"hash":"481342944363668461","title":"Alkaloid and lipid metabolism","description":"The top GO terms show multiple alkaloid catabolic/metabolic processes (alkaloid, isoquinoline, camphor, retinoic acid) together with lipid-related metabolism (triglyceride metabolic process, bile acid biosynthetic process). This suggests the cluster centers on metabolism of diverse small organic molecules, particularly alkaloids and lipids, even though some entries (ion responses, inflammatory regulation) are less cohesive. So the label captures the core theme without overstating specificity.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009822","count":2},{"id":"GO:0006641","count":2},{"id":"GO:0071615","count":2},{"id":"GO:0034653","count":2},{"id":"GO:0033076","count":2}]},{"hash":"1960505906185033255","title":"Unknown","description":"The top GO terms include oogenesis and female meiotic nuclear division, which might hint at a reproductive process, but the terms are otherwise disparate (including an obsolete biosynthesis term and a general negative regulation of phosphatase activity) and there are no edges connecting the proteins. This lack of a coherent, testable shared function makes a specific, high-confidence label inappropriate.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033585","count":1},{"id":"GO:0010923","count":1},{"id":"GO:0007143","count":1},{"id":"GO:0048477","count":1}]},{"hash":"489481443980989964","title":"Innate immune signaling and cytokine production","description":"The top GO terms point to activation of innate immune pathways and cytokine production (TNF, IFN-beta, NF-kappaB, JNK) in response to pathogen-associated signals (LPS, dsRNA, Gram-positive bacteria) and interleukin-12, indicating a cohesive immune signaling cluster. A single term about mitotic centrosome separation seems unrelated noise rather than a core feature. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007100","count":3},{"id":"GO:0042535","count":2},{"id":"GO:0045359","count":2},{"id":"GO:0046330","count":2},{"id":"GO:0050830","count":2}]},{"hash":"70082217236983467","title":"O-fucose glycosylation and Notch signaling","description":"The top GO terms center on fucose metabolism and protein O-linked fucosylation, plus the Notch signaling pathway, which together suggest a core theme of fucose-dependent modulation of signaling (Notch). Developmental terms like EMT and mesoderm formation likely reflect Notch\u2019s broader regulatory roles, while some plant-related terms may represent contextual noise in this mixed cluster.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006004","count":1},{"id":"GO:0007219","count":1},{"id":"GO:0010717","count":1},{"id":"GO:0036066","count":1},{"id":"GO:0001707","count":1}]},{"hash":"1172199792394308881","title":"TLR-NF-kB Innate Immune Signaling","description":"This cluster centers on Toll-like receptor signaling (TLR4/TLR10), detection of lipopolysaccharide, NF-kB activation via I-kappaB phosphorylation, and downstream cytokine responses (TNF, interferons) as well as dendritic cell and Th1-type immune activation, indicating a cohesive innate immune sensing and inflammatory signaling function.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042535","count":2},{"id":"GO:0002730","count":2},{"id":"GO:0034142","count":2},{"id":"GO:0007252","count":2},{"id":"GO:0034166","count":2}]},{"hash":"1007239359701518371","title":"Plant Hormone Signaling and Defense","description":"The top GO terms show multiple hormone-related responses (gibberellin, cytokinin-activated signaling, ethylene precursor ACC, salicylic acid) together with defense functions (response to chitin, regulation of antifungal innate immune response). This pattern points to proteins involved in hormone signaling with cross-talk to plant immunity and growth regulation, including development-related differentiation (atrichoblast, sclerenchyma). Thus a label emphasizing hormone signaling linked to growth and defense is appropriate.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009739","count":2},{"id":"GO:0009751","count":2},{"id":"GO:0009736","count":2},{"id":"GO:0009961","count":1},{"id":"GO:1905034","count":1}]},{"hash":"734318821358270915","title":"Vacuolar acidification and metal ion transport","description":"GO terms converge on membrane-associated processes: vacuolar acidification, V-ATPase complex assembly, and transmembrane transport of Mg2+ and Co2+ (including mitochondrial Mg2+ transport). This points to a cluster centered on vacuolar proton pumping and metal ion transport across membranes.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006613","count":1},{"id":"GO:0070072","count":1},{"id":"GO:0007035","count":1},{"id":"GO:1903830","count":1},{"id":"GO:0006824","count":1}]},{"hash":"996020182820203286","title":"Cytoskeletal assembly and proteostasis","description":"The cluster is enriched for tubulin complex assembly and cortical microtubule organization, indicating a cytoskeletal focus. It also features chaperone-mediated protein complex assembly, protein folding, and ubiquitin-proteasome system\u2013related quality control, pointing to proteostasis. Additional terms touch transcription regulation and signaling, likely reflecting multi-functional components, but the strongest signal centers on cytoskeletal organization coupled with protein quality control.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007021","count":2},{"id":"GO:0009611","count":1},{"id":"GO:0010951","count":1},{"id":"GO:0032147","count":1},{"id":"GO:0006351","count":1}]},{"hash":"460935864540708217","title":"Ribosome Biogenesis and Developmental Differentiation","description":"This cluster's terms cluster around ribosome assembly and RNA processing (SSU-rRNA maturation, ribosome biogenesis, mRNA export) alongside developmental processes (flower development, multicellular organism development, cell differentiation), suggesting a theme where protein synthesis machinery supports development.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030490","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0009908","count":1},{"id":"GO:0030154","count":1},{"id":"GO:0007275","count":1}]},{"hash":"1749895144969299152","title":"Unknown","description":"The GO terms span both immune signaling (TLR pathways, NF-kB/I-kappaB phosphorylation, LPS detection, dendritic cell cytokine production) and neuronal development processes (nerve branching, axonal fasciculation, synapse assembly), with no obvious unifying function and no reported interactions in the cluster. This makes a coherent, specific label unlikely. ","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000172","count":1},{"id":"GO:0031146","count":1},{"id":"GO:0006409","count":1},{"id":"GO:0002730","count":1},{"id":"GO:0007413","count":1}]},{"hash":"724944536520165032","title":"Unknown","description":"This cluster lacks a coherent functional theme: GO terms include plant stress responses (cold acclimation, response to water deprivation, ABA) alongside diverse mammalian developmental processes (pancreatic cell development, cartilage morphogenesis, EMT, trophoblast differentiation, left-right patterning, endocrine system development), with no unifying pathway or function linking the proteins. Therefore, a meaningful label cannot be assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009631","count":1},{"id":"GO:0009414","count":1},{"id":"GO:0009737","count":1},{"id":"GO:0003323","count":1},{"id":"GO:0060536","count":1}]},{"hash":"1377877260501661121","title":"Spliceosome-Regulated mRNA Splicing and Export","description":"The top GO terms cluster around spliceosome-driven alternative splicing and related RNA processing steps (mRNA splicing, export, modification, and stabilization) as well as ncRNA-mediated gene silencing, indicating a cohesive focus on RNA maturation and post-transcriptional regulation. Some terms appear tangential (e.g., blastocyst formation, viral translation), but the predominant signal is spliceosome-associated mRNA processing and export.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000380","count":2},{"id":"GO:0016556","count":1},{"id":"GO:0006406","count":1},{"id":"GO:0031047","count":1},{"id":"GO:0048026","count":1}]},{"hash":"1494693103071606215","title":"Unknown","description":"The terms span stress response, signaling (Rho and calcium), immune/metabolic processes, development, and lipid transport, with no single dominant process linking all four proteins and no interactions among them. This heterogeneity makes it hard to assign a cohesive, representative label.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006950","count":1},{"id":"GO:0035023","count":1},{"id":"GO:1904468","count":1},{"id":"GO:0021997","count":1},{"id":"GO:0035773","count":1}]},{"hash":"972386154382168444","title":"Ubiquitin-Dependent Proteostasis and Chromatin Regulation","description":"The terms point to a shared focus on ubiquitin-mediated protein degradation (ERAD, K48-linked ubiquitination, autoubiquitination, proteolysis) and chromatin-related regulation (histone methylation marks and transcription regulation), suggesting a cluster centered on ubiquitin signaling coupled to chromatin/modulation of transcription. Some terms are obsolete, but the core theme remains proteostasis and chromatin regulation.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061087","count":2},{"id":"GO:0030433","count":2},{"id":"GO:2001040","count":1},{"id":"GO:0042787","count":1},{"id":"GO:0000122","count":1}]},{"hash":"1472184597284653083","title":"Neuronal methylation and catecholamine metabolism","description":"Based on the GO terms, the cluster mixes methylation-related processes (protein methylation, methylation) with catecholamine metabolism (catecholamine metabolic process, negative regulation of dopamine metabolism), and includes neural development and transcription activity terms (auditory receptor cell development, transcription by RNA polymerase II). This suggests a neural module where epigenetic regulation intersects with neurotransmitter handling, rather than a single, narrow pathway. Confidence: Medium","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":2},{"id":"GO:0050668","count":1},{"id":"GO:0060117","count":1},{"id":"GO:0042135","count":1},{"id":"GO:0006479","count":1}]},{"hash":"1902932027552913653","title":"mRNA Processing and Splicing Regulation","description":"This cluster is enriched for GO terms related to mRNA stability, modification, export, and both constitutive and alternative splicing via the spliceosome, indicating a cohesive function in RNA maturation and regulation.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":4},{"id":"GO:0016556","count":3},{"id":"GO:0006406","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0048026","count":3}]},{"hash":"1459357604554168411","title":"Translation and tRNA Modification","description":"The cluster shows strong terms centered on translation (GO:0006412) and regulation of translational fidelity (GO:0006450), with tRNA queuosine biosynthesis (GO:0008616) supporting a shared link to translation and tRNA modification. A few outlier terms (cell wall modification, pectin catabolic process, visual perception) and only one edge among four proteins suggest a noisy or weakly connected set, but the dominant translation-related signals justify a translation/tRNA-focused label.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006450","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006407","count":1},{"id":"GO:0009405","count":1},{"id":"GO:0042545","count":1}]},{"hash":"1205940013291687594","title":"Chromatin remodeling and cytokine-responsive transcription","description":"GO terms center on chromatin remodeling and DNA-templated transcription, plus cellular responses to interleukin-4, TGF-beta, and steroid hormones, with accompanying developmental processes such as myoblast development and organ morphogenesis, pointing to chromatin-mediated transcriptional regulation during signaling-driven development.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":2},{"id":"GO:0071353","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0021538","count":1},{"id":"GO:0048545","count":1}]},{"hash":"1215686959881436015","title":"Growth-factor signaling and cytoskeletal remodeling","description":"This cluster centers on signaling responses to growth factors (BDNF and prolactin) and kinase activity (autophosphorylation and its regulation), with elements of cytoskeletal remodeling such as myosin II filament disassembly and calcium-dependent cell-matrix adhesion. The presence of stress-related terms (anoxia, necroptosis) suggests these signaling events can intersect with cellular stress responses, forming a cohesive theme around growth-factor\u2013mediated signaling that influences cytoskeletal dynamics and survival decisions.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1990416","count":1},{"id":"GO:0046777","count":1},{"id":"GO:0031952","count":1},{"id":"GO:0071454","count":1},{"id":"GO:0070266","count":1}]},{"hash":"2203690622629745701","title":"Proteostasis and microtubule organization","description":"The cluster features strong signals for protein folding and quality control (protein folding; chaperone-mediated protein complex assembly; ubiquitin-proteasome system) and for cytoskeletal assembly/organization (tubulin complex assembly; cortical microtubule organization), suggesting a cohesive theme around maintaining protein homeostasis while organizing microtubules. Some GO terms (strigolactone response, prostaglandin catabolism) appear peripheral or noisy in this set.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":2},{"id":"GO:0007021","count":1},{"id":"GO:0071629","count":1},{"id":"GO:0051131","count":1},{"id":"GO:0006457","count":1}]},{"hash":"1967146973355557185","title":"Embryonic organ development and patterning","description":"Most of the GO terms point to embryonic development across several organs (eye, digestive tract, ureter, Harderian gland) and to proximal/distal patterning, with some signaling (cAMP) terms. A couple of terms relate to metabolism or incidental annotations, but the dominant theme is embryonic organ development and patterning.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006540","count":4},{"id":"GO:0019545","count":4},{"id":"GO:0035799","count":4},{"id":"GO:0048566","count":4},{"id":"GO:0006068","count":4}]},{"hash":"32817765923510842","title":"Unknown","description":"The top GO terms are extremely diverse, covering viral processes, multiple organ development, nuclear transport, cytoskeletal assembly, and chromosome cohesion. There is no single cohesive function or pathway tying these proteins together, so a unified label cannot be confidently assigned.","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":1,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0016032","count":4},{"id":"GO:0010909","count":4},{"id":"GO:0060492","count":4},{"id":"GO:1904948","count":4},{"id":"GO:0072053","count":4}]},{"hash":"1226511348364501268","title":"GTPase Regulation and Ubiquitination","description":"The top GO terms emphasize positive regulation of GTPase activity and autoubiquitination, along with ubiquitin-dependent ERAD, suggesting a core function in modulating signaling via GTPases and controlling protein turnover. This can impact cell migration and various developmental processes (lung induction, midbrain dopaminergic neuron differentiation, renal development). Some additional terms about cellular structures and cohesion may reflect broader regulatory roles, but the central theme centers on signaling regulation and ubiquitin-mediated processes.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0010909","count":2}]},{"hash":"1317320266987137317","title":"Mitotic spindle and microtubule dynamics","description":"Reasoning: The top GO terms are dominated by mitosis- and microtubule-related processes (centrosome separation, metaphase chromosome recapture, microtubule regulation, plus-end-directed vesicle transport along microtubules). Some neuronal/developmental terms are present but the cohesive theme centers on microtubule dynamics in cell division and transport. Therefore, this label best captures the cluster's core function.","confidence":"Medium","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1990535","count":4},{"id":"GO:0099607","count":4},{"id":"GO:0007100","count":4},{"id":"GO:1990942","count":4},{"id":"GO:0001560","count":4}]},{"hash":"1606612361171702306","title":"Cytoskeleton remodeling and cell migration","description":"The cluster centers on cytoskeletal dynamics and movement, highlighted by terms for actin/mimicking pseudopodium assembly, cytokinesis, centriole cohesion, and microtubule regulation, plus adherens junctions and cell migration, with Supporting hints from vesicle trafficking and extracellular matrix-related biosynthesis. This pattern points to coordinated cytoskeleton remodeling driving cell movement and division.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071255","count":1},{"id":"GO:0034333","count":1},{"id":"GO:0060769","count":1},{"id":"GO:0030997","count":1},{"id":"GO:0007026","count":1}]},{"hash":"1654884447271580641","title":"Cytoskeletal remodeling and cell growth","description":"These proteins show strong associations with cytoskeleton-mediated processes: mitotic actomyosin contractile ring assembly, phagocytosis, and skeletal muscle fiber adaptation, along with multidimensional cell growth. While other terms (gene expression regulation, aging, DNA unwinding) are broader, the shared theme appears to be cytoskeletal dynamics underpinning growth, movement, and division, making a cytoskeleton-centered label most representative.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000001","count":4},{"id":"GO:0010628","count":4},{"id":"GO:0001895","count":4},{"id":"GO:0001300","count":4},{"id":"GO:0009825","count":4}]},{"hash":"778778533513603260","title":"Proteostasis and Chromatin Regulation","description":"This cluster is enriched for ubiquitin-proteasome\u2013dependent protein degradation and chromatin organization, with links to serine dephosphorylation and DNA repair. Together, these terms point to regulation of protein stability coupled to chromatin dynamics and genome maintenance, rather than a single narrowly defined function.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070262","count":2},{"id":"GO:0031497","count":2},{"id":"GO:0000209","count":2},{"id":"GO:0071560","count":2},{"id":"GO:0031146","count":2}]},{"hash":"1156185211770631607","title":"Metabolic Stress and Amino Acid Catabolism","description":"The dominant GO terms point to metabolic adaptation under nutrient limitation: cellular response to glucose starvation, positive regulation of gluconeogenesis, GMP biosynthetic process, and several amino acid catabolic pathways (L-serine, L-homocysteine, L-cysteine). Glycine betaine transport supports osmotic/solute adjustment. While a cell-cycle term is present, the metabolic themes predominate, suggesting these proteins group around metabolism and nucleotide synthesis during stress.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042149","count":2},{"id":"GO:0006565","count":2},{"id":"GO:0019343","count":2},{"id":"GO:0030071","count":2},{"id":"GO:0043418","count":2}]},{"hash":"1244897735122636609","title":"Unknown","description":"The top GO terms are highly diverse, spanning DNA replication, mitotic processes, immune signaling, placental development, protein export, ER polarization, viral response, and organ regeneration. There is no clear, single functional theme linking these proteins, making a coherent label from GO terms unsupported.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0007100","count":3},{"id":"GO:0043277","count":2},{"id":"GO:0046641","count":2},{"id":"GO:0060709","count":2}]},{"hash":"1574213962270226450","title":"Immune Regulation and Development","description":"The cluster is enriched for immune-related terms such as positive regulation of T cell proliferation, positive regulation of tolerance induction to self antigen, apoptotic cell clearance, and cellular response to virus, suggesting roles in immune modulation. It also includes developmental/differentiation and organogenesis terms (placenta development, organ regeneration) and some general cellular processes (ER polarization, protein export from nucleus), indicating a broader theme that spans immune regulation and development rather than a single, cohesive pathway.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043277","count":1},{"id":"GO:0046641","count":1},{"id":"GO:0060709","count":1},{"id":"GO:0006611","count":1},{"id":"GO:0061167","count":1}]},{"hash":"1363746762810789151","title":"Membrane Transport of Ions and Small Molecules","description":"The top GO terms show a clear pattern of transmembrane transport across membranes for a variety of substrates (nitrate/nitrite, sodium, phosphate, xenobiotics, sugars like galactose and fucose) and related processes such as neurotransmitter loading into vesicles. This suggests the cluster is functionally cohesive around transporting diverse solutes across membranes, with some metabolism-related terms accompanying it. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":3},{"id":"GO:0006004","count":2},{"id":"GO:0098700","count":2},{"id":"GO:0015757","count":2},{"id":"GO:1900754","count":2}]},{"hash":"661877478691469082","title":"Bacterial vitamin and lipid metabolism","description":"The dominant GO terms involve retinol/retinal and phylloquinone (vitamin) metabolism, plus lipid-associated and LPS biosynthesis processes, which together point to a cluster of bacterial metabolic pathways focusing on vitamins and lipid/cell-envelope components.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0042572","count":3},{"id":"GO:0061370","count":3},{"id":"GO:0008209","count":3},{"id":"GO:0042574","count":3}]},{"hash":"1440909723386028534","title":"Aromatic compound and amino acid catabolism","description":"The GO terms cluster around catabolic processes for aromatic compounds and amino acids (e.g., phenylalanine, tyrosine, homogentisate, and 4-hydroxyphenylacetate), suggesting a shared function in degradation pathways. Several terms like DNA-templated transcription and viral process appear incidental and do not redefine the main theme.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019571","count":1},{"id":"GO:0006559","count":1},{"id":"GO:0006572","count":1},{"id":"GO:0019380","count":1},{"id":"GO:0006527","count":1}]},{"hash":"1666977999211011500","title":"Spliceosome-Driven RNA Splicing and Silencing","description":"The cluster is dominated by spliceosome-related terms (conformational changes, disassembly, and regulation of mRNA splicing) and RNA silencing pathways, suggesting a core function in RNA processing and post-transcriptional regulation. A few terms about transcription-coupled repair and replication appear ancillary rather than central.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000393","count":1},{"id":"GO:0000716","count":1},{"id":"GO:0071035","count":1},{"id":"GO:0019079","count":1},{"id":"GO:0006260","count":1}]},{"hash":"171264346725863324","title":"Bacterial membrane transporters","description":"The terms cluster around transmembrane transport of diverse substrates (molybdate, methionine, thiamine, teichoic acid, glycerophosphodiester, phospholipids) and bacteriocin export/immunity, with an additional SOS response term. This points to a cohesive theme of bacterial membrane transport processes and envelope-related defenses. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045796","count":1},{"id":"GO:0001407","count":1},{"id":"GO:0015689","count":1},{"id":"GO:0043213","count":1},{"id":"GO:0015777","count":1}]},{"hash":"1822058360742629135","title":"Flavonoid Glucoside Biosynthesis","description":"The top GO terms are dominated by flavonoid glucoside biosynthetic processes (kaempferol O-glucoside, quercetin O-glucoside, cyanidin 3-O-glucoside), indicating a clear theme of flavonoid glycoside production. Other listed terms refer to various aromatic or broad metabolic processes and appear as noise relative to the flavonoid signatures. This makes the label a concise and representative summary of the cluster\u2019s function.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006711","count":3},{"id":"GO:0030259","count":3},{"id":"GO:0052696","count":3},{"id":"GO:0070980","count":3},{"id":"GO:0033330","count":3}]},{"hash":"170087506034370555","title":"Ubiquitin-Proteasome Regulation of Innate Immunity","description":"The top GO terms point to ubiquitin-dependent protein catabolic processes and proteasomal degradation, indicating a core involvement of the ubiquitin-proteasome system. Additional terms related to TLR signaling, interferon production, and dendritic cell cytokine regulation suggest that these proteins connect targeted protein turnover with innate immune signaling pathways. Together, the cluster seems to represent components linking ubiquitination-driven proteolysis to regulation of innate immune responses.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":3},{"id":"GO:2000172","count":2},{"id":"GO:0000209","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0006409","count":2}]},{"hash":"2140499871361619193","title":"Calcium-Dependent Vesicle Trafficking","description":"This cluster centers on vesicle-related processes and calcium signaling, with terms like positive regulation of vesicle fusion, cellular response to calcium, and vesicle-mediated cholesterol transport. Lipid biosynthesis regulation and Rho signaling add context to membrane dynamics and signaling crosstalk, suggesting a cohesive theme around calcium-driven vesicle trafficking and associated signaling. Confidence: Medium","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":2},{"id":"GO:1904468","count":2},{"id":"GO:0021997","count":2},{"id":"GO:0035773","count":2},{"id":"GO:0001302","count":2}]},{"hash":"847636580387665150","title":"Plant metabolism and stomatal regulation","description":"This cluster combines plant-specific processes such as stomatal closure regulation, phylloquinone and phenylpropanoid biosynthesis, plus galactose metabolism and membrane-working processes (potassium transport, membrane potential). The presence of plant-centric GO terms strongly suggests a plant metabolism/physiology theme with stomatal control, despite the small, edge-less network. ","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006012","count":2},{"id":"GO:0090333","count":1},{"id":"GO:0010163","count":1},{"id":"GO:0051260","count":1}]},{"hash":"439740893114861404","title":"Abiotic stress signaling and lipid metabolism","description":"The top terms include several abiotic stress responses (water deprivation, flooding, sucrose) alongside lipid metabolism (lipid A and phospholipid biosynthesis) and phosphorylation/dephosphorylation, suggesting a theme of stress-responsive metabolic signaling, particularly involving lipid pathways. Given the limited number of proteins and overlapping yet not tightly coupled functions, the label is plausible but not definitive.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009245","count":1},{"id":"GO:2001289","count":1},{"id":"GO:0046085","count":1},{"id":"GO:0016310","count":1},{"id":"GO:0016311","count":1}]},{"hash":"449178488699444945","title":"Plant stress response and autophagy","description":"The terms cluster around plant-specific stress responses and defense signaling (aerenchyma formation, salicylic acid signaling, camalexin biosynthesis) together with autophagy-related processes (piecemeal microautophagy of the nucleus, vacuolar protein processing) and cell-wall remodeling (pectin catabolic process), suggesting a cohesive theme of plant stress adaptation linked to autophagy.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034727","count":2},{"id":"GO:0010618","count":2},{"id":"GO:0006624","count":2},{"id":"GO:0080151","count":2},{"id":"GO:2000124","count":2}]},{"hash":"895763570700834415","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0052889","count":2},{"id":"GO:0002097","count":1},{"id":"GO:0050665","count":1},{"id":"GO:0009083","count":1},{"id":"GO:0009435","count":1}]},{"hash":"929457478548915384","title":"Regulatory control of translation and cell cycle","description":"This cluster shows two strong terms for translation and regulation of the cell cycle, along with several regulatory processes (transcriptional repression, signaling regulation, and ubiquitination) and a negative control of growth, implying a broad regulatory module coordinating protein synthesis with cell growth and signaling.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071157","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0000209","count":1},{"id":"GO:0007257","count":1},{"id":"GO:0071360","count":1}]},{"hash":"1536313957438581373","title":"Acetylation-Linked Amine and Sugar Metabolism","description":"The terms cluster around acetylation events (N6- and N-terminal acetylation, propionylation) and metabolism of amines (polyamines like spermidine, putrescine, spermine) and amino sugars (glucosamine, N-acetylglucosamine), with supporting metabolism like mycothiol biosynthesis. This suggests a shared theme of acetylation/modification coupled to amine and sugar metabolism rather than a single, narrow pathway.","confidence":"Medium","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045150","count":4},{"id":"GO:0046208","count":4},{"id":"GO:0006041","count":4},{"id":"GO:0032918","count":4},{"id":"GO:0006044","count":4}]},{"hash":"440631719835099662","title":"Phytochrome-driven circadian signaling","description":"This cluster shows strong enrichment for far-red and red light signaling and phototransduction, plus positive regulation of circadian rhythm and transcriptional regulation, all pointing to light-perceived, circadian processes typical of phytochrome signaling in plants. Other terms about adenosine metabolism and generic cellular processes are incidental and do not define the core theme. ","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046085","count":1},{"id":"GO:0016310","count":1},{"id":"GO:0016311","count":1},{"id":"GO:0006195","count":1},{"id":"GO:0010018","count":1}]},{"hash":"789410487414321964","title":"Osmoprotectant stress response","description":"The cluster centers on cellular responses to desiccation and heat, with biosynthesis of osmoprotectants like glucosylglycerol and trehalose, suggesting a shared osmoprotectant-mediated stress response. Other annotations (dephosphorylation, ppGpp biosynthesis, amino acid and purine metabolism) appear less defining for the cluster\u2019s core function. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071465","count":1},{"id":"GO:0016311","count":1},{"id":"GO:0090441","count":1},{"id":"GO:0070415","count":1},{"id":"GO:0034605","count":1}]},{"hash":"894845315679212242","title":"tRNA aminoacylation and translation","description":"The top GO terms are dominated by lysyl-tRNA aminoacylation and mitochondrial tRNA charging, plus overall translation, suggesting the cluster centers on the protein synthesis machinery, particularly tRNA charging in mitochondria and cytosol. Other terms like DNA replication/repair and telomere maintenance may reflect ancillary or multi-functional roles, but the core theme is translation-related processes.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006430","count":1},{"id":"GO:0070145","count":1},{"id":"GO:0070154","count":1},{"id":"GO:0010833","count":1},{"id":"GO:0071915","count":1}]},{"hash":"650263626680943168","title":"Ribosome biogenesis and translation","description":"The proteins are annotated with translation-related processes and ribosomal RNA maturation, suggesting roles in assembling and regulating ribosomes and protein synthesis.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0000470","count":1},{"id":"GO:0006417","count":1},{"id":"GO:0000462","count":1}]},{"hash":"1641992548725166929","title":"Organic compound catabolism","description":"The cluster shows strong enrichment for multiple organic compound catabolic processes (camphor, carbazole, alkane, leucine) and related metabolic steps (2-oxoglutarate metabolism), suggesting a shared theme of breakdown of organic molecules. Some terms (detoxification, mitochondrial electron transport) may reflect broader metabolic context but do not negate the main catabolic focus.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019383","count":2},{"id":"GO:0046232","count":2},{"id":"GO:0006103","count":1},{"id":"GO:0006552","count":1},{"id":"GO:0006120","count":1}]},{"hash":"1553993352039831270","title":"Unknown","description":"The GO terms span ion transport, acidification, various metabolic processes, transcription regulation, differentiation, and even bacterial flagellum assembly, with no single unifying function. The mix suggests inconsistent or heterogeneous annotations rather than a coherent protein cluster function, so a concise, representative label cannot be assigned.","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006814","count":1},{"id":"GO:0006933","count":1},{"id":"GO:0007035","count":1},{"id":"GO:0044780","count":1},{"id":"GO:0006355","count":1}]},{"hash":"50819432559553310","title":"Unknown","description":"The terms show diverse prokaryotic metabolic and cellular processes (photosynthesis, chemiosmotic electron transport, methanogenesis, sulfate reduction), plus flagellum assembly and tRNA processing. There is no single, common function tying them together, so Unknown.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019483","count":1},{"id":"GO:0008033","count":1},{"id":"GO:0015942","count":1},{"id":"GO:0022900","count":1},{"id":"GO:0019684","count":1}]},{"hash":"1833661828722545020","title":"Unknown","description":"The GO terms indicate two disparate themes\u2014energy metabolism (photosynthesis, electron transport, proton transport) and DNA replication/repair/recombination\u2014without any edges tying the proteins together, so there isn\u2019t a single representative function for this cluster.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":1},{"id":"GO:0006122","count":1},{"id":"GO:0022904","count":1},{"id":"GO:1902600","count":1},{"id":"GO:0030420","count":1}]},{"hash":"258608382211819029","title":"Unknown","description":"The GO terms span two largely unrelated themes\u2014cilia/left-right symmetry processes and plant light-response/photosynthesis\u2014without a single cohesive function tying all three proteins together, making it inappropriate to assign a specific, representative label.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007368","count":1},{"id":"GO:0070286","count":1},{"id":"GO:0044458","count":1},{"id":"GO:0009768","count":1},{"id":"GO:1904964","count":1}]},{"hash":"2168885301337040205","title":"Chaperone-Mediated Folding and Stabilization","description":"Dominant GO terms point to chaperone activity and protein folding/stabilization (e.g., chaperone-mediated folding/refolding, protein stabilization, chaperone complex assembly) and related localization processes, including mitochondrial intermembrane space import. Immune signaling terms (IL-6 production, B cell cytokine production) are present but less central to the core theme. Overall, the cluster seems centered on proteostasis and chaperone-assisted maturation/localization functions.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2000778","count":3},{"id":"GO:0050821","count":3},{"id":"GO:0051973","count":3},{"id":"GO:0051086","count":3},{"id":"GO:0051085","count":3}]},{"hash":"136690481351322200","title":"Fatty acid metabolism and biosynthesis","description":"The top GO terms are dominated by fatty-acyl-CoA catabolic and biosynthetic processes (long-chain and medium-chain) and palmitic acid biosynthesis, pointing to a shared function in fatty acid metabolism that encompasses both synthesis and degradation, with a minor presence of unrelated processes that do not redefine the cluster.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036116","count":1},{"id":"GO:0035338","count":1},{"id":"GO:0045717","count":1},{"id":"GO:1900535","count":1},{"id":"GO:0010124","count":1}]},{"hash":"378632851319264187","title":"Embryonic Development and Signaling","description":"The top GO terms cluster around embryonic development events (fin morphogenesis, skeletal joint development, olfactory bulb development) and signaling pathways (BMP signaling, salicylic acid\u2013mediated signaling). Though some biosynthetic/process terms appear, the dominant theme is embryonic development coupled with signaling, suggesting this cluster represents early development and tissue patterning processes.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008101","count":2},{"id":"GO:0035118","count":2},{"id":"GO:0035884","count":2},{"id":"GO:0021772","count":2},{"id":"GO:0072498","count":2}]},{"hash":"1206946686294877701","title":"Prostaglandin and lipid metabolism cluster","description":"The top GO terms are dominated by prostaglandin biosynthesis and lipid metabolism (prostaglandin biosynthetic process, triglyceride metabolic process, bile acid biosynthesis), with supporting signals from related small-molecule metabolism terms. There are some outliers (alkaloid metabolism, ion response), but the strongest, recurring theme is lipid signaling and prostaglandin-related metabolism, justifying a lipid/prostaglandin-focused label.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":2},{"id":"GO:0009822","count":1},{"id":"GO:0006641","count":1},{"id":"GO:0071615","count":1},{"id":"GO:0034653","count":1}]},{"hash":"1037264442286034200","title":"Endosomal-Lysosomal Trafficking","description":"Based on the dominant GO terms endosome to lysosome transport and positive regulation of late endosome to lysosome transport, plus related vesicle trafficking terms (melanosome transport, apical protein localization), the cluster most strongly reflects endosomal-lysosomal transport processes. Some other terms may be incidental annotations. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008333","count":3},{"id":"GO:1902824","count":3},{"id":"GO:0045176","count":3},{"id":"GO:0010629","count":3},{"id":"GO:0030521","count":3}]},{"hash":"1995220368173286918","title":"Unknown","description":"The top GO terms are highly diverse, including hormonal response (estradiol), tissue-specific processes (lens fiber morphogenesis), aging, muscle contraction, and multiple negative regulatory and stress-response processes. This lack of a unifying function across the terms suggests no single coherent theme ties the proteins together, so a specific functional label cannot be confidently assigned.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032355","count":2},{"id":"GO:0050821","count":2},{"id":"GO:0070309","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0030308","count":2}]},{"hash":"25011536503047394","title":"Ribosome assembly and amino acid starvation response","description":"The strongest signals are ribosomal small subunit assembly and cellular response to amino acid starvation, indicating a theme around ribosome biogenesis and nutrient-stress regulation. Additional terms related to plant shoot development and other processes may reflect broader functional contexts or annotation noise, but the core cluster appears tied to translation machinery and stress response.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000028","count":2},{"id":"GO:0034198","count":2},{"id":"GO:0090506","count":2},{"id":"GO:2000032","count":2},{"id":"GO:0006407","count":2}]},{"hash":"1696078667313412385","title":"Malate/Pyruvate Metabolism and TCA Cycle","description":"These proteins are enriched for malate and pyruvate metabolic processes and the tricarboxylic acid cycle, pointing to a core central carbon metabolism theme. Additional terms like NADP metabolism regulation and protein tetramerization hint at redox regulation and oligomeric enzyme assembly within metabolic pathways, while responses to hypoxia or starvation reflect metabolic adaptation under stress. Overall, the cluster centers on central energy metabolism involving malate and the TCA cycle.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006108","count":3},{"id":"GO:0043464","count":2},{"id":"GO:0006090","count":2},{"id":"GO:0051262","count":2},{"id":"GO:1902031","count":2}]},{"hash":"1053636838851830545","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":3},{"id":"GO:0090617","count":3},{"id":"GO:0042793","count":3},{"id":"GO:1905639","count":3},{"id":"GO:1900865","count":3}]},{"hash":"2151624016618209544","title":"Neuronal protein modification and autophagy","description":"The terms point to post-translational modification (sumoylation, ubiquitination), autophagy-related processes (mitophagy, aggrephagy) and apoptosis regulation, plus neuronal development context (GnRH neuron development) and neurotransmitter secretion control. This suggests a cluster centered on neuronal protein homeostasis and stress response, integrating modification-based regulation with autophagic clearance.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":3},{"id":"GO:1902236","count":2},{"id":"GO:0021888","count":2},{"id":"GO:1904049","count":2},{"id":"GO:0008625","count":2}]},{"hash":"1876140434087741665","title":"Mitochondrial respiration and iron homeostasis","description":"The GO terms cluster around mitochondrial function and iron handling, with key signals for the respiratory chain (succinate to ubiquinone and succinate dehydrogenase activity) and iron-related processes (intracellular iron ion homeostasis, response to iron(II) ion, Fe-S cluster coordination). The presence of cytochrome c release regulation also ties to mitochondrial metabolism and apoptosis control. Some terms appear peripheral or obsolete, but the dominant theme is mitochondria-linked energy production and iron-sulfur biology, suggesting this label captures the core function of the cluster.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006121","count":1},{"id":"GO:1904234","count":1},{"id":"GO:0019230","count":1},{"id":"GO:0042542","count":1},{"id":"GO:0006879","count":1}]},{"hash":"169780001402046123","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":2},{"id":"GO:0019354","count":1},{"id":"GO:0000453","count":1},{"id":"GO:0050843","count":1},{"id":"GO:0055114","count":1}]},{"hash":"66297502241086004","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006616","count":1},{"id":"GO:0044781","count":1},{"id":"GO:0006614","count":1},{"id":"GO:0036498","count":1},{"id":"GO:0051301","count":1}]},{"hash":"2156030916462387200","title":"Unknown","description":"The terms cover immune-related neutrophil homeostasis, multiple folate and nucleotide biosynthesis processes, ribosome biogenesis, development, signal transduction, and even bacterial peptidoglycan synthesis. There is no single coherent biological theme tying these GO terms together, so a concise, specific label cannot be assigned beyond Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001780","count":1},{"id":"GO:0009113","count":1},{"id":"GO:0048702","count":1},{"id":"GO:0035999","count":1},{"id":"GO:0009257","count":1}]},{"hash":"139467853381389125","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002938","count":1},{"id":"GO:0000453","count":1},{"id":"GO:0006014","count":1},{"id":"GO:0006098","count":1},{"id":"GO:0009052","count":1}]},{"hash":"1368696438605756093","title":"Ribosome Assembly and Translation","description":"The top GO terms cluster around ribosome biogenesis, ribosomal subunit assembly, and translation, indicating a shared role in ribosome production and protein synthesis. Despite no edges among the three proteins in this cluster, their functional annotations converge on ribosome-related processes, suggesting they participate in ribosome assembly or function.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000028","count":1},{"id":"GO:0006407","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0042254","count":1}]},{"hash":"509782301335527871","title":"Terpenoid/isoprenoid biosynthesis","description":"The proteins are annotated with several terpenoid/isoprenoid biosynthetic processes (farnesyl diphosphate, geranyl/geranylgeranyl diphosphate, monoterpene, cholesterol/quinone biosynthesis), suggesting involvement in the mevalonate pathway and downstream terpenoid assembly. Other terms (protein transport, RNA decay) are ancillary and do not define the core function. ","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045337","count":1},{"id":"GO:0006695","count":1},{"id":"GO:1901663","count":1},{"id":"GO:0033384","count":1},{"id":"GO:0043693","count":1}]},{"hash":"1540628539576581551","title":"Cofactor and Metabolite Biosynthesis","description":"These proteins appear tied to multiple biosynthetic pathways, including porphyrin/heme precursor (protoporphyrinogen IX) biosynthesis, biotin biosynthesis, beta-alanine biosynthesis, antibiotic biosynthesis, and several amino acid-related biosynthetic/catabolic processes. The common thread is production of small molecules and cofactors rather than a single specific function, supporting a biosynthesis-focused cluster.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006782","count":2},{"id":"GO:0009102","count":2},{"id":"GO:0019878","count":2},{"id":"GO:0010121","count":1},{"id":"GO:0006593","count":1}]},{"hash":"358709135795392370","title":"ER Folding and MHC I Antigen Presentation","description":"The cluster centers on ER-associated processes: endoplasmic reticulum unfolded protein response and protein folding, plus peptide antigen assembly with MHC class I, which together indicate ER-mediated peptide processing and loading for antigen presentation. Immune-related terms (innate immune signaling, dendritic cell chemotaxis) reinforce an immune-cell context, but the core theme is ER quality control tied to MHC I antigen presentation.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"protein folding","top_go_terms":[{"id":"GO:0030968","count":3},{"id":"GO:1900026","count":3},{"id":"GO:0048488","count":3},{"id":"GO:0048387","count":3},{"id":"GO:0002502","count":3}]},{"hash":"118868742979655148","title":"Nuclear RNA Splicing and DNA Repair","description":"The top GO terms cluster around spliceosome-driven splicing and its regulation (GO:0000393, GO:0048026, GO:0016441, GO:0031047), plus transcription-coupled nucleotide-excision repair (GO:0000716, GO:0006283), along with snoRNA release from pre-rRNA and nuclear RNA degradation. This points to a cohesive theme of nuclear RNA processing and quality control, with an accompanying role in DNA repair pathways that are coupled to transcription. Some other terms (viral genome replication, DNA replication) are less central to this core function, but do not dominate the set.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000393","count":3},{"id":"GO:0000716","count":3},{"id":"GO:1990417","count":3},{"id":"GO:0071035","count":3},{"id":"GO:0019079","count":3}]},{"hash":"1842866405246357069","title":"RNA Splicing and Post-Transcriptional Regulation","description":"These proteins cluster around RNA processing and regulation after transcription: spliceosomal splicing and its regulation, mRNA export from the nucleus, mRNA stabilization, and ncRNA/miRNA-mediated silencing. The consolidated GO terms point to a cohesive function in RNA maturation and post-transcriptional control, despite a few outliers. ","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016556","count":1},{"id":"GO:0006406","count":1},{"id":"GO:0031047","count":1},{"id":"GO:0048026","count":1},{"id":"GO:0000381","count":1}]},{"hash":"701909155297579734","title":"Translational Regulation","description":"The top GO terms show translation and positive regulation of translation, indicating proteins linked to protein synthesis and its upregulation; the cluster centers on translation-related functions.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0045727","count":1}]},{"hash":"674007673605649203","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000393","count":1},{"id":"GO:0071035","count":1},{"id":"GO:0000724","count":1},{"id":"GO:0061820","count":1},{"id":"GO:0000467","count":1}]},{"hash":"2067243197807787162","title":"Cytoskeleton-driven cell division and remodeling","description":"The terms point to cytoskeletal processes: mitotic actomyosin contractile ring assembly, phagocytosis, and skeletal muscle fiber adaptation all rely on cytoskeletal remodeling; mitochondrion inheritance reflects organelle distribution linked to cell division, suggesting a unifying theme of cytoskeleton-mediated division and remodeling, even though some terms are unrelated or obsolete.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000001","count":3},{"id":"GO:0010628","count":3},{"id":"GO:0001895","count":3},{"id":"GO:0001300","count":3},{"id":"GO:0009825","count":3}]},{"hash":"1044966574286187683","title":"Unknown","description":"There are no edges, no triangles, and no GO terms or term frequencies to identify a common function, so a meaningful label cannot be inferred from the cluster's data.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2254809920049164962","title":"Plant meiosis and gametophyte development","description":"The terms cluster around meiosis: double-strand break repair and reciprocal meiotic recombination, together with developmental processes for both male (pollen) and female (embryo sac) gametophytes in plants. This suggests a cohesive theme of meiotic DNA repair linked to plant gametophyte development, justifying the label.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006302","count":1},{"id":"GO:0009553","count":1},{"id":"GO:0009555","count":1},{"id":"GO:0007131","count":1}]},{"hash":"931126585845843200","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":1},{"id":"GO:0019068","count":1},{"id":"GO:0039651","count":1},{"id":"GO:0039702","count":1},{"id":"GO:0071031","count":1}]},{"hash":"2244118855611033583","title":"Fungal osmotic stress response and glucan biosynthesis","description":"The terms point to osmotic/osmolyte-related responses (water deprivation, flooding, sucrose, mannitol) and fungal cell-wall polysaccharide biosynthesis (alpha-glucans), with accompanying lipid biosynthesis. This suggests proteins involved in adjusting the fungal cell envelope and membrane components under osmotic stress, rather than a single isolated pathway. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009414","count":1},{"id":"GO:0008654","count":1},{"id":"GO:0009413","count":1},{"id":"GO:0070600","count":1},{"id":"GO:0070630","count":1}]},{"hash":"285024077622152744","title":"Unknown","description":"The two top GO terms indicate unrelated processes (activation of protein kinase activity and ribosome biogenesis). With only three proteins and no coherent shared function, there isn't a clear theme tying these proteins together, so a specific, representative label cannot be confidently assigned.","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032147","count":1},{"id":"GO:0042254","count":1}]},{"hash":"2115010274479787683","title":"Broad Developmental Processes","description":"These proteins span a range of developmental and differentiation processes across multiple tissues (epithalamus, pancreas, ureter, muscle) and include differentiation signals (TGF-beta, steroid hormone responses). Because no single function dominates, a broad label like \"Broad Developmental Processes\" best summarizes the cluster.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021538","count":1},{"id":"GO:0048545","count":1},{"id":"GO:0045662","count":1},{"id":"GO:0071560","count":1},{"id":"GO:0010909","count":1}]},{"hash":"912207888967187745","title":"Epidermal keratinization and skin development","description":"The cluster shows clear emphasis on epidermal biology: keratinization, skin development, and regulation of epidermal cell division, with supporting hints from Golgi localization and nuclear export processes that can relate to epithelial protein processing. This pattern suggests a functional theme around epidermal differentiation and keratinocyte maturation rather than general metabolic or signaling roles.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051291","count":1},{"id":"GO:0030307","count":1},{"id":"GO:0032869","count":1},{"id":"GO:0043154","count":1},{"id":"GO:0031424","count":1}]},{"hash":"2001692505359104467","title":"Unknown","description":"The GO terms are diverse, including serine dephosphorylation, proteoglycan biosynthesis regulation, several organ development terms (lung, renal inner medulla, midbrain dopaminergic neuron differentiation), protein catabolic regulation, apoptosis signaling, centromeric cohesion, nucleus-vacuole junction assembly, and an obsolete Wnt-EMT term. There is no single cohesive function or pathway linking these terms, so a specific, representative label cannot be inferred.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070262","count":2},{"id":"GO:0010909","count":2},{"id":"GO:0060492","count":2},{"id":"GO:1904948","count":2},{"id":"GO:0042176","count":2}]},{"hash":"125059364200716978","title":"Ubiquitin-dependent proteostasis and chaperone signaling","description":"The top GO terms converge on ubiquitination processes (K63-linked ubiquitination, autoubiquitination) and ERAD-related pathways, along with positive regulation of chaperone-mediated protein complex assembly, indicating a focus on proteome quality control and proteostasis under stress. The presence of stress-related terms (ethanol, chitin, ABA) further supports a proteostasis-centered function rather than a single metabolic pathway. ","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090359","count":2},{"id":"GO:0071361","count":2},{"id":"GO:0010200","count":2},{"id":"GO:0008626","count":2},{"id":"GO:0030579","count":2}]},{"hash":"852036827474960082","title":"Angiogenesis and Proliferation Regulation","description":"This cluster\u2019s strongest signal is terms related to angiogenesis and its regulation, plus regulation of cell population proliferation, suggesting a shared role in vascular growth and proliferation control. Other terms (digestion, melanocyte migration, transcription regulation) are more diverse and less cohesive with the vascular theme, so the overall connection is moderate. Confidence: Medium","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045766","count":2},{"id":"GO:0014068","count":2},{"id":"GO:0042127","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0045944","count":2}]},{"hash":"1621418471791631882","title":"Microtubule dynamics and mitotic spindle functions","description":"The top GO terms cluster around microtubule regulation, plus-end transport along microtubules, centrosome separation, spindle\u2013microtubule attachments, and chromosome movements during mitosis. While a neuron-related term appears, the strongest recurring theme is microtubule-based processes in cell division and intracellular transport, so this name captures the cluster\u2019s core function.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1990535","count":3},{"id":"GO:0099607","count":3},{"id":"GO:0007100","count":3},{"id":"GO:1990942","count":3},{"id":"GO:0001560","count":3}]},{"hash":"2047724391306937247","title":"Unknown","description":"The GO terms span many unrelated biological processes (pigment granule maturation, methionine cycle, mRNA export, ATP biosynthesis regulation, viral processes, TGF-beta response, molybdate transport, transcription initiation, centriole elongation, and MAVS-related viral interactions), with no clear, single function tying the proteins together.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048757","count":1},{"id":"GO:0033353","count":1},{"id":"GO:0006406","count":1},{"id":"GO:2001171","count":1},{"id":"GO:0016032","count":1}]},{"hash":"1378992476716412465","title":"Camalexin biosynthesis and plant defense signaling","description":"This cluster\u2019s top GO terms center on plant defense and secondary metabolism: camalexin biosynthesis, defense response to bacterium, jasmonic acid metabolism, and plant-type hypersensitive response regulation, plus responses to UV-B. These together point to a theme of defense signaling and phytoalexin production in plants. Some metabolic terms (e.g., galactonate, benzoate) are more general, but the defense- and camalexin-related terms suggest a cohesive, defense-focused group, albeit with modest evidence since there are no interactions among proteins.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034194","count":1},{"id":"GO:0010120","count":1},{"id":"GO:0009816","count":1},{"id":"GO:2000030","count":1},{"id":"GO:0010046","count":1}]},{"hash":"488480921827067051","title":"Muscle calcium and metal ion transport","description":"The GO terms are dominated by ion transport and homeostasis, especially calcium ion transport and calcium signaling, with additional copper, manganese, and polyamine transport and maintenance of electrochemical gradients. Terms like relaxation of skeletal muscle and negative regulation of heart contraction point to muscle/heart calcium dynamics, suggesting these proteins participate in ion transport and calcium homeostasis in muscle cells. The label captures the main theme without overcommitting to a single pathway. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006825","count":2},{"id":"GO:1901205","count":2},{"id":"GO:0090076","count":2},{"id":"GO:0030026","count":2},{"id":"GO:0010248","count":2}]},{"hash":"1141335610977341132","title":"Protein Complex Assembly and Nuclear Transport","description":"Top GO terms emphasize protein self-assembly and interactions (homooligomerization, heterotrimerization, heterotetramerization) and nuclear-related processes (tRNA export, regulation of protein import into nucleus). This pattern points to clusters involving assembly of protein complexes and trafficking into/within the nucleus, which best fits the predominant signals despite some peripheral terms like retina development or virus transport.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0070208","count":2},{"id":"GO:0060041","count":2},{"id":"GO:0075733","count":1},{"id":"GO:0042306","count":1}]},{"hash":"2244939790964119711","title":"Unknown","description":"No GO terms or interaction structure are provided; with only isolated proteins and no connections, there\u2019s no clear shared function to name, so the cluster is Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"145818600958777159","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":1},{"id":"GO:0090617","count":1},{"id":"GO:1905639","count":1},{"id":"GO:1900865","count":1},{"id":"GO:0042793","count":1}]},{"hash":"540120291313120776","title":"Bacterial cytokinesis and septum formation","description":"The GO terms are dominated by cell division, division septum assembly, cell septum assembly, and FtsZ-dependent cytokinesis, which strongly indicate bacterial cytokinesis machinery; other terms like cytoplasmic microtubule organization and neuron migration appear incidental or reflect multifunctional annotations, but the core signal is bacterial cell division processes.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0000917","count":2},{"id":"GO:0071353","count":2},{"id":"GO:0090529","count":2},{"id":"GO:0031122","count":2}]},{"hash":"2271820335379319657","title":"Proteostasis and Cytoskeleton Regulation","description":"This cluster centers on ubiquitin-mediated proteolysis (polyubiquitination and SCF-dependent proteasomal degradation) and cytoskeletal dynamics (microtubule polymerization and Rho signaling), suggesting a theme of protein turnover linked to cytoskeletal regulation, with supporting signals from related developmental and signaling processes.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2000323","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0000209","count":2},{"id":"GO:0046785","count":2},{"id":"GO:1904948","count":2}]},{"hash":"1885350094106014234","title":"Ubiquitin-like protein modification and autophagy","description":"Top GO terms indicate multiple ubiquitin-like modifications (sumoylation, urmylation, neddylation) and autophagy processes (macroautophagy, piecemeal microautophagy of the nucleus), suggesting a cluster centered on post-translational modification by ubiquitin-like proteins and related autophagy regulation. While some other terms are present, they are less cohesive with the main theme. Confidence: High","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":3},{"id":"GO:0034727","count":2},{"id":"GO:0032447","count":2},{"id":"GO:0050832","count":2},{"id":"GO:0009228","count":2}]},{"hash":"718388866099610092","title":"Fructose and Glucose Metabolism","description":"These proteins share GO terms centered on fructose and glucose metabolism (fructose metabolic process, fructose 2,6-bisphosphate metabolic process, gluconeogenesis, and related phosphorylation steps) and on regulatory aspects of glycolytic flux (dephosphorylation, negative regulation of glucose catabolic to lactate via pyruvate). While one term mentions brain development and a couple relate to metal response, the dominant signal is carbohydrate metabolism and its regulation, suggesting a role in controlling glucose/fructose utilization rather than developmental signaling.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":1},{"id":"GO:0016311","count":1},{"id":"GO:0046835","count":1},{"id":"GO:0006094","count":1},{"id":"GO:0071279","count":1}]},{"hash":"422364495212902308","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0006168","count":1},{"id":"GO:0032264","count":1},{"id":"GO:0006178","count":1}]},{"hash":"1481748441652996003","title":"Calcium and metal ion transport in muscle","description":"This cluster shows strong signals for calcium ion transport and homeostasis (calcium transmembrane transport; Golgi calcium ion homeostasis) plus other metal ion transport (copper, manganese) and related electrochemical gradient maintenance. The presence of muscle/heart-related terms (skeletal muscle relaxation, negative regulation of heart contraction) suggests a broader theme of ion transport influencing muscle physiology. Overall, calcium-centric ion transport appears to be the core thread linking these terms, with auxiliary metal ion transport supportive of the theme.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006825","count":1},{"id":"GO:1901205","count":1},{"id":"GO:0090076","count":1},{"id":"GO:0016311","count":1},{"id":"GO:0030026","count":1}]},{"hash":"1593271217560530865","title":"Unknown","description":"The top GO terms span extracellular carbohydrate transport, lipopolysaccharide and polysaccharide biosynthesis, chromosome segregation/plasmid partitioning, and various peptide methylation processes, with several terms marked obsolete. This mix shows no clear, shared function or pathway tying the proteins together, so a coherent label cannot be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006859","count":1},{"id":"GO:0009103","count":1},{"id":"GO:0045226","count":1},{"id":"GO:0007059","count":1},{"id":"GO:0030541","count":1}]},{"hash":"1281269857942322554","title":"Unknown","description":"The GO terms are too diverse to imply a single cohesive function for these three proteins; they touch on signaling regulation (calcineurin-NFAT, TNF), development (placenta), cell cycle (centrosome duplication, spindle-related), nuclear transport, and axon regeneration. This scattered set makes a unified label unlikely, so Unknown.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051534","count":3},{"id":"GO:0045071","count":3},{"id":"GO:0001893","count":3},{"id":"GO:0051298","count":3},{"id":"GO:0042535","count":3}]},{"hash":"1500656821272526460","title":"Amino acid biosynthesis and metabolism","description":"This cluster's terms predominantly point to amino acid biosynthesis/metabolism (methionine, threonine, lysine) and related nutrient processing, with gluconeogenesis and excretion as broader context. A few annotations (e.g., serotonin biosynthesis, obsolete terms) appear noisy, but the core signal is amino acid metabolism.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033353","count":1},{"id":"GO:0042427","count":1},{"id":"GO:0006094","count":1},{"id":"GO:0019877","count":1},{"id":"GO:0009089","count":1}]},{"hash":"2003871059009495465","title":"RNA Pol II Transcription Regulation","description":"Two top terms indicate transcription control by RNA polymerase II and DNA-templated transcription, which is the main shared function among the proteins. The other GO terms point to stress and signaling responses (unfolded protein response, nitrosative stress\u2013induced apoptosis, glucose starvation) and calcium signaling, which may reflect context-specific regulation rather than core function. Thus the cluster is best described by transcription regulation type, with secondary stress-response attributes.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045944","count":2},{"id":"GO:0006351","count":2},{"id":"GO:1990442","count":1},{"id":"GO:0042149","count":1},{"id":"GO:0045872","count":1}]},{"hash":"1541281176104533952","title":"RNA processing and splicing regulation","description":"The cluster is dominated by GO terms related to nuclear mRNA maturation and spliceosome-associated regulation, including polyadenylation, mRNA modification, export, and regulation of (alternative) splicing. These indicate a cohesive functional module around RNA processing and spliceosome control, with transcription and ncRNA silencing as related regulatory contexts; a couple of developmental terms appear incidental rather than defining the core function. ","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":2},{"id":"GO:0016556","count":1},{"id":"GO:0006406","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0031047","count":1}]},{"hash":"1229817255403309625","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0061158","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0031564","count":1},{"id":"GO:0045947","count":1}]},{"hash":"2042461975659535794","title":"DNA Repair and Replication","description":"Based on the top GO terms, the cluster is dominated by DNA damage response and repair mechanisms (UV-C response, translesion synthesis, NER) and DNA replication, suggesting a genome maintenance theme. Some terms are development or transcription-related, which may reflect pleiotropy or annotation noise in a small cluster with no interactions. Therefore, the label is provisional but representative of the core function.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071494","count":1},{"id":"GO:0070987","count":1},{"id":"GO:0042276","count":1},{"id":"GO:0006297","count":1},{"id":"GO:0006261","count":1}]},{"hash":"1809993513724218622","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0016032","count":2},{"id":"GO:1903762","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0006296","count":2}]},{"hash":"243087277931846264","title":"Amino acid catabolism fueling central carbon metabolism","description":"This small cluster centers on core energy metabolism: leucine and other amino acid catabolism feeding into central carbon pathways such as the TCA cycle, 2-oxoglutarate metabolism, glycolysis, and gluconeogenesis. The GO terms collectively point to management of carbon flux and energy production, with malonyl-CoA biosynthesis linking to broader metabolic context. Despite the single reported edge, the dominant theme is cohesive central carbon metabolism driven by amino acid catabolism.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":2},{"id":"GO:0019629","count":2},{"id":"GO:0006103","count":1},{"id":"GO:0006814","count":1},{"id":"GO:0006552","count":1}]},{"hash":"981591603788377674","title":"Ubiquitin-Proteasome and TNF-NF-\u03baB Signaling","description":"The top terms point to ubiquitin-dependent protein degradation (SCF- and ERAD pathways, K48-linked ubiquitination), which ties to the proteasome system, along with TNF signaling and NF-\u03baB\u2013inducing kinase activity, and related regulation of transcription and apoptosis. This suggests a cohesive cluster centered on ubiquitin-mediated turnover and inflammatory signaling that can influence gene expression and cell fate decisions.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0007250","count":2},{"id":"GO:1901253","count":2}]},{"hash":"376123955092526248","title":"Plant secondary metabolite biosynthesis","description":"The GO terms cluster around plant-specific biosynthetic pathways: anthocyanin pigment biosynthesis, lignin production, and sterol biosynthesis, with related oxidation-reduction context. This points to plant secondary metabolism rather than general metabolic processes. ","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0016126","count":2},{"id":"GO:0009718","count":2},{"id":"GO:0042573","count":1},{"id":"GO:0045777","count":1}]},{"hash":"2049997365519182837","title":"Unknown","description":"The listed GO terms are highly heterogeneous (immune activation and costimulation, host-symbiont entry, metabolism, behavior, proteolysis, and tissue remodeling) with no clear shared function tying the proteins together, so a coherent cluster label cannot be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042110","count":1},{"id":"GO:0046718","count":1},{"id":"GO:0031295","count":1},{"id":"GO:0015996","count":1},{"id":"GO:0036343","count":1}]},{"hash":"1744297011782126397","title":"Fatty acid oxidation and amino acid catabolism","description":"The cluster\u2019s terms converge on lipid and amino acid breakdown, including fatty acid beta-oxidation (and medium-chain fatty acids) and L-leucine catabolism, with a link to carnitine biosynthesis and regulation of gluconeogenesis, indicating an energy-metabolism theme. Some terms relate to development or steroid biosynthesis, which are less central, suggesting the core function is metabolic catabolism rather than a single developmental process.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045329","count":1},{"id":"GO:0006111","count":1},{"id":"GO:0006552","count":1},{"id":"GO:0009791","count":1},{"id":"GO:0033539","count":1}]},{"hash":"1816792525648683027","title":"Methylation and Biosynthesis Pathways","description":"These proteins show a mix of methylation-related activities (RNA and histone methylation, mRNA capping, arginine hydroxylation) and several biosynthetic processes (sterol, ubiquinone, and biotin biosynthesis), suggesting a common theme around enzymatic modifications and metabolic biosynthesis.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030961","count":1},{"id":"GO:0016126","count":1},{"id":"GO:0043985","count":1},{"id":"GO:0001300","count":1},{"id":"GO:0006744","count":1}]},{"hash":"842727145432153546","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":1},{"id":"GO:0090617","count":1},{"id":"GO:0042793","count":1},{"id":"GO:1905639","count":1},{"id":"GO:1900865","count":1}]},{"hash":"164843501884717216","title":"Fungal Cell Wall Remodeling via Vesicle Trafficking","description":"The terms include fungal-type cell wall organization and beta-D-glucan catabolic process, indicating a fungal cell wall remodeling theme. They also point to secretion and vesicle trafficking processes (calcium-dependent exocytosis, SNARE regulation, endosome-to-lysosome transport, synaptic vesicle maturation, contractile vacuole discharge), suggesting that vesicle-mediated secretion drives wall remodeling and related transport in fungi.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006076","count":1},{"id":"GO:0031505","count":1},{"id":"GO:0045956","count":1},{"id":"GO:0051291","count":1},{"id":"GO:0008333","count":1}]},{"hash":"543137248130651954","title":"RNA Pol II Transcription Regulation","description":"The terms cluster around regulation of RNA Polymerase II transcription, including termination and elongation control (including exosome-dependent termination) and pathways linked to calcium/NFAT signaling that drive transcription. Some items are obsolete, but the dominant theme is transcriptional regulation by RNA Pol II, with a possible connection to calcium-triggered transcription via NFAT.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051533","count":1},{"id":"GO:0006379","count":1},{"id":"GO:0010526","count":1},{"id":"GO:0070940","count":1},{"id":"GO:0006369","count":1}]},{"hash":"745848875799959237","title":"Unknown","description":"There are only 3 proteins with no edges and no shared GO terms to anchor a common function, and although five more proteins were re-added by ReCIPE, there is no connectivity or enrichment to define a single representative function for this cluster.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]}]