[{"hash":"2261090635598896417","title":"Mitochondrial translation and energy metabolism","description":"The cluster\u2019s top GO terms cluster around mitochondrial protein synthesis (translation and ribosomal subunit assembly), mitochondrial ATP synthase complex assembly, lipoylation, thiamine biosynthesis, and central metabolism (TCA cycle), suggesting a coherent theme of mitochondrial translation machinery coupled to energy production and cofactor biosynthesis.","confidence":"High","size":29,"edges":405,"triangles":3627,"max_degree":28,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0030488","count":3},{"id":"GO:0006099","count":2},{"id":"GO:0000027","count":2}]},{"hash":"1465424681634166187","title":"Excitatory synapse assembly and AMPA receptor regulation","description":"The cluster is dominated by GO terms tied to excitatory synapses: synapse assembly, AMPA receptor activity regulation, synaptic vesicle clustering, presynaptic terminal organization, and regulation of postsynaptic potentials, indicating a cohesive role in building excitatory synapses and modulating glutamatergic signaling. While a few terms like response to xenobiotic stimulus and gibberellin-mediated signaling appear, they seem ancillary to the main synaptic theme.","confidence":"High","size":29,"edges":405,"triangles":3627,"max_degree":28,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":15},{"id":"GO:2000969","count":14},{"id":"GO:0048789","count":14},{"id":"GO:1904861","count":14},{"id":"GO:2000809","count":14}]},{"hash":"112229780483978378","title":"Ribosome Biogenesis and rRNA Maturation","description":"Dominant GO terms describe maturation and processing of rRNA (SSU/LSU and 5.8S) and large subunit biogenesis, pointing to a core function in ribosome assembly and rRNA maturation. Some secondary terms (mRNA splicing, protein complex assembly, ER\u2013Golgi transport) appear but do not override the ribosome-focused signal.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000466","count":5},{"id":"GO:0000398","count":5},{"id":"GO:0000462","count":5},{"id":"GO:0042273","count":5},{"id":"GO:0000463","count":5}]},{"hash":"2209554515624436237","title":"Mitochondrial metabolite transport and cofactor movement","description":"The cluster is dominated by GO terms for transmembrane transport of various metabolites and cofactors (thiosulfate, thiamine pyrophosphate, pyridoxal phosphate, citrate, deoxynucleotides, manganese), along with mitochondrial-related functions (regulation of mitochondrial membrane potential and oxidative stress response). This suggests a coherent theme around mitochondrial transport of small molecules and cofactors, despite a few outliers. ","confidence":"Medium","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1990314","count":3},{"id":"GO:0051666","count":2},{"id":"GO:0051881","count":2},{"id":"GO:0015709","count":2},{"id":"GO:0031921","count":2}]},{"hash":"771972756396556686","title":"Apoptosis and innate immune signaling","description":"The cluster is dominated by GO terms for apoptotic processes, intrinsic apoptotic signaling, pyroptotic inflammatory response, innate immune response, and protein ubiquitination, suggesting proteins that regulate programmed cell death and inflammatory signaling. ER stress-related apoptotic signaling and DNA-templated transcription appear as secondary associations, consistent with stress-induced apoptosis and transcriptional control in development or stress responses. The presence of ubiquitination supports regulation of these pathways. Overall, the pattern points to a cohesive function in cell death regulation and immune activation.","confidence":"High","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090307","count":20},{"id":"GO:0006915","count":18},{"id":"GO:0045087","count":18},{"id":"GO:0016567","count":17},{"id":"GO:1990001","count":17}]},{"hash":"515174616927392949","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":5},{"id":"GO:0019068","count":4},{"id":"GO:0015074","count":4},{"id":"GO:0030260","count":4},{"id":"GO:0075713","count":4}]},{"hash":"1743451569262179101","title":"Redox metabolism and chromatin regulation","description":"The top terms cluster around redox processes (oxidation-reduction, redox homeostasis, mitochondrial electron transport) and metabolism (2-oxoglutarate), alongside chromatin-related regulation (positive regulation of chromatin binding, DNA methylation-related terms and methylation). This suggests a theme where redox/metabolic state interfaces with chromatin modification and epigenetic regulation, possibly via 2-oxoglutarate\u2013dependent processes. Some terms are obsolete or broad, but the core pattern points to redox-linked metabolism affecting chromatin regulation.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0018013","count":5},{"id":"GO:0045454","count":4},{"id":"GO:0035563","count":4},{"id":"GO:0043046","count":4}]},{"hash":"1088274533554818271","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0071031","count":3},{"id":"GO:0019068","count":2},{"id":"GO:0030260","count":2}]},{"hash":"1127240295604161758","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by GO terms for ribosome biogenesis, translation, translation reinitiation, and rRNA maturation, suggesting a core role in assembling ribosomes and protein synthesis. Additional terms related to transcription regulation and DNA transposition are present but less represented, so the primary theme remains ribosome-related.","confidence":"High","size":29,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007338","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0032197","count":2},{"id":"GO:0015074","count":2}]},{"hash":"2242896213101935049","title":"Retrotransposons and Proviral Integration","description":"The cluster is dominated by GO terms related to DNA transposition, retrotransposition, DNA integration, and proviral latency, pointing to mobilizable genetic elements and genome integration events (e.g., GO:0006313, GO:0032197, GO:0015074, GO:0075713). While a few terms touch on host development, the strongest signal is mobile genetic elements and virus-host genome interactions, justifying a focus on retrotransposons and proviral integration.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046718","count":2},{"id":"GO:0006313","count":1},{"id":"GO:0075732","count":1},{"id":"GO:0032197","count":1},{"id":"GO:0015074","count":1}]},{"hash":"2259983902589026965","title":"Vertebrate eye development","description":"The top GO terms are dominated by eye-related morphogenesis and patterning\u2014camera-type eye development, embryonic eye morphogenesis, left/right pattern formation\u2014along with multicellular organism development and transcription by RNA polymerase II. This suggests a coherent theme of vertebrate eye formation and regulatory gene expression, despite the presence of some unrelated terms.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060972","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0048048","count":3},{"id":"GO:0006366","count":3},{"id":"GO:0060441","count":3}]},{"hash":"1273531747803492576","title":"Unknown","description":"The GO terms are very diverse (meiosis pairing, transcription, ER protein handling, NK regulation, eye and wing development, ER localization/ERAD). There is no single cohesive function linking these proteins, so a specific functional label is not supported.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007129","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0030970","count":1},{"id":"GO:0032815","count":1},{"id":"GO:0042676","count":1}]},{"hash":"421559589515618726","title":"Nuclear genome maintenance and RNA processing","description":"This set of terms centers on nuclear DNA metabolism and genome stability (DNA repair via homologous recombination, immunoglobulin V(D)J and general recombination, DNA ligation in recombination, telomere/chromatin dynamics) and also on RNA processing in the nucleolus (rRNA maturation, rRNA processing). The presence of a deneddylation term suggests broader regulatory control of these nuclear processes, supporting a cohesive theme of genome maintenance coupled with RNA maturation. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000338","count":2},{"id":"GO:0051102","count":1},{"id":"GO:0000466","count":1},{"id":"GO:0002328","count":1},{"id":"GO:0071919","count":1}]},{"hash":"230440463949563250","title":"Ubiquitin-mediated proteolysis and cell cycle control","description":"This cluster is dominated by GO terms related to ubiquitination and proteasomal degradation (SCF-dependent ubiquitin tagging and protein catabolic processes, protein polyubiquitination) and several cell cycle-related processes (DNA replication initiation regulation, G1 DNA damage checkpoint signaling). The presence of circadian rhythm regulation terms suggests broader timing control linked to ubiquitin signaling. Together, these points indicate a cohesive theme around ubiquitin-proteasome\u2013mediated protein turnover that governs cell cycle progression and related regulatory pathways.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":11},{"id":"GO:0060386","count":9},{"id":"GO:0000083","count":9},{"id":"GO:1902916","count":9},{"id":"GO:0042752","count":9}]},{"hash":"67528851031547427","title":"Ubiquitin-mediated proteostasis and neuronal stress response","description":"The cluster centers on ubiquitin-dependent protein catabolic processes and polyubiquitination, highlighting protein turnover and proteostasis. It also includes neural context via synapse assembly in innervation and stress-response terms tied to heavy metals (cadmium, methylmercury) and oxidative stress\u2013induced neuronal apoptosis, suggesting a link between protein quality control and neuronal stress pathways. A circadian rhythm regulation term implies broader regulatory roles as well. Overall, these proteins likely function in maintaining neuronal protein homeostasis while mounting stress responses.","confidence":"High","size":29,"edges":8,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0031571","count":10},{"id":"GO:0042787","count":10},{"id":"GO:0060386","count":10},{"id":"GO:1903378","count":10},{"id":"GO:0000083","count":10}]},{"hash":"1739463792067496474","title":"Ribosome biogenesis and translation regulation","description":"Based on the dominant GO terms, the proteins are linked to transcription and translation processes as well as rRNA maturation and processing (DNA-templated transcription, translation, maturation of SSU rRNA, regulation of translation, and rRNA processing regulation). This points to a cohesive theme around ribosome biogenesis and control of protein synthesis, with some ancillary nucleotide metabolism terms likely incidental. The cluster therefore most plausibly represents gene expression machinery centered on ribosome assembly and translation regulation.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0000462","count":2},{"id":"GO:0006417","count":2},{"id":"GO:0006203","count":1}]},{"hash":"1928747966587006739","title":"Retrotransposition and proviral integration","description":"This cluster is best described by processes governing genome mobility and proviral life cycles: DNA integration, DNA transposition, retrotransposition, and establishment of integrated proviral latency, along with viral entry into the host nucleus. These together suggest a cluster of retrotransposons and integrated provirus activity rather than a single metabolic pathway.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":3},{"id":"GO:0039651","count":3},{"id":"GO:0075713","count":3},{"id":"GO:0043547","count":2},{"id":"GO:0046677","count":2}]},{"hash":"787719049073524631","title":"Diverse substrate catabolism","description":"The top GO terms show catabolic processes for a wide range of substrates (chlorophyll, uracil, prostaglandin, stilbene, phosphatidylserine, monoacylglycerol, 1,2-dichloroethane, etc.), indicating proteins involved in breaking down diverse compounds rather than a single pathway. A couple of terms (like C-terminal demethylation) are outliers/obsolete, but the shared theme is broad catabolic activity.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019260","count":2},{"id":"GO:1990577","count":2},{"id":"GO:0052651","count":2},{"id":"GO:0009086","count":2},{"id":"GO:1905344","count":2}]},{"hash":"1453308261807175424","title":"Amino acid biosynthesis and related metabolism","description":"The cluster is enriched for multiple amino acid biosynthetic processes (lysine via aminoadipic acid, leucine, histidine, isoleucine) and also includes core metabolic pathways such as the TCA cycle, biotin and heme biosynthesis, porphyrinogen production, and fatty acid homeostasis, suggesting a cohesive set of enzymes involved in primary metabolism and cofactor biosynthesis.","confidence":"High","size":28,"edges":106,"triangles":79,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019878","count":12},{"id":"GO:0006099","count":7},{"id":"GO:0009102","count":6},{"id":"GO:0009098","count":6},{"id":"GO:0009097","count":6}]},{"hash":"1011719907801606702","title":"Seed lipid biosynthesis and transport","description":"The top GO terms are dominated by fatty acid biosynthetic processes (various chain lengths), fatty acid transport/import, and seed coat development, pointing to lipid metabolism and handling in seeds. ancillary catabolic terms may reflect broader seed metabolite turnover but the core theme is seed lipid synthesis and trafficking.","confidence":"High","size":28,"edges":9,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006633","count":10},{"id":"GO:0043041","count":9},{"id":"GO:0000038","count":9},{"id":"GO:1902987","count":9},{"id":"GO:0010214","count":9}]},{"hash":"973081583053026517","title":"Ubiquitin-Regulated Mitosis, Apoptosis, and Pyroptosis","description":"The cluster's top GO terms cluster around ubiquitination, spindle assembly, and programmed cell death, with strong signals for innate immune\u2013related pyroptosis. This points to proteins involved in ubiquitin-mediated regulation of mitosis and apoptosis, linked to inflammatory signaling. The presence of older, less-relevant terms is minor and does not change the overall pattern.","confidence":"High","size":28,"edges":15,"triangles":3,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":19},{"id":"GO:0090307","count":19},{"id":"GO:0006915","count":19},{"id":"GO:0045087","count":19},{"id":"GO:1990001","count":19}]},{"hash":"2253118531426694042","title":"Translation and antibiotic stress response","description":"Most top GO terms are related to translation (translation, regulation of translational fidelity, translational termination) and to cellular responses to translation inhibitors (cycloheximide) and antibiotics, indicating a cluster enriched for protein synthesis machinery and its regulation under chemical stress. A few terms like carnitine biosynthetic process and intracellular potassium ion homeostasis are less central, but the dominant theme centers on translation and inhibitor-responsive processes. Overall, this label captures the main function represented by the cluster.","confidence":"Medium","size":28,"edges":63,"triangles":191,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0055114","count":4},{"id":"GO:0046677","count":3},{"id":"GO:0006450","count":3},{"id":"GO:0045329","count":2}]},{"hash":"1809037341629467309","title":"Transmembrane transporter proteins","description":"The top GO terms are dominated by various transmembrane transport activities (sialic acid, potassium, arabinose, galactose, phosphate, vitamin) plus related processes like neurotransmitter loading into synaptic vesicles, indicating a cluster of membrane transporters with diverse substrates. The absence of edges suggests these proteins may be functionally related by transport role rather than forming a tight interaction network. Therefore the label \"Transmembrane transporter proteins\" best captures the shared function.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":5},{"id":"GO:0071805","count":5},{"id":"GO:0042128","count":5},{"id":"GO:0015751","count":5},{"id":"GO:0098700","count":5}]},{"hash":"1385476736987179451","title":"Ribosome biogenesis and TORC1-regulated translation","description":"The dominant GO terms center on ribosome assembly and translation control\u2014translation reinitiation, formation of translation preinitiation complex, and maturation of SSU-rRNA\u2014along with positive regulation of TORC1 signaling, which ties to growth and proliferation. While other terms touch on transcription, vesicle transport, and development, the core signal converges on ribosome biogenesis and TORC1\u2011driven protein synthesis. ","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0002188","count":5},{"id":"GO:1904263","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0008283","count":5},{"id":"GO:0006888","count":4}]},{"hash":"935009793396842866","title":"Synaptic plasticity and cytoskeletal remodeling","description":"This cluster is enriched for long-term synaptic potentiation and multiple receptor-mediated signaling pathways (EGFR, Ephrin, Wnt), plus positive regulation of actin polymerization and substrate adhesion-dependent cell spreading. Together, these terms point to coordinated signaling that strengthens synapses and remodels the cytoskeleton, with polarity and GTPase regulation as related network features. Overall, the core theme is neuronal synaptic signaling coupled to cytoskeletal changes.","confidence":"High","size":28,"edges":136,"triangles":142,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0060291","count":5},{"id":"GO:0046580","count":4},{"id":"GO:0007173","count":4},{"id":"GO:1900026","count":4},{"id":"GO:0048013","count":4}]},{"hash":"2181968322013832188","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0046677","count":4},{"id":"GO:0006412","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0006446","count":3}]},{"hash":"341583147951195073","title":"Ubiquitin-Proteasome\u2013Mediated Proteostasis and Cell Cycle Regulation","description":"The top GO terms are dominated by ubiquitin-dependent protein catabolic processes and proteasomal degradation, including SCF-dependent pathways and polyubiquitination, indicating a core role in proteostasis. Additional terms point to circadian rhythm regulation and cell cycle checkpoints, suggesting linkage between protein turnover and cell cycle control. Together, these themes support a label centered on ubiquitin-proteasome\u2013mediated proteostasis and cell-cycle regulation.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":7},{"id":"GO:0042787","count":7},{"id":"GO:1903378","count":7},{"id":"GO:0060386","count":6},{"id":"GO:0000083","count":6}]},{"hash":"1203577281716802614","title":"RNA processing and transcription regulation","description":"The proteins appear linked by RNA metabolism and transcription control processes: regulation of nuclear-transcribed mRNA poly(A) tail shortening; regulation of phosphorylation of RNA polymerase II CTD; DNA-templated transcription; and mRNA processing, pointing to a shared role in RNA metabolism and transcription regulation. Other GO terms (insulin signaling, redox homeostasis, development) may reflect broader or secondary annotations rather than a core feature of this cluster.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060211","count":2},{"id":"GO:1901407","count":2},{"id":"GO:0008286","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0006260","count":2}]},{"hash":"1952622615013903436","title":"Unknown","description":"The terms include development-related processes (myoblast fusion, skeletal system development, multicellular organism development), general cellular processes (DNA-templated transcription, ER-Golgi transport, mitotic cell cycle), stress and defense responses (ER-stress\u2013induced apoptosis, cadmium response, defense against Gram-positive bacteria), and nutrient-responsive growth. The wide spread of functions provides no single cohesive theme to bind the cluster, so a specific label is not supported.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007520","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0050830","count":2}]},{"hash":"519416053839168773","title":"Ubiquitin-Dependent Protein Degradation","description":"The dominant GO terms point to ubiquitin-mediated proteolysis, including SCF-dependent proteasomal ubiquitin-dependent protein catabolic process and protein polyubiquitination, indicating a cluster centered on protein turnover via the ubiquitin\u2013proteasome system. While there are related stress and cell-cycle terms, the core function across terms is ubiquitin-driven degradation.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":6},{"id":"GO:0042787","count":5},{"id":"GO:0071276","count":5},{"id":"GO:0000209","count":4},{"id":"GO:0031571","count":3}]},{"hash":"1935674672831332573","title":"Unknown","description":"The GO terms are highly diverse (spliceosome disassembly, DNA damage response to X-ray, intra-Golgi transport, B cell differentiation, small GTPase signaling, ER unfolded protein response, vascular permeability, focal adhesion regulation, and PKC signaling), and there is no clear shared function or pathway connecting them, plus the network metrics show no edges or clusters. This suggests heterogeneous annotations rather than a single cohesive functional theme.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000390","count":2},{"id":"GO:0010165","count":2},{"id":"GO:0006891","count":1},{"id":"GO:0008272","count":1},{"id":"GO:0030183","count":1}]},{"hash":"757855123670246534","title":"Nutrient-responsive transcription regulation","description":"The top GO terms center on DNA-templated transcription and regulation of transcription from RNA polymerase II promoter under various nutrient- and condition-related cues (oleic acid, nonfermentable carbon sources, starvation). This points to a cohesive theme of transcriptional control in response to nutrients, with some links to metabolism-related biosynthetic processes, supporting a label focused on nutrient-triggered transcription regulation.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0045122","count":4},{"id":"GO:2001158","count":4},{"id":"GO:0043457","count":4},{"id":"GO:1904741","count":4}]},{"hash":"504386888931516268","title":"Ribosome biogenesis and translation initiation","description":"This cluster shows strong enrichment for ribosome biogenesis (ribosome biogenesis; ribosomal large subunit biogenesis) and formation of the translation preinitiation complex, with supporting RNA processing terms, indicating a core protein-synthesis machinery theme. While there are also cell cycle and development terms, the ribosome/translation signals dominate.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0001731","count":3},{"id":"GO:0000070","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0042273","count":3}]},{"hash":"1924973629869713444","title":"Neuronal ubiquitin-proteasome proteostasis","description":"This cluster is strongly enriched for ubiquitin-dependent proteolysis and ubiquitination-related processes (UPS) with SCF and proteasomal involvement, indicating a proteostasis-focused module. The presence of neuronal-specific terms such as synapse assembly and neuron-intrinsic apoptotic signaling under oxidative stress, along with stress response to metals and circadian regulation, suggests a connected network managing protein turnover and stress responses in neurons. While there are some cell-cycle and transcription-related terms, they can be linked to broader regulatory stress pathways. ","confidence":"High","size":28,"edges":147,"triangles":238,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":6},{"id":"GO:0031146","count":6},{"id":"GO:0031571","count":5},{"id":"GO:0060386","count":5},{"id":"GO:1903378","count":5}]},{"hash":"1507747204625052390","title":"Ubiquitin-Dependent Protein Degradation and DNA Metabolism","description":"The top GO terms cluster around ubiquitin-mediated protein turnover, including ubiquitin-dependent proteolysis, ERAD, and autoubiquitination, alongside several DNA-focused processes such as DNA replication, DNA integration, and histone catabolic processes. While there are a couple of terms mentioning host-virus interactions, the dominant signal is ubiquitin-dependent degradation coupled with DNA metabolism, suggesting a functional link between protein turnover and genome/chromatin dynamics.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042787","count":8},{"id":"GO:0006260","count":6},{"id":"GO:0030433","count":6},{"id":"GO:0085020","count":5},{"id":"GO:0036205","count":5}]},{"hash":"2303665856125367106","title":"Vesicle trafficking and Golgi-endosome transport","description":"Top GO terms indicate enrichment for vesicle formation and transport processes, including multivesicular body assembly, endosome-to-lysosome transport, retrograde Golgi-to-ER transport, and Golgi organization, as well as protein transport and exosomal secretion. This points to a cohesive theme of intracellular trafficking between Golgi, endosomes, lysosomes, and secretory pathways, justifying a vesicle trafficking\u2013centric label.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036258","count":3},{"id":"GO:0008333","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0032258","count":3},{"id":"GO:0007030","count":3}]},{"hash":"1798086228141437104","title":"RNA Pol I Transcription and Ribosome Biogenesis","description":"The top terms point to nucleolar transcription by RNA polymerase I and ribosome biogenesis (e.g., RNA Pol I transcription, preinitiation complex assembly, nucleolar rRNA transcription, ribosome biogenesis), with a few transcription-related terms supporting a unified transcription-first/nucleolar module. A single unrelated term (heart development) appears as a minor outlier, but the core theme is transcription by Pol I and ribosome production.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0007507","count":2},{"id":"GO:0043433","count":2},{"id":"GO:0006362","count":1},{"id":"GO:0042254","count":1}]},{"hash":"412473534009851426","title":"Migration and differentiation regulation","description":"The top GO terms point to regulation of cell migration, chemotaxis, and lamellipodium morphogenesis, with notes on oligodendrocyte differentiation, indicating a shared theme of motility and development. Signaling modulation (negative regulation of protein kinase activity) further supports coordinated regulation of these processes. Some metabolic terms appear as noise, but the strongest pattern is regulation of cell movement and differentiation.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0045719","count":2},{"id":"GO:2000394","count":2},{"id":"GO:0030334","count":2}]},{"hash":"27200126990645391","title":"Mitotic regulation and inflammatory cell death","description":"The top GO terms cluster around mitotic spindle assembly and ubiquitination (cell-cycle control), along with apoptotic and pyroptotic inflammatory responses and innate immune signaling. This suggests a unit that links cell division regulation with inflammatory cell death pathways and cytoskeletal remodeling during mitosis.","confidence":"Medium","size":27,"edges":340,"triangles":2661,"max_degree":26,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0090307","count":6},{"id":"GO:0016567","count":5},{"id":"GO:0006915","count":5},{"id":"GO:0045087","count":5},{"id":"GO:1990001","count":5}]},{"hash":"1092056106807437295","title":"Epigenetic Regulation in Development","description":"The cluster shows a strong bias toward chromatin regulation and RNA processing (positive regulation of chromatin binding, histone methylation, alternative splicing) along with developmental signals (embryonic and cerebral cortex development). Although a few outlier terms relate to metabolism or immune response, the dominant theme is transcriptional/epigenetic control during development.","confidence":"Medium","size":27,"edges":59,"triangles":12,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":10},{"id":"GO:0009228","count":6},{"id":"GO:0001701","count":6},{"id":"GO:0032496","count":5},{"id":"GO:0045793","count":5}]},{"hash":"707597681989118819","title":"Neuronal endocannabinoid signaling and lipid catabolism","description":"Label reflects dominance of endocannabinoid-related signaling terms (regulation of endocannabinoid signaling, retrograde trans-synaptic signaling by endocannabinoid) together with lipid catabolic processes (triglyceride, diacylglycerol, monoacylglycerol catabolism) and synaptic GPCR signaling (glutamate receptor pathway). Some terms appear noisy (cellulose catabolic, obsolete neurotransmitter biosynthetic process, MVB disassembly), but the core theme points to lipid-based neuronal signaling and endocannabinoid-mediated communication.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0019433","count":9},{"id":"GO:2000124","count":8},{"id":"GO:0030245","count":6},{"id":"GO:0042136","count":6},{"id":"GO:0046340","count":6}]},{"hash":"92798100670133673","title":"RNA Processing and Translation Machinery","description":"The top GO terms are dominated by translation (cytosolic and mitochondrial) and spliceosome-related steps, pointing to a cohesive set of proteins involved in RNA processing and protein synthesis. While a few terms appear peripheral (e.g., DNA replication, antibiotic response, BDNF signaling), the dominant theme is RNA processing and the translation/splicing machinery, including mitochondrial translation, justifying this label.","confidence":"High","size":27,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0000742","count":2},{"id":"GO:0006260","count":2},{"id":"GO:1990416","count":2}]},{"hash":"1451536144935802125","title":"DNA Damage Checkpoints and Mitosis","description":"The cluster centers on cell cycle control and DNA damage response, with terms for G1 and G2/M checkpoints, DNA replication, and mitotic progression, plus related ubiquitin-proteasome turnover and ER stress\u2013related pathways, all of which fit a module coordinating replication, division, and stress signaling.","confidence":"High","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0031571","count":3},{"id":"GO:0000086","count":3},{"id":"GO:0070059","count":3},{"id":"GO:0000278","count":3}]},{"hash":"2048860984967972297","title":"Transmembrane Transport of Ions and Metabolites","description":"The cluster is enriched for transmembrane transport terms across membranes for a range of substrates (sialic acid, potassium, arabinose, galactose, fucose, phosphate, vitamins) and a vesicle-loading term for neurotransmitters, pointing to membrane transport as the shared function.","confidence":"High","size":27,"edges":83,"triangles":0,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":7},{"id":"GO:0071805","count":7},{"id":"GO:0042128","count":7},{"id":"GO:0015751","count":7},{"id":"GO:0098700","count":7}]},{"hash":"2097944046841899027","title":"mRNA splicing and processing","description":"Predominant themes are spliceosome-mediated mRNA maturation and processing, including splicing, splice-site recognition, and regulation of mRNA poly(A) tail and export; a few translation initiation terms are present but do not define the cluster.","confidence":"High","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0002188","count":12},{"id":"GO:0001731","count":12},{"id":"GO:0045292","count":11},{"id":"GO:0006378","count":11},{"id":"GO:0031047","count":10}]},{"hash":"751532133258094281","title":"Ubiquitin-Proteasome-Mediated Protein Degradation","description":"The cluster is dominated by GO terms for ubiquitin-dependent protein catabolic process, protein polyubiquitination, and SCF-dependent proteasomal degradation, indicating a core role in protein turnover. Additional terms on peroxisome import, circadian rhythm regulation, and synapse assembly can be linked to ubiquitination-driven control of protein localization, clock function, and neural connectivity, respectively. Together they define a functional theme around proteostasis and ubiquitin signaling.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:0051865","count":3},{"id":"GO:0000083","count":3},{"id":"GO:0016558","count":3},{"id":"GO:0060386","count":2}]},{"hash":"337569881900751991","title":"Cellular stress signaling and translation control","description":"This cluster centers on stress-related signaling (JNK cascade; ER-stress\u2013linked apoptotic signaling), together with regulation of transcription and translation initiation, plus proteasomal degradation. The convergence of these processes suggests a cohesive cellular stress response module that modulates gene expression, protein synthesis, and turnover under stress, hence the label. ","confidence":"Medium","size":27,"edges":24,"triangles":0,"max_degree":24,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0001731","count":3},{"id":"GO:0032436","count":3},{"id":"GO:0006446","count":3},{"id":"GO:0007254","count":3}]},{"hash":"986817489741793820","title":"Insect cuticle development and immune signaling","description":"Most prominent terms center on chitin-based cuticle development and ecdysis, typical of insect development, with additional immune signaling terms (NF-kappaB activation, IL-8 production, cellular response to IL-1) and general developmental processes, indicating a cluster of proteins tied to cuticle biology and associated immune regulation across species. Some carbohydrate catabolism terms are present but secondary.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":5},{"id":"GO:0000272","count":4},{"id":"GO:0007250","count":3},{"id":"GO:0040003","count":3},{"id":"GO:0030324","count":3}]},{"hash":"1340925217787915578","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":5},{"id":"GO:0019068","count":4},{"id":"GO:0000398","count":4},{"id":"GO:0030260","count":4},{"id":"GO:0075713","count":4}]},{"hash":"529892868627932","title":"Fatty acid biosynthesis and lipid transport","description":"The cluster centers on lipid-related biosynthesis and handling, with multiple GO terms for fatty acid biosynthesis (GO:0006633), long-chain and very-long-chain fatty acid metabolism/transport (GO:0044539, GO:0001579, GO:0000038), and related lipid processes like lipopolysaccharide biosynthesis (GO:0055114 and GO:0009103) and seed coat\u2013associated lipid pathways. The repeated emphasis on fatty acid production and membrane/lipid-derived components suggests a cohesive theme around lipid biosynthesis and transport, justifying this label.","confidence":"High","size":26,"edges":2,"triangles":0,"max_degree":1,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0055114","count":11},{"id":"GO:0009103","count":7},{"id":"GO:1902987","count":7},{"id":"GO:0042619","count":7},{"id":"GO:0043041","count":6}]},{"hash":"792353286433079542","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000480","count":5},{"id":"GO:0000472","count":5},{"id":"GO:0000447","count":5},{"id":"GO:0050731","count":5},{"id":"GO:2000601","count":5}]},{"hash":"287350822676744508","title":"Innate antiviral signaling and membrane transport","description":"Top GO terms point to innate antiviral signaling via Toll-like receptors (TLR3/7/9) and several transmembrane transport processes (sialic acid, xenobiotic, phosphate, potassium, fucose). This combination suggests a functional theme around antiviral sensing linked with membrane transport activities, consistent with a cohesive cluster rather than random associations.","confidence":"Medium","size":26,"edges":11,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0075522","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0034138","count":2},{"id":"GO:0034154","count":2},{"id":"GO:0034162","count":2}]},{"hash":"1556207350474767578","title":"Symbiont-driven immune modulation and barrier biosynthesis","description":"This cluster combines immune-related processes (antigen presentation via MHC II, regulation of MHC II biosynthesis, symbiont-mediated suppression of host adaptive immunity) with ubiquitination pathways (protein polyubiquitination, ubiquitin-like modifications) and barrier biosynthesis (suberin/cutin). The overlap suggests a theme of host defense regulation and barrier formation in the context of symbiotic interactions, linking immune modulation to protective plant-like barrier processes across the host\u2013symbiont interface.","confidence":"Medium","size":26,"edges":34,"triangles":15,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0060576","count":1},{"id":"GO:0060628","count":1},{"id":"GO:0039648","count":1},{"id":"GO:1900490","count":1},{"id":"GO:0010345","count":1}]},{"hash":"2174883292346553315","title":"Transcription and Translation Regulation with Proteostasis","description":"The cluster centers on both transcriptional control (DNA-templated transcription) and various modes of translational regulation (translation reinitiation, preinitiation complex formation, IRES-dependent initiation, and regulation of translational initiation), plus proteasomal protein turnover. This combination points to a cohesive theme of gene expression regulation at transcriptional and translational levels with proteostasis.","confidence":"High","size":26,"edges":5,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032436","count":6},{"id":"GO:0006351","count":5},{"id":"GO:0002188","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0075525","count":5}]},{"hash":"2289417274789779612","title":"Unknown","description":"The top GO terms are a mix of unrelated processes (various catabolic processes for different substrates, detoxification, insulin secretion regulation, cell adhesion, T cell activation, and proteolysis), giving no single, coherent function for the cluster. This makes a specific, representative label unreliable.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0030245","count":8},{"id":"GO:0042136","count":8},{"id":"GO:0046340","count":8},{"id":"GO:0015996","count":6},{"id":"GO:0098869","count":6}]},{"hash":"942643401258526496","title":"Viral translation initiation and virion assembly","description":"The GO terms cluster around translation initiation processes (IRES-dependent viral translation, preinitiation complex formation, regulation of translational initiation) along with virion assembly and host-entry processes, suggesting proteins involved in viral infection and hijacking of host translation. Additional terms on mRNA export/splicing and DNA integration point to broader virus-host interaction in replication and genome integration. Overall, the dominant theme is viral translation and assembly functions.","confidence":"Medium","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0006406","count":2},{"id":"GO:0075525","count":2},{"id":"GO:0001731","count":2}]},{"hash":"1392012242107927564","title":"Chromosome replication and meiotic chromatin silencing","description":"This cluster is dominated by nuclear processes tied to chromosome maintenance and meiotic chromatin state, including DNA replication, mitotic chromosome condensation, centromeric cohesion, and silent mating-type locus heterochromatin formation, as well as meiotic DSB regulation. While a few terms point to broader cellular transport roles, the core signal is chromosome dynamics and meiotic chromatin regulation.","confidence":"Medium","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":11},{"id":"GO:0030466","count":9},{"id":"GO:0006260","count":9},{"id":"GO:0006888","count":8},{"id":"GO:0051754","count":6}]},{"hash":"146465691513577582","title":"ER protein folding and redox regulation","description":"The most represented terms point to protein folding in the endoplasmic reticulum and redox-related processes (deglutathionylation, oxidative stress response, redox regulation), suggesting a cluster of proteins involved in protein maturation under oxidative conditions. Some terms like \"viral process\" or \"regulation of DNA binding\" appear as outliers and may reflect annotation noise or multifunctionality. Overall, the cluster seems driven by redox-associated protein quality control rather than a single cohesive pathway.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006662","count":1},{"id":"GO:0033158","count":1},{"id":"GO:0080058","count":1},{"id":"GO:1903026","count":1}]},{"hash":"1345748961010915371","title":"Ubiquitin-regulated TNF-NF-\u03baB signaling and apoptosis","description":"The top GO terms cluster around ubiquitin-dependent protein catabolic processes, TNF and NF-\u03baB signaling, and regulation of apoptosis. This points to a coherent theme where ubiquitination modulates TNF pathway activity and downstream cell fate decisions, matching the emphasis on ubiquitin-related processes and TNF/NF-\u03baB signaling in the cluster.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:1903265","count":6},{"id":"GO:0042981","count":5},{"id":"GO:0007250","count":5},{"id":"GO:0085020","count":5}]},{"hash":"300662620890436413","title":"Cell division and ribosome biogenesis","description":"The strongest signals are cell division and ribosome biogenesis, as shown by GO:0051301 (cell division) and GO:0042254 (ribosome biogenesis) with supporting terms like mitotic spindle assembly and intracellular transport, indicating a core role in cellular growth and division. Some annotations such as brain development and cadmium response are broader and likely reflect pleiotropy or general cellular annotations rather than a single pathway. Given the lack of explicit interactions (edges) in this cluster, the label should reflect a general cellular proliferation/biogenesis theme rather than a specific pathway.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0000747","count":2},{"id":"GO:0000492","count":2},{"id":"GO:0000920","count":2}]},{"hash":"284051152696594114","title":"Cell Morphogenesis and Organ Regeneration","description":"The top GO terms highlight cell morphogenesis and animal organ regeneration, suggesting a developmental remodeling theme. While other terms touch on processes like apoptotic clearance and spindle-kinetochore interactions, the dominant signal centers on morphogenesis and tissue regeneration rather than a single biochemical pathway. Some terms are obsolete, which weakens the coherence, but the primary theme remains developmental remodeling.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051973","count":4},{"id":"GO:0000902","count":4},{"id":"GO:0031532","count":4},{"id":"GO:0014043","count":3},{"id":"GO:0007070","count":3}]},{"hash":"1041086834995350719","title":"Unknown","description":"The GO terms are highly diverse, including retrotransposition and DNA integration (transposon-like activity), nutrient and maltose metabolism, N-glycan processing, heart morphogenesis, neuromuscular control, fungal beta-glucan biosynthesis, and vacuolar sequestration. This lack of a single shared function or pathway, plus zero edges, suggests no cohesive functional cluster. Therefore Unknown with None.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":3},{"id":"GO:0007584","count":2},{"id":"GO:0032197","count":2},{"id":"GO:0015074","count":2},{"id":"GO:0006491","count":2}]},{"hash":"1618261045717329765","title":"Epigenetic Silencing and Transposon Regulation","description":"The top GO terms point to DNA methylation and chromatin modification (including siRNA-directed methylation and histone modifications) that repress transcription, plus retrotransposon activity (DNA integration, retrotransposition). This suggests a functional cluster centered on epigenetic regulation of transcription and suppression of transposable elements.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0015074","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0000122","count":2},{"id":"GO:0032197","count":2},{"id":"GO:0010390","count":1}]},{"hash":"1865866658763337295","title":"Ribosome biogenesis and RNA processing","description":"The top terms are dominated by ribosome-related processes (ribosomal large subunit biogenesis; maturation of SSU- and 5.8S rRNA) and RNA processing (mRNA splicing via spliceosome; rRNA maturation). There are also multiple hits for ubiquitination/ER-associated degradation, which aligns with protein quality control in ribosome assembly. Although there are a couple of terms like mitotic spindle assembly and brain development, the core signal strongly points to ribosome biogenesis and RNA processing as the cluster\u2019s central function. ","confidence":"High","size":25,"edges":85,"triangles":149,"max_degree":23,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090307","count":7},{"id":"GO:0007420","count":5},{"id":"GO:0051260","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0000466","count":5}]},{"hash":"600552102930653007","title":"Translation machinery and cell cycle proteins","description":"The cluster is dominated by translation-related terms (translation, cytoplasmic translation, ribosomal subunit assembly) and cell-cycle processes (cell cycle, cell division, chromosome segregation, exit from mitosis), indicating a set of proteins tied to protein synthesis and mitotic progression.","confidence":"High","size":25,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0046677","count":4},{"id":"GO:0007605","count":2},{"id":"GO:0000027","count":2},{"id":"GO:0010458","count":2}]},{"hash":"1782921823001935030","title":"EGFR/Wnt signaling and cell migration cluster","description":"This cluster is enriched for pathways that regulate cell signaling, adhesion, polarity, and movement, including EGFR signaling, canonical Wnt signaling, filopodium assembly, and endosomal trafficking, along with regulation of fibroblast migration and cell spreading. These features point to a coherent theme of signaling-driven cell migration and polarity, supported by multiple related GO terms.","confidence":"Medium","size":25,"edges":238,"triangles":1201,"max_degree":24,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1900026","count":5},{"id":"GO:0033144","count":4},{"id":"GO:0007173","count":4},{"id":"GO:0090263","count":4},{"id":"GO:0043552","count":4}]},{"hash":"706740760442228793","title":"Transcriptional Regulation of Metabolic Biosynthesis","description":"The dominant signals are transcription-related (DNA-templated transcription; positive/negative regulation of transcription from RNA polymerase II promoter under various nutrients and carbon sources). A minority of terms tie to metabolic biosynthesis (aflatoxin, lysine, pyrimidine nucleotide biosynthesis) and respiration regulation. This suggests a cluster of proteins that primarily regulate transcription to control metabolic pathways.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0045122","count":1},{"id":"GO:2001158","count":1},{"id":"GO:0043457","count":1},{"id":"GO:1904741","count":1}]},{"hash":"363973871872009369","title":"Unknown","description":"The top GO terms are diverse (mitochondrial DNA repair, DNA damage response, heat-shock/chromatin puffing, developmental axis specification, amyloid-beta response) with some obsolete terms, so there is no clear, single function tying the proteins together.","confidence":"","size":25,"edges":9,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:1904646","count":1},{"id":"GO:0090298","count":1},{"id":"GO:0006288","count":1},{"id":"GO:0008069","count":1},{"id":"GO:0035080","count":1}]},{"hash":"2268293375433473632","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0002188","count":3},{"id":"GO:0071560","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0000472","count":3},{"id":"GO:0000447","count":3}]},{"hash":"2151855339599250304","title":"NF-\u03baB Signaling and Apoptosis Regulation","description":"Proteins in this cluster are enriched for NF-\u03baB\u2013related signaling, apoptosis regulation, and ubiquitination, particularly TNF-mediated pathways and K6-linked ubiquitination, suggesting a role in inflammatory signaling and cell fate decisions via ubiquitin-dependent regulation. Some terms are obsolete or tangential (voltage-gated K channel regulation, X-inactivation dosage compensation), but the dominant pattern is NF-\u03baB activation and apoptotic control.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042981","count":5},{"id":"GO:0007250","count":5},{"id":"GO:0085020","count":5},{"id":"GO:0033209","count":5},{"id":"GO:1903762","count":5}]},{"hash":"2009046098405336261","title":"Gene Expression and Proteostasis","description":"The cluster centers on core gene expression processes (DNA-templated transcription, mRNA splicing, DNA replication) and translation initiation, alongside protein handling pathways (ER-to-Golgi transport, unfolded protein response, aggresome assembly) and organelle dynamics (mitochondrial fission). This combination suggests a theme around transcription/translation machinery with proteostasis and stress-related quality control, rather than a single isolated pathway.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0000398","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0043029","count":3}]},{"hash":"2277885698027789136","title":"Retroviral DNA Integration and Proviral Latency","description":"The top terms center on retroviral life cycle steps: reverse transcription (RNA-templated DNA synthesis), DNA integration into the host genome, and the establishment of proviral latency, with supporting roles in DNA repair/recombination and host-virus interactions. This suggests the proteins function together in retroviral replication and maintenance of latent provirus.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0075732","count":4},{"id":"GO:0015074","count":4},{"id":"GO:0046718","count":4},{"id":"GO:0039651","count":4}]},{"hash":"519685292701844535","title":"Unknown","description":"The top terms split between cytoskeletal assembly (microspike/filopodium) and a grab-bag of disparate processes (glutathione transport, seed development, DNA integration, retrotransposition, growth hormone secretion), with no clear cohesive function or network structure. This suggests no single, interpretable cluster function, so Unknown with None confidence. ","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030035","count":2},{"id":"GO:0046847","count":2},{"id":"GO:0051515","count":1},{"id":"GO:0098709","count":1},{"id":"GO:0048316","count":1}]},{"hash":"165127009785351949","title":"Developmental Translation Initiation and Ribosome Biogenesis","description":"These proteins are enriched for translation-related processes (translation reinitiation; formation of translation preinitiation complex) and maturation of ribosomal RNA, suggesting a core role in protein synthesis machinery. The concurrent appearance of multicellular development and cell proliferation terms indicates this synthesis capacity is tied to developmental growth. While a few terms point to vesicle transport or GPCR signaling, these are less prominent, so the central theme centers on translation initiation and ribosome biogenesis in development.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0002188","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0001731","count":4},{"id":"GO:0008283","count":4},{"id":"GO:0008284","count":4}]},{"hash":"708433578723578263","title":"Membrane lipid signaling and polarity regulation","description":"The terms cluster around lipid-based signaling (phosphatidylinositol dephosphorylation, regulation of phosphatidylcholine biosynthesis, PKC signaling) and processes involving cell polarity and membrane remodeling (establishment of cell polarity, dendritic spine modification, glutamate secretion). Developmental and differentiation terms appear but can be connected to signaling and morphogenesis across contexts. Overall, the proteins appear linked by lipid-mediated signal transduction influencing cell architecture and synaptic modulation.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046856","count":2},{"id":"GO:0030183","count":1},{"id":"GO:2000114","count":1},{"id":"GO:2001246","count":1},{"id":"GO:0051452","count":1}]},{"hash":"1840811693235234746","title":"Ubiquitin-Dependent Proteolysis and Neuronal Stress Response","description":"The cluster is strongly enriched for ubiquitination-related processes (ubiquitin-dependent protein catabolic process, protein polyubiquitination, regulation of polyubiquitination) and includes neuronal-related terms (synapse assembly, neuron-specific apoptotic signaling) along with cellular stress responses to metals (cadmium, methylmercury) and circadian rhythm regulation. This pattern suggests a group of proteins involved in ubiquitin-mediated protein turnover that also participate in neuronal stress responses and synaptic organization.","confidence":"Medium","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:0000209","count":7},{"id":"GO:0031571","count":6},{"id":"GO:0060386","count":6},{"id":"GO:1903378","count":6}]},{"hash":"1784334028689120609","title":"Unknown","description":"The terms are scattered across DNA replication, mitotic processes, various plant carbohydrate catabolic steps (xylan, cellulose, starch), nitrogen response, circadian rhythm, pollen hydration, protein heterooligomerization, and kinase regulation, with no single dominant function. There are no edges and no cohesive enrichment to tie the proteins to one theme, so a reliable label cannot be assigned.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043137","count":1},{"id":"GO:0007084","count":1},{"id":"GO:0045493","count":1},{"id":"GO:0030245","count":1},{"id":"GO:0005983","count":1}]},{"hash":"87986074555084962","title":"Diverse Catabolic Metabolism and Stress Response","description":"The top terms indicate a broad set of catabolic pathways (galactose, sorbitol, glucose, amino acids via the Ehrlich pathway, formaldehyde) and oxidation-related processes, plus environmental stress responses (lipopolysaccharide and copper ion). This suggests a cluster focused on versatile catabolic metabolism coupled with stress responsiveness, rather than a single specific pathway.","confidence":"Medium","size":24,"edges":243,"triangles":1389,"max_degree":23,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0019518","count":8},{"id":"GO:0032496","count":8},{"id":"GO:0055114","count":7},{"id":"GO:0033498","count":7},{"id":"GO:0000947","count":7}]},{"hash":"1941331076933722886","title":"Bacterial metabolism and cell wall biosynthesis","description":"This cluster is driven by terms related to glycolysis, peptidoglycan biosynthesis, and transmembrane transport of amino acids (D-alanine/D-serine), along with cell wall organization and regulation of cell shape, suggesting a focus on bacterial energy metabolism and cell envelope biosynthesis. Some outlier terms (e.g., liver development, obsolete oxidation-reduction) appear noisy, but the core signals point to bacterial metabolic processes and cell wall assembly.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0001889","count":3},{"id":"GO:0042594","count":3},{"id":"GO:0006096","count":3},{"id":"GO:0008360","count":3}]},{"hash":"1268628184784927875","title":"Transcriptional Regulation & Chromatin Remodeling","description":"The cluster's top GO terms are dominated by DNA-templated transcription and chromatin remodeling, with DNA integration also appearing, indicating components of transcriptional control and chromatin dynamics. Other terms about biosynthetic regulation are present but appear as secondary or ancillary functions, suggesting the core theme is transcription regulation with associated chromatin remodeling.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0015074","count":4},{"id":"GO:0043044","count":4},{"id":"GO:0045122","count":4},{"id":"GO:2001158","count":4}]},{"hash":"1706873487401888778","title":"DNA Metabolism and Programmed Cell Death with Innate Immunity","description":"Most terms relate to DNA metabolism (transposition, recombination, replication) and chromosome handling (mitotic spindle), with additional signals for ubiquitination and for apoptotic/pyroptotic and innate immune responses (including viral entry into the nucleus). Since there is no single cohesive complex, the cluster appears to span DNA metabolism and cell-death/immune pathways, hence the label.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006313","count":8},{"id":"GO:0006915","count":7},{"id":"GO:0006310","count":5},{"id":"GO:0016567","count":4},{"id":"GO:0090307","count":4}]},{"hash":"342666709075561757","title":"Lipid and Steroid Metabolism","description":"The top terms are dominated by lipid-related biosynthetic and metabolic processes (poly-hydroxybutyrate, very long-chain fatty acids, mycolic acids, 3-keto-sphinganine, retinol, and C21-steroid hormone metabolism), with a few outliers like transcription regulation and drug response. This points to a cohesive theme of lipid/steroid metabolism, including specialized microbial lipid pathways such as mycolic acid synthesis, making this an appropriate, specific cluster label.","confidence":"High","size":24,"edges":78,"triangles":102,"max_degree":14,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":24},{"id":"GO:0042619","count":24},{"id":"GO:0006710","count":22},{"id":"GO:0006666","count":22},{"id":"GO:0006355","count":22}]},{"hash":"1792317527593875643","title":"Fungal secondary metabolism and sporulation","description":"The GO terms point to fungal-specific processes: ascospore formation, antibiotic biosynthesis, and riboflavin biosynthesis all align with fungal secondary metabolism and development. Xylan catabolic activity also fits a fungal capability to degrade plant material, while transcription and basic metabolic regulation are broader but still contextual. Overall, the cluster seems centered on fungal metabolism and sporulation rather than a single straightforward pathway.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016311","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0045493","count":3},{"id":"GO:0045820","count":3},{"id":"GO:0017000","count":2}]},{"hash":"352001416901669376","title":"Aromatic compound catabolism","description":"The top GO terms are dominated by catabolic processes for aromatic compounds (3-phenylpropionate, stilbene, uracil) and the beta-ketoadipate pathway, with some biosynthetic terms (antibiotic, biotin) also present. This suggests the cluster centers on metabolism and breakdown of aromatic and related small molecules, hence a label focusing on aromatic compound catabolism is most representative.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0017000","count":14},{"id":"GO:0009102","count":13},{"id":"GO:0055114","count":11},{"id":"GO:0098869","count":10},{"id":"GO:0019380","count":9}]},{"hash":"609805156088593578","title":"Metabolic Biosynthesis Regulation","description":"Top terms show multiple biosynthetic processes (polyamine, lysine, pyrimidine, aflatoxin) and their positive regulation, plus regulation of cellular respiration and transcription in response to nitrogen status and a cadmium response. This points to a theme of how metabolism and secondary metabolism are regulated rather than a single pathway, justifying a label focused on biosynthesis regulation within metabolism.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046686","count":2},{"id":"GO:0006596","count":2},{"id":"GO:0045122","count":2},{"id":"GO:2001158","count":2},{"id":"GO:0043457","count":2}]},{"hash":"1071373434725984186","title":"Ubiquitin-regulated Wnt and immune signaling","description":"The cluster is enriched for protein deubiquitination and both positive and negative regulation of canonical Wnt signaling, plus multiple immune signaling pathways (T cell receptor, Fc-epsilon receptor, TNF) and antigen processing. These terms together point to a cohesive role for ubiquitin-dependent control of signaling cascades, especially Wnt, with broader involvement in immune signaling.","confidence":"Medium","size":24,"edges":266,"triangles":1821,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":11},{"id":"GO:0090090","count":7},{"id":"GO:0051436","count":7},{"id":"GO:0050852","count":7},{"id":"GO:0090263","count":7}]},{"hash":"2214098110112447474","title":"DNA replication and innate immune/apoptotic responses","description":"This cluster shows enrichment in DNA metabolic processes (recombination, integration, replication) and cell-cycle-related activity (mitotic spindle assembly) alongside innate immune and apoptotic pathways (including pyroptosis and ubiquitination), suggesting a group of proteins linked to DNA processing and programmed cell death with immune signaling, possibly connected to proviral latency mechanisms.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":5},{"id":"GO:0006915","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0015074","count":4},{"id":"GO:0006260","count":4}]},{"hash":"1825363758622205548","title":"Host factors in viral replication and immune response","description":"Top GO terms repeatedly point to viral processes (viral life cycle, virion assembly, viral release from host cell) and to immune cell dynamics (leukocyte migration). This suggests a cluster of host proteins that participate in viral infection and immune response, possibly regulatory or structural factors co-opted by viruses. Additional terms like DNA-templated transcription and protein peptidyl-prolyl isomerization reflect general cellular machinery broadly involved during infection; a few unrelated terms may reflect annotation noise but do not override the central theme. ","confidence":"Medium","size":24,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0019076","count":2},{"id":"GO:0050900","count":2},{"id":"GO:2000276","count":2},{"id":"GO:0034389","count":2}]},{"hash":"1141185914351558304","title":"Unknown","description":"The top GO terms span transcription regulation, Golgi retention, vesicle formation, cell division, translation, autophagy, endocytosis, and other broad cellular processes. With 0 edges/triangles and no cohesive function linking the terms, there isn\u2019t a single interpretable theme for this cluster. Therefore, the label Unknown with None confidence.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032968","count":3},{"id":"GO:0045053","count":3},{"id":"GO:0043457","count":2},{"id":"GO:0070676","count":2},{"id":"GO:0051301","count":2}]},{"hash":"931373881623598524","title":"Filopodium and lamellipodium assembly","description":"The cluster is dominated by GO terms for actin-based protrusion formation (microspike, filopodium, lamellipodium assemblies) and related signaling (Rho) and adhesion-dependent spreading, pointing to actin cytoskeleton remodeling and protrusive structure formation as the core function. Some terms are obsolete or less directly related, but the main signal supports this theme.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030035","count":4},{"id":"GO:0046847","count":4},{"id":"GO:0060124","count":3},{"id":"GO:1904424","count":3},{"id":"GO:0043552","count":3}]},{"hash":"1104641819400583034","title":"Post-transcriptional RNA Processing and Decay","description":"The cluster is dominated by RNA metabolism: mRNA processing, decay (NMD, decapping), and miRNA-mediated silencing with stress granule localization, pointing to post-transcriptional regulation of gene expression as the common theme.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043085","count":2},{"id":"GO:0030420","count":2},{"id":"GO:0006351","count":2},{"id":"GO:1903608","count":1},{"id":"GO:0000184","count":1}]},{"hash":"1387936910146596384","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000492","count":1},{"id":"GO:0006338","count":1},{"id":"GO:0031063","count":1},{"id":"GO:0048254","count":1},{"id":"GO:0033617","count":1}]},{"hash":"2182347012659655783","title":"Dopamine metabolism and chemical stress responses","description":"The cluster is driven by dopamine-related terms (dopamine catabolic process; positive regulation of dopamine metabolic process), suggesting a dopamine-centered module. Several \"response to\" terms indicate exposure to chemicals and stressors (xenobiotic stimulus, ethanol, corticosterone, aluminum ion), pointing to chemical/xenobiotic handling as a shared function. A metabolic term (thiamine biosynthetic process) appears but does not override the main dopamine-chemical-response theme. Together, these terms imply a cluster of proteins involved in dopamine metabolism with broader chemical exposure responses.","confidence":"Medium","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":10},{"id":"GO:0043046","count":10},{"id":"GO:0042420","count":9},{"id":"GO:0042135","count":9},{"id":"GO:0042493","count":9}]},{"hash":"1094895589194431730","title":"Ribosome Core and Translation Regulation","description":"The proteins cluster around ribosome function and translation: translation itself, initiation/termination, ribosome assembly/disassembly, and even selenocysteine incorporation. The antibiotic response term further supports a ribosome-centric theme, as many antibiotics target the ribosome. This makes \u201cRibosome Core and Translation Regulation\u201d an appropriate, representative label.","confidence":"High","size":23,"edges":253,"triangles":1771,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":22},{"id":"GO:0046677","count":5},{"id":"GO:0000027","count":3},{"id":"GO:0006413","count":3},{"id":"GO:0032790","count":3}]},{"hash":"999405280949724330","title":"Redox Metabolism and Stress Response","description":"This cluster is driven by multiple redox- and metabolism-related terms (oxidative/reduction processes, oxidant detoxification, redox homeostasis, 2-oxoglutarate metabolism) alongside diverse metabolic activities (nitrate assimilation, antibiotic biosynthesis, tRNA wobble modification, uracil catabolism). The common thread appears to be cellular metabolism with emphasis on redox balance and stress-related responses, rather than a single narrow function.","confidence":"Medium","size":23,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":10},{"id":"GO:0002098","count":7},{"id":"GO:0017000","count":6},{"id":"GO:0042128","count":5},{"id":"GO:0009409","count":4}]},{"hash":"1514850889677242729","title":"Seed coat lipid biosynthesis and phenylpropanoid metabolism","description":"This cluster is enriched for fatty acid biosynthesis and transport (including very long and long-chain FA), seed coat development, and phenylpropanoid metabolism, suggesting plant seed lipid production and lignin/phenolic pathways. An outlier term on nonribosomal peptide activation does not alter the overall theme.","confidence":"High","size":23,"edges":85,"triangles":110,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1902987","count":6},{"id":"GO:0006633","count":6},{"id":"GO:0043041","count":5},{"id":"GO:0000038","count":5},{"id":"GO:0010214","count":5}]},{"hash":"1730476014496863780","title":"Multi-Substrate Catabolism","description":"The cluster shows a spectrum of catabolic processes across amino acids, sugars, fatty acids, and small molecules (e.g., threonine to glycine, galactose, glucose, sorbitol, formaldehyde), with some accompanying stress-response terms (lipopolysaccharide and copper ion). This suggests proteins involved in broad degradation pathways rather than a single pathway. ","confidence":"High","size":23,"edges":143,"triangles":548,"max_degree":18,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0019518","count":6},{"id":"GO:0032496","count":6},{"id":"GO:0033498","count":5},{"id":"GO:0000947","count":5},{"id":"GO:0019595","count":5}]},{"hash":"795826086397700568","title":"Neuronal signaling and development regulators","description":"This cluster centers on regulation of signaling pathways tied to neural development and function, including hippocampus development, axonogenesis regulation, calcium-dependent exocytosis, and JNK signaling, with supporting cues from Wnt signaling and dopamine response. An immune signaling term (T cell receptor pathway) appears as a less central anchor, but the dominant theme is neural signaling and development regulation.","confidence":"Medium","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090263","count":8},{"id":"GO:1903351","count":6},{"id":"GO:0043552","count":6},{"id":"GO:0045956","count":6},{"id":"GO:0050852","count":6}]},{"hash":"1397835812388976104","title":"Transmembrane transport of metabolites and cofactors","description":"The cluster is dominated by GO terms for transporting nutrients and cofactors across membranes, including phosphate, nitrate, thiosulfate, citrate, deoxynucleotides, thiamine pyrophosphate, and pyridoxal phosphate. There are also related mitochondrial transport and membrane potential terms, supporting a cohesive theme of membrane-associated transport processes for small molecules and cofactors. This makes a concise, precise label: transmembrane transport of metabolites and cofactors.","confidence":"High","size":23,"edges":13,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":9},{"id":"GO:0042128","count":6},{"id":"GO:0070542","count":6},{"id":"GO:0051881","count":5},{"id":"GO:0015709","count":5}]},{"hash":"1782595382951546888","title":"Oxidative phosphorylation","description":"This cluster\u2019s top GO terms are dominated by mitochondrial electron transport (NADH to ubiquinone) and proton-motive force\u2013driven ATP synthesis, indicating oxidative phosphorylation as the core function. Some RNA processing terms are present but are less frequent and may reflect annotation noise or additional roles; the main signal is energy production in mitochondria.","confidence":"Medium","size":23,"edges":242,"triangles":1549,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0006120","count":2},{"id":"GO:0043280","count":2},{"id":"GO:0099132","count":2},{"id":"GO:0015986","count":2},{"id":"GO:0031053","count":1}]},{"hash":"904915069356226568","title":"Ubiquitin-Mediated Apoptosis and Innate Immunity","description":"These proteins are dominated by GO terms related to ubiquitination, apoptosis, pyroptosis, and innate immune responses, with additional, less central hints of DNA replication and cell cycle processes. The strongest shared theme appears to be ubiquitin-dependent regulation of cell death and inflammatory/immune signaling, rather than a single structural function. Thus, the label reflects the core functional cluster: ubiquitin-mediated regulation of apoptosis and innate immunity.","confidence":"High","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0016567","count":22},{"id":"GO:0090307","count":22},{"id":"GO:0006915","count":22},{"id":"GO:0045087","count":22},{"id":"GO:1990001","count":22}]},{"hash":"1135216187416801396","title":"Developmental and stress-induced apoptotic signaling","description":"These proteins cluster around apoptosis-related processes tied to development and cellular stress, including ER stress\u2013driven intrinsic apoptosis, neuron and glial apoptotic pathways, TGF-beta signaling, and ubiquitination. The presence of DNA repair and cell cycle terms suggests integration with DNA damage responses during development, supporting a cohesive theme of programmed cell death in stressed developmental contexts.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071560","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0070059","count":2},{"id":"GO:0000724","count":2},{"id":"GO:0007584","count":2}]},{"hash":"688571477820871714","title":"Germline RNA Silencing and Spermatogenesis Regulation","description":"The top GO terms point to miRNA- and ncRNA-mediated post-transcriptional gene silencing, plus germline stem cell maintenance, regulation of stem cell proliferation, and spermatid development. This suggests a functional cluster centered on RNA silencing mechanisms in the germline and their link to germline development and spermatogenesis. Some terms are obsolete, but the core signal is coherent around RNA-based regulation in germline cells.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035278","count":3},{"id":"GO:0000335","count":2},{"id":"GO:0007286","count":2},{"id":"GO:0030718","count":2},{"id":"GO:1901224","count":2}]},{"hash":"1506776911871533619","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0072553","count":1},{"id":"GO:0010048","count":1},{"id":"GO:0031442","count":1},{"id":"GO:0021529","count":1}]},{"hash":"1485601737651830849","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006336","count":1},{"id":"GO:0010923","count":1},{"id":"GO:0035042","count":1},{"id":"GO:0034589","count":1},{"id":"GO:0006068","count":1}]},{"hash":"930995258328498858","title":"Nuclear envelope and chromatin organization","description":"These proteins show GO terms centered on chromatin organization, nuclear pore complex assembly, mitotic nuclear membrane reassembly, and related transport processes, suggesting a nuclear-structure/transport\u2013focused cluster. While there are some outlier terms (e.g., ABA response, taste perception), the dominant signals relate to nuclear organization and nuclear\u2013membrane transport. The lack of strong interconnections among members means the label is the best-fit broad theme, with moderate confidence.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006336","count":1},{"id":"GO:0010923","count":1},{"id":"GO:0035042","count":1},{"id":"GO:0051292","count":1},{"id":"GO:0032596","count":1}]},{"hash":"885514987549746479","title":"Muscle cytoskeleton and integrin signaling","description":"The cluster centers on actin cytoskeleton dynamics and muscle-related functions: integrin-mediated signaling points to cell-ECM adhesion, while terms like positive regulation of skeletal muscle tissue growth, negative regulation of muscle relaxation, microspike and terminal web assembly, and even mitotic contractile ring actin filament bundle assembly all tie to actin-based structures and force generation in muscle and epithelial contexts. This suggests a cohesive theme of muscle cytoskeleton organization with adhesion signaling.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007229","count":2},{"id":"GO:2000009","count":1},{"id":"GO:0048633","count":1},{"id":"GO:1903033","count":1},{"id":"GO:1903477","count":1}]},{"hash":"1785479444703162282","title":"Unknown","description":"This cluster lists GO terms from several unrelated areas\u2014transposable-element activity (retrotransposition, DNA integration), osmotic and water balance (osmotic stress, intracellular water homeostasis, ion transport), lipid and ubiquinone metabolism (lipid homeostasis, tocopherol cyclase, ubiquinone biosynthesis), and even neuronal development (Purkinje cell layer morphogenesis). The lack of a single coherent functional theme and no connecting edges among members suggests the proteins do not share a common biological role, so a specific functional label is not supported.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032197","count":2},{"id":"GO:0015074","count":2},{"id":"GO:0071470","count":2},{"id":"GO:0009992","count":2},{"id":"GO:0034220","count":2}]},{"hash":"648530784733345056","title":"Developmental signaling and trafficking","description":"Top terms cluster around developmental processes (spinal cord and retina development, pigmentation) and intracellular transport/signaling (ER-to-Golgi vesicle transport, GTPase activity regulation, GPCR signaling). This suggests a theme of developmental programs tied to vesicle trafficking and signaling; some terms about translation and rRNA processing may reflect multi-functionality but do not override the main pattern.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0006888","count":4},{"id":"GO:0021510","count":4},{"id":"GO:0007568","count":4},{"id":"GO:0043473","count":4}]},{"hash":"354975168159709182","title":"Auxin transport and signaling","description":"The Top Terms include three plant-specific auxin processes: auxin export across the plasma membrane, auxin polar transport, and auxin-activated signaling pathway, pointing to a plant auxin transport/signaling module. Other terms (L-threonine biosynthesis, methionine salvage, RNA methylation, phosphorylation, antibiotic response, SREBP signaling) appear broader or unrelated, suggesting some background signals or multifunctional proteins. Overall, the cluster seems best described by auxin transport/signaling, with moderate confidence given the mixed functions.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009088","count":3},{"id":"GO:0016310","count":3},{"id":"GO:0019509","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0019284","count":3}]},{"hash":"2057531480795457612","title":"Neuronal Proteostasis and Stress Response","description":"This cluster is dominated by ubiquitin-dependent degradation terms (SCF-dependent proteasomal proteolysis, ubiquitin-dependent proteolysis, and protein polyubiquitination), indicating a core focus on proteostasis through the ubiquitin\u2013proteasome system. The presence of neuron-related stress and damage terms (neuronal apoptotic signaling under oxidative stress), along with chemical stress responses (heavy metals) and circadian regulation, suggests a cohesive theme of neuronal protein quality control coupled to stress response rather than a single signaling pathway.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":8},{"id":"GO:0042787","count":7},{"id":"GO:0031571","count":6},{"id":"GO:0060386","count":6},{"id":"GO:1903378","count":6}]},{"hash":"1220350843441834341","title":"Diverse membrane transporters","description":"The top GO terms center on transmembrane transport of a wide range of substrates (ions, sugars, vitamins) and related vesicular transport, indicating a cluster of transporter proteins with broad substrate specificity.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":3},{"id":"GO:0015739","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0015751","count":2},{"id":"GO:0098700","count":2}]},{"hash":"115510885693225669","title":"Membrane Transporters for Xenobiotics and Nutrients","description":"The terms cluster around transmembrane transport of diverse substrates, especially xenobiotics (xenobiotic transmembrane transport, xenobiotic export, doxorubicin transport), vitamins, osmolytes (glycine betaine, taurine), ions (potassium), and lipids (ceramide), plus Type I secretion system\u2013related protein secretion. This indicates a cohesive group of membrane transport proteins with broad substrate scope, including xenobiotics and nutrients.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006855","count":22},{"id":"GO:0035461","count":22},{"id":"GO:0042891","count":13},{"id":"GO:0071805","count":12},{"id":"GO:0030253","count":12}]},{"hash":"576106778623640892","title":"Chromatin remodeling and transcriptional regulation","description":"The cluster is enriched for chromatin remodeling and transcription regulation terms (chromatin remodeling, negative regulation of transcription by RNA Pol II, histone modification), with additional links to nucleosome positioning/density and DNA methylation signals. The presence of spindle assembly and centrosome cycle hints at a mitotic context, suggesting these proteins coordinate chromatin state with cell division. Overall, this cluster likely represents chromatin-based epigenetic regulation of gene expression, especially during mitosis.","confidence":"High","size":22,"edges":103,"triangles":208,"max_degree":20,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":10},{"id":"GO:0043044","count":8},{"id":"GO:0051225","count":8},{"id":"GO:0007098","count":8},{"id":"GO:0098532","count":8}]},{"hash":"362636318216866305","title":"Developmental growth and cell cycle control","description":"Enrichment for developmental processes (skeletal system development, liver development) together with cell-cycle activities (cell division, mitotic cell cycle) and transcription suggests a cluster centered on growth and tissue formation. Additional terms point to signaling and cellular logistics (TGF-beta response, lipopolysaccharide response, ER-to-Golgi transport, potassium homeostasis) that support proliferation and differentiation. Overall, this cluster likely represents proteins involved in developmental growth and regulation of the cell cycle, with supporting secretory and transcriptional functions.","confidence":"Medium","size":22,"edges":14,"triangles":6,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001501","count":6},{"id":"GO:0051301","count":6},{"id":"GO:0030007","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0007568","count":4}]},{"hash":"1174818255126285417","title":"Vacuolar acidification and ion homeostasis","description":"The top GO terms cluster around vacuole organization/targeting to vacuole, vacuolar acidification, and proton transmembrane transport, along with sodium ion and other ion homeostasis. This combination strongly suggests a core function in vacuolar proton pumping and maintenance of ion gradients (e.g., V-ATPase\u2013driven processes). A couple of unrelated nuclear RNA processing terms appear marginally, but the dominant signal is vacuolar function and ion regulation.","confidence":"High","size":22,"edges":136,"triangles":357,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0007033","count":2},{"id":"GO:0006623","count":2},{"id":"GO:0015991","count":2},{"id":"GO:0006626","count":2},{"id":"GO:0006814","count":2}]},{"hash":"1135828027049422537","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":81,"triangles":57,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0016554","count":2},{"id":"GO:1905639","count":2},{"id":"GO:0031426","count":2},{"id":"GO:0090617","count":2},{"id":"GO:0080156","count":2}]},{"hash":"2107061558230367453","title":"Ubiquitination-Linked Cell Death and Innate Immunity","description":"The cluster centers on ubiquitination, mitotic spindle assembly, apoptosis, and pyroptotic/inflammatory responses, pointing to a coherent theme where ubiquitin signaling regulates both cell division and programmed cell death within an innate immune context. Minor terms like mRNA decay and DNA repair are present but far less represented, suggesting they are not primary drivers of this cluster\u2019s function.","confidence":"High","size":22,"edges":116,"triangles":242,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":18},{"id":"GO:0090307","count":18},{"id":"GO:0006915","count":18},{"id":"GO:0045087","count":18},{"id":"GO:1990001","count":18}]},{"hash":"1395568426323959798","title":"Ribosome biogenesis and RNA splicing regulation","description":"This cluster shows strong signals for ribosome biogenesis and maturation of rRNA, plus multiple spliceosome-related RNA processing and splicing regulatory terms, plus translation. The shared theme is RNA metabolism linked to ribosome assembly and mRNA processing/translation control, justifying a combined label.","confidence":"Medium","size":22,"edges":147,"triangles":655,"max_degree":17,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":8},{"id":"GO:0000398","count":4},{"id":"GO:0031047","count":3},{"id":"GO:0000462","count":3},{"id":"GO:0042273","count":3}]},{"hash":"223769826098320096","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0000209","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000447","count":2}]},{"hash":"166827253487497180","title":"Mitotic spindle and chromosome segregation","description":"The dominant GO terms point to mitosis and spindle function: mitotic cell cycle, attachment of spindle microtubules to the kinetochore, and sister chromatid biorientation, with positive regulation of microtubule polymerization. While there are chromatin-related and DNA repair terms present (histone deubiquitination, RITS complex assembly, mismatch repair), the clearest pattern across the terms is mitotic spindle dynamics and chromosome segregation.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016578","count":1},{"id":"GO:1904802","count":1},{"id":"GO:0043569","count":1},{"id":"GO:0051987","count":1},{"id":"GO:1990758","count":1}]},{"hash":"1436582479264396631","title":"Unknown","description":"The GO terms include DNA transposition/integration (mobility) and arginyl/glycyl tRNA aminoacylation (translation) with only one hit per term and no network edges, suggesting two unrelated processes. Because there is no cohesive functional theme across the 22 proteins, a single interpretable label cannot be assigned.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006313","count":1},{"id":"GO:0015074","count":1},{"id":"GO:0006420","count":1},{"id":"GO:0006426","count":1}]},{"hash":"1653121042973492701","title":"Proteostasis and Neuronal Stress Response","description":"The cluster shows strong enrichment for ubiquitin-dependent protein catabolism and proteasomal degradation (SCF complex\u2013related and general ubiquitination), along with stress-related processes such as oxidative-stress\u2013induced neuronal apoptotic signaling, DNA damage checkpoints, and metal ion responses. This suggests a coherent theme of protein homeostasis under cellular stress, particularly in neuronal contexts, with some links to circadian regulation. ","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":8},{"id":"GO:0042787","count":7},{"id":"GO:0031571","count":6},{"id":"GO:0060386","count":6},{"id":"GO:1903378","count":6}]},{"hash":"306698438526431981","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019380","count":2},{"id":"GO:0010124","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0042493","count":2}]},{"hash":"1926693961218051347","title":"Retinoic Acid Signaling and Development","description":"Dominant GO terms are retinol and retinal metabolic processes and cellular response to retinoic acid, indicating a core retinoid signaling theme. The inclusion of developmental terms for nose and pancreas suggests this cluster may reflect retinoic acid\u2013driven developmental programs across tissues, with additional signaling and metabolic context (e.g., cAMP response). A few terms like GABA shunt and the obsolete arginine catabolic term are less central or possibly annotation artifacts. Overall, the cluster appears to represent retinoic acid\u2013related metabolism and signaling with developmental roles.","confidence":"High","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":20},{"id":"GO:0042574","count":20},{"id":"GO:0071300","count":19},{"id":"GO:0006540","count":19},{"id":"GO:0031016","count":19}]},{"hash":"1204164132987935989","title":"Multisystem Development and Organogenesis","description":"The terms point to developmental roles across multiple tissues: heart development, Schwann cell development, and angiogenesis, plus visual perception, indicating organogenesis and tissue differentiation. The presence of DNA-templated transcription suggests regulatory control driving these developmental programs. Overall, a cohesive multisystem development theme emerges rather than a single pathway.","confidence":"High","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0055114","count":8},{"id":"GO:0046826","count":8},{"id":"GO:0014850","count":7},{"id":"GO:0007275","count":7}]},{"hash":"1867606717316303696","title":"Mitochondrial Transport and Membrane Potential Regulation","description":"The top terms point to transport of a variety of metabolites and ions across mitochondrial membranes (phosphate, citrate, thiamine pyrophosphate, pyridoxal phosphate, manganese, deoxynucleotides, thiosulfate), along with regulation of mitochondrial membrane permeability and membrane potential, and a response to oxidative stress. This suggests a cohesive function centered on mitochondrial transport and ion/redox regulation within the organelle.","confidence":"High","size":21,"edges":98,"triangles":200,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":12},{"id":"GO:0046902","count":11},{"id":"GO:0051881","count":10},{"id":"GO:0015709","count":10},{"id":"GO:0031921","count":10}]},{"hash":"610194753828777697","title":"Mitochondrial translation and Fe-S cluster biogenesis","description":"The dominant signal is mitochondrial-related translation and rRNA maturation (translation, SSU rRNA maturation) alongside mitochondrial inner membrane and respiratory assembly processes (cristae formation, ATP synthase assembly, proton-motive force\u2013driven ATP synthesis). Fe-S cluster assembly and iron homeostasis terms further indicate maturation of Fe-S proteins, a key mitochondrial cofactor biogenesis pathway that often accompanies translation and respiratory complex assembly. Together, these terms point to a cohesive mitochondrial module focusing on ribosome function, rRNA processing, Fe-S biogenesis, and respiratory complex biogenesis.","confidence":"High","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0015986","count":2},{"id":"GO:0016226","count":1},{"id":"GO:0097428","count":1},{"id":"GO:0009399","count":1}]},{"hash":"2243292667839906952","title":"Skeletal Muscle Calcium Signaling and Oxidative Stress Response","description":"The top GO terms center on calcium handling and contraction in skeletal muscle (regulation of calcium release and ryanodine receptor activity) together with oxidative stress responses (redox homeostasis, oxidant detoxification, arsenic response, toxin catabolism) and DNA repair. This suggests a cohesive cluster of proteins involved both in calcium-mediated muscle contraction and cellular defense against oxidative/detox stress, with some broader metabolic links. Confidence in this label is high due to the strong calcium signaling/muscle contraction signals paired with detox and redox terms.","confidence":"High","size":21,"edges":202,"triangles":1189,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0014810","count":18},{"id":"GO:0071243","count":18},{"id":"GO:0009072","count":18},{"id":"GO:0019852","count":18},{"id":"GO:0045454","count":18}]},{"hash":"2164694137529198814","title":"Calcium-Driven Signaling and Trafficking","description":"This cluster centers on calcium-dependent signaling and vesicle trafficking between the ER and Golgi (calcium detection; calcineurin-NFAT pathway; ER-Golgi transport), with related themes in cytoskeletal remodeling and developmental transitions (EMT, actomyosin assembly) and cell cycle regulation. An outlier term (lipid A biosynthesis) likely reflects annotation noise, but the core pattern is calcium-mediated signaling linked to membrane trafficking.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009245","count":5},{"id":"GO:0070940","count":4},{"id":"GO:0051533","count":4},{"id":"GO:0006888","count":3},{"id":"GO:0050774","count":3}]},{"hash":"294599538220634336","title":"Apoptosis and innate immune signaling","description":"This cluster is enriched for apoptotic and inflammatory terms (apoptotic process, pyroptotic inflammatory response, innate immune response) and protein ubiquitination, suggesting a set of proteins involved in death signaling and immune activation. The presence of mitotic spindle assembly and chromatin methylation terms indicates some dispersion into cell cycle and epigenetic regulation, but the strongest shared signal relates to apoptosis/inflammation rather than a single pathway.","confidence":"Medium","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":5},{"id":"GO:0016567","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0045087","count":3},{"id":"GO:1990001","count":3}]},{"hash":"1834214046867161658","title":"Synaptic vesicle exocytosis regulation","description":"The cluster's terms center on regulated vesicle trafficking and secretion, including regulation of synaptic vesicle exocytosis, calcium-dependent exocytosis, and ER-Golgi transport, with brain development and protein localization to the plasma membrane supporting a neuronal vesicle-traffic theme.","confidence":"High","size":21,"edges":5,"triangles":0,"max_degree":4,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:2000300","count":6},{"id":"GO:0031384","count":6},{"id":"GO:0007420","count":6},{"id":"GO:0010796","count":6},{"id":"GO:0043497","count":5}]},{"hash":"1725814254313611129","title":"Developmental signaling and cytoskeleton regulation","description":"The top GO terms cluster around signaling pathways (cellular response to TGF-beta, ephrin receptor signaling, positive regulation of GTPase and tyrosine phosphorylation, and IP3 biosynthesis) and cytoskeletal control (barbed-end actin filament capping), with developmental processes such as cranial skeletal development and B cell differentiation also represented. This suggests a cohesive theme of signal transduction guiding development and cytoskeletal dynamics, with lipid catabolism playing a less central role among the terms.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009395","count":4},{"id":"GO:0071560","count":3},{"id":"GO:0051016","count":3},{"id":"GO:0050731","count":3},{"id":"GO:0043547","count":3}]},{"hash":"211304682318747504","title":"RNA silencing and chromosome condensation","description":"This cluster is driven by RNA regulatory processes: miRNA-mediated gene silencing, regulatory ncRNA-mediated post-transcriptional silencing, translation reinitiation, and mRNA splice site recognition. It also includes meiotic and mitotic chromosome condensation and regulation of meiotic DSB formation, suggesting a link between RNA-based regulation and chromosome dynamics during cell division. Peripheral terms like TORC1 signaling and tRNA gene clustering are present but less central to the core theme.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":3},{"id":"GO:0035278","count":2},{"id":"GO:0038202","count":2},{"id":"GO:0016246","count":2},{"id":"GO:0070058","count":2}]},{"hash":"2043288478828458973","title":"Multi-tissue Development Signaling","description":"The GO terms span development across tissues (muscle, tubule morphogenesis, analia development) and signaling pathways (cAMP response, B cell receptor signaling, pro-T cell differentiation), suggesting a broad set of proteins involved in general developmental processes and signaling rather than a single cohesive pathway. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051591","count":3},{"id":"GO:0050853","count":3},{"id":"GO:0045497","count":2},{"id":"GO:0072156","count":2},{"id":"GO:0045496","count":2}]},{"hash":"474756378058841196","title":"Cortical neuron migration and microtubule dynamics","description":"This cluster centers on cerebral cortex development and neuron migration, with several microtubule-related processes (nucleation, centrosome duplication/separation, vesicle transport along microtubules, retrograde axonal transport) and centrosome activities, suggesting a group of proteins coordinating cortical neuron positioning and cytoskeletal transport.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021987","count":1},{"id":"GO:0007020","count":1},{"id":"GO:0051298","count":1},{"id":"GO:0001764","count":1},{"id":"GO:0008090","count":1}]},{"hash":"25019074074721457","title":"Unknown","description":"The top GO terms are heterogeneous, including ether lipid biosynthesis, chromatin localization, CAAX-box protein processing, negative regulation of mitochondrial fusion, nuclear envelope organization, and cell wall modification, with few shared functions tying the proteins together. The lack of a cohesive theme and absence of network connections make it inappropriate to assign a specific, salient label to this cluster.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008611","count":2},{"id":"GO:0071169","count":2},{"id":"GO:0030327","count":1},{"id":"GO:0010637","count":1},{"id":"GO:0071432","count":1}]},{"hash":"1318363297790808111","title":"Bacterial energy metabolism and biosynthesis","description":"The top GO terms cluster around central carbon metabolism and energy production in bacteria: TCA cycle and oxaloacetate metabolism, fatty acid beta-oxidation, multiple amino acid catabolic pathways (valine, lysine) and aromatic compound catabolism (phenylacetate). Quinone biosynthesis (phylloquinone, menaquinone) points to electron transport components, while antibiotic biosynthetic process hints at secondary metabolite production. The presence of a regulatory term (response to cAMP) supports coordinated metabolic regulation. Together, these terms reflect a cohesive metabolic energy production and biosynthesis theme rather than a single narrow function.","confidence":"High","size":20,"edges":189,"triangles":1122,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":9},{"id":"GO:0033512","count":7},{"id":"GO:0006107","count":6},{"id":"GO:0006635","count":6},{"id":"GO:0010124","count":6}]},{"hash":"345823711860929025","title":"Hormone biosynthesis and metabolic signaling","description":"The top GO terms point to steroid hormone biosynthesis (C21-steroid), retinoid/retinal metabolism, thyroid hormone response, and norepinephrine metabolism, all anchored by signals like PI3K/AKT regulation and peptide-responsive cellular signaling. This suggests a cohesive theme around endocrine/metabolic processes and hormone-responsive pathways, rather than a single narrow function, warranting a label centered on hormone biosynthesis and metabolic signaling.","confidence":"Medium","size":20,"edges":190,"triangles":1140,"max_degree":19,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0042572","count":13},{"id":"GO:0042574","count":12},{"id":"GO:0055114","count":11},{"id":"GO:0046370","count":11},{"id":"GO:0051897","count":10}]},{"hash":"749654176070034730","title":"Bacterial metabolism, metal transport, and sporulation","description":"The cluster includes multiple bacterial-related processes: nitrate assimilation, denitrification, copper/iron/arsenate ion transport, sporulation with FtsZ-dependent cytokinesis, and broader metabolic/secondary metabolism activities (antibiotic biosynthesis, lignin catabolic process). These terms point to a cohesive theme of bacterial nutrient processing and environmental response, including metal ion handling and sporulation, rather than a single specialized pathway. Confidence: Medium","confidence":"","size":20,"edges":13,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":11},{"id":"GO:0042128","count":8},{"id":"GO:0017000","count":7},{"id":"GO:0046274","count":6},{"id":"GO:0043093","count":6}]},{"hash":"1517729777930423707","title":"Steroid and Lipid Metabolism","description":"The cluster\u2019s top GO terms indicate lipid and steroid processing (androgen metabolic process, testosterone biosynthetic process, triglyceride metabolic process, response to fatty acid) alongside energy-production processes (aerobic respiration, proton transmembrane transport), which together point to a metabolic/mitochondrial context. Some terms like DNA-templated transcription and kidney development seem less central, possibly reflecting broader cellular roles. Overall, the dominant signal is lipid/steroid metabolism linked to mitochondrial energy production.","confidence":"Medium","size":20,"edges":22,"triangles":3,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0051289","count":3},{"id":"GO:0070542","count":3},{"id":"GO:0009060","count":3},{"id":"GO:1902600","count":3},{"id":"GO:0010193","count":2}]},{"hash":"1961511151895479103","title":"Neural development and axon growth","description":"This cluster is dominated by neural development and axon-related processes (axonogenesis, hippocampus and Schwann cell development, axon extension), with associated signaling (dopamine response, calcium-dependent exocytosis, JNK cascade). A few terms (DNA replication, T cell signaling) are less representative. ","confidence":"High","size":20,"edges":9,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":18},{"id":"GO:1903351","count":16},{"id":"GO:0045956","count":16},{"id":"GO:0050852","count":16},{"id":"GO:0033138","count":16}]},{"hash":"557887776264464731","title":"DNA replication and cell cycle regulation","description":"The top terms cluster around DNA replication, mitotic cell cycle, and cell division, with positive regulation of nuclear processes and the centrosome cycle, indicating involvement in replication machinery and cell-cycle control. Additional terms like SOS response and histone exchange reflect chromatin/damage-related context, and potassium ion transport appears less central. Overall, the dominant theme is cell-cycle progression and DNA replication.","confidence":"High","size":20,"edges":15,"triangles":2,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0000278","count":6},{"id":"GO:0046827","count":6},{"id":"GO:0051301","count":5},{"id":"GO:0006813","count":5}]},{"hash":"826950945492734546","title":"Unknown","description":"The top GO terms cover a broad set of regulatory processes across signaling, cytoskeleton, chromatin, and development, with no single shared function tying all 20 proteins together.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071560","count":2},{"id":"GO:0051016","count":2},{"id":"GO:0000747","count":2},{"id":"GO:0050731","count":2},{"id":"GO:0030702","count":2}]},{"hash":"1146325847353988945","title":"Innate immune signaling and transcription regulation","description":"This cluster is dominated by terms tied to innate immune signaling (NOD1 pathway, macrophage-related differentiation, chemokine and MIP-1 alpha production) and transcription/chromatin processes (DNA-templated transcription, nucleosome assembly). A few development-related terms appear but the immune signaling and transcription themes best unify the set.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006334","count":2},{"id":"GO:0018230","count":1},{"id":"GO:0021707","count":1},{"id":"GO:0048733","count":1}]},{"hash":"630509749238457553","title":"Membrane transporters for diverse substrates","description":"The top GO terms indicate transport across membranes for a wide range of substrates (sialic acid, phosphate ions, potassium and sodium ions, arabinose, fucose, xenobiotics) and even vesicular loading of neurotransmitters, pointing to a cluster of membrane transporter proteins with varied substrate specificity rather than a single substrate focus.","confidence":"High","size":20,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":3},{"id":"GO:0035435","count":3},{"id":"GO:0006004","count":3},{"id":"GO:0006855","count":3},{"id":"GO:0071805","count":3}]},{"hash":"1328056051661887172","title":"Unknown","description":"The top GO terms are scattered across lipid metabolism, nuclear envelope organization, transcription, immune signaling, and diverse developmental processes (left-right patterning, cartilage morphogenesis, placental and pancreatic development, EMT). There is no clear shared function or pathway linking these proteins, so a specific label cannot be inferred. ","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071072","count":1},{"id":"GO:1903740","count":1},{"id":"GO:0006998","count":1},{"id":"GO:0042797","count":1},{"id":"GO:0032728","count":1}]},{"hash":"377002345204924673","title":"Transposons and Proviral Integration","description":"The terms point to mobile genetic elements: DNA transposition, retrotransposition, DNA integration, proviral latency, and plasmid maintenance, with viral/symbiont entry into host cells. This suggests a cohesive theme around transposable elements and proviral integration, despite some general housekeeping terms present.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006364","count":1},{"id":"GO:0006313","count":1},{"id":"GO:0075732","count":1},{"id":"GO:0032197","count":1},{"id":"GO:0015074","count":1}]},{"hash":"985193782900851415","title":"Developmental Translational Initiation Regulation","description":"The proteins dominate terms related to translation initiation (formation of translation preinitiation complex, cytoplasmic translational initiation, and negative regulation of translational initiation) alongside developmental processes (in utero embryonic development, ovarian follicle development, oligodendrocyte development, presynapse assembly). This suggests a cluster centered on developmental programs that are tightly coordinated by translational control. Some broader terms like energy homeostasis and germ cell proliferation fit into developmental contexts but do not outweigh the core theme of translational initiation regulation in development.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001701","count":2},{"id":"GO:1905696","count":1},{"id":"GO:0001541","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0002183","count":1}]},{"hash":"427614629282783959","title":"Membrane Transport of Ions and Small Molecules","description":"The top GO terms are dominated by various forms of transmembrane transport (sodium, potassium, phosphate, arabinose, sialic acid, xenobiotics) and a vesicle-related term (neurotransmitter loading into synaptic vesicle), suggesting the proteins function together in transporting ions and small molecules across membranes, with vesicle-mediated transport also represented. A few metabolism-related terms appear but do not override the clear transport-focused signal.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":5},{"id":"GO:0035435","count":5},{"id":"GO:0006004","count":5},{"id":"GO:0006855","count":5},{"id":"GO:0071805","count":5}]},{"hash":"2181630425662409716","title":"Cell Cycle and Ribosome Biogenesis","description":"The dominant GO terms are cell cycle and cell division, plus ribosome biogenesis, which together point to proliferative growth and increased protein synthesis as the core function of this cluster. A few incidental terms related to stress responses, DNA integration, and antibiotic biosynthesis appear but do not define the primary theme. Therefore the label reflects the central biology of the group.","confidence":"High","size":20,"edges":2,"triangles":0,"max_degree":1,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0007049","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0042220","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0042254","count":3}]},{"hash":"716607848544437279","title":"Skeletal Muscle Differentiation and Transcription","description":"The top GO terms point to DNA-templated transcription and skeletal muscle cell differentiation, with supporting terms like skeletal muscle fiber development and activation of protein kinase activity. Although several unrelated terms appear (plants, flower development, viral latency), the strongest signals consistently relate to transcriptional regulation and muscle differentiation, suggesting this cluster centers on muscle development programs governed by transcriptional activity.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0035914","count":2},{"id":"GO:0032147","count":1},{"id":"GO:1902064","count":1},{"id":"GO:0072156","count":1}]},{"hash":"103126934985889985","title":"Immune and Developmental Signaling","description":"The GO terms point to inflammatory/immune pathways (NF-kappaB activation, IL-8 production, apoptotic processes) alongside diverse developmental annotations (lung, cartilage, insect cuticle/ecdysis, and mechanosensing). This suggests a mix of stress-related signaling rather than a single cohesive function, so a broad label like immune and developmental signaling captures the shared theme with moderate confidence.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070317","count":2},{"id":"GO:0030324","count":1},{"id":"GO:0018990","count":1},{"id":"GO:0007250","count":1},{"id":"GO:0072606","count":1}]},{"hash":"8452934788495180","title":"Nutrient-Responsive Transcription and RNA Methylation","description":"The cluster centers on transcription regulation in response to nutrient cues (nitrogen catabolite activation and carbon-source\u2013responsive transcription) along with RNA modification activities (rRNA and tRNA methylation). There are additional links to nucleotide biosynthesis and various catabolic processes, suggesting a coordinated module tying transcriptional control to RNA modification and metabolism. Confidence: Medium","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0070476","count":6},{"id":"GO:0009236","count":6},{"id":"GO:0030488","count":6},{"id":"GO:2001158","count":6}]},{"hash":"2155489451642146439","title":"Ubiquitin-Proteasome Regulation & Cell Cycle","description":"The top GO terms are dominated by ubiquitination and proteasomal degradation (protein polyubiquitination, ubiquitin-dependent protein catabolic process, SCF-dependent proteasomal degradation) and regulation of DNA replication initiation and G1 checkpoint signaling, pointing to control of the cell cycle via ubiquitin pathways. While a few terms touch circadian rhythm and synapse assembly, the central theme is proteostasis through the ubiquitin\u2013proteasome system and its impact on cell cycle regulation. This makes the label a focused, representative interpretation of the cluster\u2019s function.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060386","count":6},{"id":"GO:0000083","count":6},{"id":"GO:1902916","count":6},{"id":"GO:0042752","count":6},{"id":"GO:0000209","count":6}]},{"hash":"1664292411724631724","title":"Unknown","description":"The top GO terms form a scattered mix of carbohydrate metabolism (galactose, sorbitol, inositol catabolic) and transcriptional regulation (negative regulation of transcription by RNA polymerase II), with many obsolete annotations. There are no edges connecting proteins, so no shared function emerges. This cluster is best labeled Unknown.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006012","count":1},{"id":"GO:0043433","count":1},{"id":"GO:0006061","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0019310","count":1}]},{"hash":"658747512838684538","title":"Transcriptional Regulation of Metabolic Pathways","description":"The terms cluster around DNA-templated transcription and positive regulation of transcription from RNA polymerase II, with mentions of nutrient- and signal-responsive regulation (nitrogen catabolite activation, oleic acid-induced transcription). They also include various biosynthetic and catabolic processes (lysine biosynthesis, pyrimidine biosynthesis, proline and urea catabolism, aflatoxin biosynthesis), suggesting a theme where transcriptional control coordinates metabolic pathways. This supports a coherent label focused on transcriptional regulation linked to metabolism.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0045122","count":1},{"id":"GO:2001158","count":1},{"id":"GO:0043457","count":1},{"id":"GO:1904741","count":1}]},{"hash":"138775414104605093","title":"Small-molecule catabolism","description":"Top GO terms are dominated by catabolic processes for diverse small molecules (ketone, monosaccharide, glycerol, nucleotides, and related small compounds) with a nearby cellular response term; the common theme appears to be the breakdown/metabolism of varied organic substrates rather than a single pathway, justifying the label as small-molecule catabolism. Some regulatory terms are present but do not define the cluster's main function.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042182","count":1},{"id":"GO:0039534","count":1},{"id":"GO:0046365","count":1},{"id":"GO:0097237","count":1},{"id":"GO:0046835","count":1}]},{"hash":"1280136297192752001","title":"Ubiquitin-Dependent Protein Degradation & ERAD","description":"The top GO terms are dominated by ubiquitin-related processes: ubiquitin-dependent proteolysis, multiple linkage-specific deubiquitination (K48, K63, K11), and ERAD-related pathways, with additional notes on monoubiquitination and trafficking to endosomes/vacuoles. DNA replication and repair terms may reflect ubiquitin\u2019s role in genome maintenance, suggesting a cohesive theme of ubiquitin-mediated protein turnover and quality control.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006511","count":2},{"id":"GO:0070536","count":2},{"id":"GO:0035871","count":2},{"id":"GO:0071108","count":2},{"id":"GO:0000012","count":2}]},{"hash":"684629208841799621","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":120,"triangles":348,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0070365","count":7},{"id":"GO:0045984","count":7},{"id":"GO:0006207","count":7},{"id":"GO:0019240","count":7},{"id":"GO:0071400","count":7}]},{"hash":"670422795453325550","title":"Cerebellar development and cell-cycle regulation","description":"This cluster shows strong signals for cerebellar neural development, including cerebellar cortex formation and Bergmann glial cell differentiation, suggesting a focus on cerebellar development. It also includes cell cycle control terms (G1/S transition, negative regulation of cyclin-dependent kinase activity, and negative regulation of cell proliferation), indicating coordination between proliferation and differentiation in neural progenitors. Some signaling terms (insulin and T cell receptor signaling) are present but do not define the main theme. Overall, the core theme appears to be cerebellar development with linked cell-cycle regulation.","confidence":"Medium","size":19,"edges":171,"triangles":969,"max_degree":18,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045736","count":11},{"id":"GO:0050852","count":11},{"id":"GO:2001275","count":11},{"id":"GO:0034501","count":11},{"id":"GO:0060020","count":11}]},{"hash":"909562144783381061","title":"Xenobiotic Detoxification and Lipid Metabolism","description":"The top GO terms cluster around processing xenobiotics (insecticide metabolism, organofluorine metabolism, coumarin catabolic process) and lipid-related oxidation (fatty acid omega-oxidation), suggesting a functional group focused on detoxification and lipid metabolism. Additional terms about inflammation regulation and cell adhesion may reflect linked pathways or dataset noise, but the core signal points to xenobiotic and lipid metabolic activities.","confidence":"Medium","size":19,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0017143","count":17},{"id":"GO:0010760","count":17},{"id":"GO:0070365","count":17},{"id":"GO:0090350","count":17},{"id":"GO:0071603","count":17}]},{"hash":"698049111745926408","title":"Mitotic spindle assembly and chromosome segregation","description":"This cluster is dominated by GO terms related to cell cycle, cell division, microtubule nucleation/organization, kinetochore localization, and spindle pole body duplication, pointing to proteins involved in mitotic spindle function and chromosome segregation. Some overlap with DNA replication reflects broader cell-cycle coordination.","confidence":"High","size":19,"edges":85,"triangles":159,"max_degree":17,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007049","count":7},{"id":"GO:0051301","count":7},{"id":"GO:0030182","count":6},{"id":"GO:0007020","count":6},{"id":"GO:1903087","count":6}]},{"hash":"1527944314508565044","title":"Unknown","description":"The top terms show a mix of lipid metabolism (ergosterol biosynthesis, unsaturated fatty acid biosynthesis, sphingolipid metabolism), nitrogen/oxidative processes (oxidation-reduction, nitric oxide biosynthetic process, nitrate assimilation), and differentiation/development signals (retinoic acid response, CNS myelin maintenance, sebaceous gland differentiation), plus mitochondrial inheritance. This lack of a single unifying biological theme makes it unclear what functional label best represents the cluster. ","confidence":"","size":19,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006809","count":2},{"id":"GO:0000001","count":2},{"id":"GO:0032286","count":2},{"id":"GO:0042128","count":2}]},{"hash":"1244758485799250638","title":"N-terminal and polyamine acetylation","description":"The top GO terms cluster around acetylation processes: multiple N-terminal peptidyl acetylations (serine, glutamic acid, methionine) and polyamine acetylation (spermidine, spermine), including melatonin biosynthesis via acetyltransferases. This points to acetyltransferase enzymes and acetylation pathways as the core function of the group, with a few outliers likely reflecting broader enzyme roles.","confidence":"High","size":19,"edges":152,"triangles":687,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0017198","count":18},{"id":"GO:0060358","count":17},{"id":"GO:0032918","count":17},{"id":"GO:0019491","count":17},{"id":"GO:0071962","count":17}]},{"hash":"1325421377998620926","title":"Xenobiotic metabolism and immune-vascular regulation","description":"The cluster includes several detoxification-related terms such as insecticide metabolism, organofluorine metabolism, coumarin catabolic process, and fatty acid omega-oxidation, alongside immune and vascular regulation terms like negative regulation of macrophage chemotaxis, negative regulation of chronic inflammatory response, and endothelial cell-cell adhesion. This combination suggests a theme around xenobiotic/lipid metabolism coupled with immune-vascular regulatory functions, rather than a single narrow pathway. ","confidence":"Medium","size":19,"edges":16,"triangles":1,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0017143","count":2},{"id":"GO:0010760","count":2},{"id":"GO:0070365","count":2},{"id":"GO:0090350","count":2},{"id":"GO:0071603","count":2}]},{"hash":"1730539655171207156","title":"TGF-\u03b2/BMP signaling regulation","description":"The top GO terms cluster around modulation of transforming growth factor beta (TGF-\u03b2) and bone morphogenetic protein (BMP) pathways, including negative regulation of BMP signaling and TGF-\u03b2 receptor signaling, plus cellular responses to TGF-\u03b2. There is also related phosphatase activity (peptidyl-threonine dephosphorylation) and connections to broader signaling networks (e.g., NF-\u03baB). While some plant- or development-specific terms appear, the dominant theme is regulation of TGF-\u03b2/BMP signaling, suggesting this label best represents the cluster\u2019s function.","confidence":"High","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042006","count":4},{"id":"GO:0035970","count":4},{"id":"GO:0030514","count":4},{"id":"GO:0000173","count":4},{"id":"GO:0042347","count":4}]},{"hash":"2071125778567147204","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":113,"triangles":385,"max_degree":17,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":12},{"id":"GO:0048026","count":12},{"id":"GO:0071038","count":10},{"id":"GO:0071051","count":10},{"id":"GO:0071042","count":10}]},{"hash":"1430171888263055777","title":"Retroviral integration and latency","description":"The GO terms cluster around retroviral processes: DNA replication/recombination, DNA integration, and establishment of proviral latency, plus viral entry into the host nucleus and RNA-templated DNA biosynthesis (reverse transcription). These collectively point to the retroviral life cycle and provirus maintenance, with some host interaction signals (e.g., modulation of RNA silencing). Therefore, the label Retroviral integration and latency captures the principal function of this cluster.","confidence":"High","size":19,"edges":8,"triangles":0,"max_degree":3,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":11},{"id":"GO:0006260","count":11},{"id":"GO:0075732","count":9},{"id":"GO:0015074","count":9},{"id":"GO:0046718","count":9}]},{"hash":"1037855089743309241","title":"Proteolysis and peptide metabolism cluster","description":"The strongest shared function among the proteins is proteolytic processing and peptide regulation, as reflected by GO terms for general and membrane proteolysis, protein autoprocessing, digestion, and amyloid-beta metabolism via APP biosynthesis regulation. While a couple of terms relate to heart development or behavior, the prominent proteolysis-related annotations best unify this cluster.","confidence":"Medium","size":19,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0060347","count":2},{"id":"GO:0002803","count":2},{"id":"GO:0016540","count":2},{"id":"GO:0042756","count":2},{"id":"GO:0006508","count":2}]},{"hash":"207677930421215068","title":"Retroelement Transposition and Proviral Latency","description":"This cluster is dominated by GO terms for retrotransposition, DNA transposition, DNA integration, and establishment of integrated proviral latency, pinpointing proteins involved in mobilizing and integrating genetic elements and maintaining proviral states. The inclusion of viral/symbiont entry and host apoptosis terms suggests interactions between transposable/proviral elements and host cells, consistent with provirus activation and latency dynamics. While some terms touch broader signaling pathways (TORC1, TGF-beta), the core theme centers on transposable elements and proviral latency.","confidence":"High","size":19,"edges":48,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0032197","count":3},{"id":"GO:0015074","count":3},{"id":"GO:0006313","count":2},{"id":"GO:0075732","count":2},{"id":"GO:0046718","count":2}]},{"hash":"2279361464126935915","title":"mRNA splicing, export, and translation initiation","description":"The GO terms are centered on mRNA processing (splicing, splice site recognition, alternative splicing, poly(A) tail regulation), mRNA export from the nucleus, and translation initiation/reinitiation, with an additional note on ncRNA-mediated gene silencing. This pattern suggests a cohesive module coordinating mRNA maturation and early steps of translation. ","confidence":"High","size":19,"edges":45,"triangles":72,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":3},{"id":"GO:0002188","count":2},{"id":"GO:0006376","count":2},{"id":"GO:0060211","count":2},{"id":"GO:0000380","count":2}]},{"hash":"1004059106470546642","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0071951","count":1},{"id":"GO:0006413","count":1},{"id":"GO:0033320","count":1}]},{"hash":"934060944805701274","title":"Transcriptional Regulation and Apoptosis","description":"The most represented terms point to regulation of transcription by RNA polymerases I and II and transcription elongation, with additional references to translational fidelity and apoptosis signaling. This suggests a functional theme centered on gene expression control coupled with cellular stress/apoptotic responses, rather than a single enzymatic activity. While some terms are obsolete or indirect, the shared thread appears to be transcriptional regulation linked to cell fate decisions.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045943","count":1},{"id":"GO:0045903","count":1},{"id":"GO:0032786","count":1},{"id":"GO:1904788","count":1},{"id":"GO:0071619","count":1}]},{"hash":"1778737158105619984","title":"Diverse membrane sugar and ion transporters","description":"GO terms indicate a collection of proteins involved in transmembrane transport of a variety of substrates, including sugars (sialic acid, arabinose, galactose, fucose), ions (potassium, phosphate), vitamins, and other metabolites, as well as processes like neurotransmitter loading into vesicles. This points to a cohesive theme of membrane transport activity across different substrates, rather than a single specific pathway. Therefore, the cluster is best described as Diverse membrane sugar and ion transporters. ","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":1},{"id":"GO:0071805","count":1},{"id":"GO:0042128","count":1},{"id":"GO:0015751","count":1},{"id":"GO:0098700","count":1}]},{"hash":"2305390181063705227","title":"Unknown","description":"The top GO terms across the proteins cover several distinct biological areas: vacuole fusion, ion transport, sphingolipid/ceramide biosynthesis, neurotransmitter reuptake, collagen synthesis, neuromuscular control, and even fungal response. This spread suggests no single cohesive function or pathway linking the cluster, making a concise, representative label unreliable.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042144","count":2},{"id":"GO:0035435","count":2},{"id":"GO:0046513","count":1},{"id":"GO:0051935","count":1},{"id":"GO:1905045","count":1}]},{"hash":"1347459160500173133","title":"Neural development and cocaine response","description":"This cluster is dominated by neural- and brain-related GO terms (cerebellar cortex development, hippocampus development, brain development) and a behavioral response to cocaine, suggesting a focus on neural development processes and cocaine-associated behavior. Some unrelated terms (e.g., cell cycle) appear but do not override the brain-development signal. ","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055129","count":2},{"id":"GO:0007095","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0048148","count":2},{"id":"GO:0007507","count":2}]},{"hash":"1729629190614320812","title":"Bacterial catabolic metabolism and quinone biosynthesis","description":"The GO terms cluster around multiple catabolic processes for varied substrates (mandelate, galactonate, glucarate, amino acids) and enzymes involved in biosynthesis of quinones (phylloquinone, menaquinone), pointing to a broad metabolic program in bacteria rather than a single pathway. An outlier term (DNA integration) exists, but the dominant theme is metabolism.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":2},{"id":"GO:0019596","count":1},{"id":"GO:0019394","count":1},{"id":"GO:0034194","count":1},{"id":"GO:0016998","count":1}]},{"hash":"1662805642551694894","title":"Developmental Regulation and Organ Stress Responses","description":"The terms cluster around transcriptional regulation, developmental processes (heart development, liver regeneration, cardiac hypertrophy under stress), and broader signaling/modulation of cellular activities (cell division, kinase activity), suggesting proteins that participate in developmental signaling and organ stress responses. Some outliers (IgA isotype switching, cellulose catabolic process) may reflect annotation noise rather than a coherent functional theme, so the label is a cautious generalization rather than a precise, single pathway.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045944","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0006469","count":2},{"id":"GO:0097421","count":2},{"id":"GO:0014898","count":2}]},{"hash":"287400440720770462","title":"Angiogenesis and vascular development","description":"This cluster is dominated by vascular-related terms: labyrinthine layer blood vessel development and angiogenesis (both 6), pointing to a primary theme of blood vessel formation, possibly in the labyrinthine region. Other terms reflect broader regulatory and signaling contexts (Wnt, transcription, cell cycle, exocytosis, dopamine response, T cell signaling) but do not override the vascular focus. ","confidence":"Medium","size":18,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060716","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0001525","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0006349","count":5}]},{"hash":"538567483851681106","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":151,"triangles":784,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":6},{"id":"GO:2001295","count":5},{"id":"GO:0042759","count":5},{"id":"GO:0051591","count":4},{"id":"GO:0006546","count":4}]},{"hash":"1071615806945143159","title":"Core Metabolism and Translation","description":"The cluster shows a mix of fundamental cellular processes, including various metabolic biosynthesis/catabolic activities, cytoplasmic translation, cell division, and stress-related regulatory steps. This pattern points to broad, housekeeping cellular functions rather than a single specific pathway, so a concise label like Core Metabolism and Translation captures the common theme. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0055114","count":9},{"id":"GO:0051301","count":5},{"id":"GO:0009228","count":5},{"id":"GO:0008203","count":4},{"id":"GO:0015945","count":4}]},{"hash":"32254148971123681","title":"Gene Expression and RNA Processing","description":"The top GO terms cluster around transcription, RNA modification (guanine-N7 methylation), rRNA maturation, and translation reinitiation, suggesting a core theme of gene expression machinery and RNA processing. Some terms (vesicle transport and GPCR signaling) are less connected to this core, but the strongest signals point to transcription/translation and RNA maturation processes.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0036265","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0016049","count":2},{"id":"GO:0070212","count":2}]},{"hash":"105156425159274201","title":"Polysaccharide and cell-surface biosynthesis","description":"This cluster is dominated by GO terms for biosynthesis of glycans and cell-surface components: lipopolysaccharide core and O-antigen, colanic acid, galactose, GDP-mannose, and ADP-L-glycero-beta-D-manno-heptose biosynthetic processes, plus poly-hydroxybutyrate biosynthesis. These terms point to carbohydrate polymer and envelope component assembly, with a few plant-specific biosynthetic terms appearing as outliers. Overall, the theme is carbohydrate and cell-surface biosynthesis.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0042619","count":5},{"id":"GO:0009244","count":3},{"id":"GO:0006012","count":3},{"id":"GO:0080110","count":3}]},{"hash":"703515141382168318","title":"Nutrient-Driven Transcriptional Regulation","description":"This cluster centers on transcriptional regulation from RNA polymerase II promoters in response to nutrient status (carbon and nitrogen sources), including nitrogen catabolite activation and carbon-source\u2013dependent transcription. It also includes regulation of various metabolic and secondary metabolism processes (proline, urea, GABA catabolism, pyrimidine biosynthesis, and aflatoxin biosynthesis), suggesting a cohesive theme of nutrient-responsive transcriptional control, particularly in fungi. Confidence: Medium.","confidence":"","size":18,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:2001158","count":6},{"id":"GO:0001080","count":6},{"id":"GO:1901714","count":6},{"id":"GO:1900399","count":6}]},{"hash":"106066805163457073","title":"Gene Expression and Energy Metabolism","description":"The cluster combines gene expression processes (DNA-templated transcription and translation) with energy-related activities (photosynthesis, nonphotochemical quenching, mitochondrial electron transport, proton transport), plus assorted metabolic and catabolic processes. This suggests a cohesive theme around cellular energy production linked to gene expression, despite some diverse substrate-specific pathways. ","confidence":"Medium","size":18,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0042203","count":1},{"id":"GO:0010196","count":1}]},{"hash":"700023695135551226","title":"RNA processing and translation regulation","description":"The top GO terms cluster around mRNA processing and metabolism (splicing via spliceosome, splice site recognition, alternative splicing, mRNA stability and poly(A) tail regulation) as well as translation initiation/reinitiation and regulatory ncRNA-mediated silencing. This pattern points to a group of proteins coordinating mRNA maturation with control of translation, rather than a single isolated function.","confidence":"High","size":18,"edges":35,"triangles":20,"max_degree":9,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1901407","count":10},{"id":"GO:0002188","count":9},{"id":"GO:0001731","count":9},{"id":"GO:0010610","count":9},{"id":"GO:0045292","count":9}]},{"hash":"725941366885570499","title":"DNA repair and ribosome biogenesis","description":"The cluster contains GO terms centered on DNA recombination, homologous recombination\u2013mediated repair, and gamma radiation\u2013related DNA damage response, plus DNA integration, suggesting a core theme of genome maintenance. It also includes translation and ribosome biogenesis terms, indicating concurrent protein synthesis activities. Overall, these functions point to DNA damage response together with ribosome biogenesis, though there is some breadth that could reflect additional cellular processes or host interactions.","confidence":"Medium","size":18,"edges":126,"triangles":478,"max_degree":17,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":3},{"id":"GO:0006412","count":3},{"id":"GO:1990414","count":2},{"id":"GO:0010569","count":2},{"id":"GO:0071480","count":2}]},{"hash":"1282829464274857844","title":"DNA Transposition and Retrotransposition Machinery","description":"This cluster is enriched for GO terms related to DNA transposition, retrotransposition, DNA integration, and RNA-templated DNA synthesis, with additional signals from DNA replication and recombination. Taken together, the terms point to proteins involved in genome mobility and maintenance, particularly transposon/retroelement\u2013associated processes.","confidence":"High","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006313","count":3},{"id":"GO:0070987","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0042276","count":2},{"id":"GO:0000060","count":2}]},{"hash":"1269549735826798237","title":"Glucose-Glycogen Metabolism and Nutrient Response","description":"The term set is dominated by glucose metabolism and glycogen-related processes (glucose metabolic process, positive regulation of glycogen catabolic process, glycophagy) and growth forms tied to nutrient limitation (invasive growth in response to glucose limitation, pseudohyphal growth), suggesting a theme of carbohydrate handling and energy management under scarcity. A few outliers (lens development, GPI anchor biosynthesis, bacillithiol biosynthesis) may be incidental annotations rather than core cluster features.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045819","count":2},{"id":"GO:0006006","count":2},{"id":"GO:0002088","count":2},{"id":"GO:0001403","count":2},{"id":"GO:0007124","count":2}]},{"hash":"364454766574963774","title":"Endomembrane Vesicle Trafficking","description":"This cluster is dominated by GO terms for vesicle transport within the secretory pathway, especially ER\u2013Golgi transport and endocytosis, plus protein targeting to vacuole, indicating a shared role in endomembrane trafficking and cargo routing. Some unrelated terms appear but do not override the central trafficking signal.","confidence":"Medium","size":18,"edges":15,"triangles":1,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006890","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0006623","count":2},{"id":"GO:0006897","count":2},{"id":"GO:0001824","count":1}]},{"hash":"729202174063725292","title":"RNA Pol II transcription machinery and protein quality control","description":"The cluster is dominated by RNA polymerase II\u2013related processes: transcription initiation, regulation, preinitiation complex assembly, and elongation regulation, indicating core transcription machinery involvement. Intersecting terms highlight proteostasis and chaperone-mediated protein assembly and ubiquitin-proteasome\u2013mediated quality control, suggesting a link between transcriptional control and protein folding/ turnover. A few terms about tubulin complex assembly and microtubule organization hint at broader cellular structure supporting transcription. Overall, the proteins likely participate in transcription regulation with supporting proteostasis mechanisms.","confidence":"Medium","size":18,"edges":8,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006457","count":1},{"id":"GO:0071629","count":1},{"id":"GO:0032968","count":1},{"id":"GO:0051131","count":1},{"id":"GO:0043622","count":1}]},{"hash":"1242241364482664404","title":"Eye pigment biosynthesis and vesicle trafficking","description":"The top GO terms cluster around eye pigmentation (ommochrome biosynthesis, eye pigmentation) and vesicle trafficking/docking (vesicle tethering, docking, Golgi to endosome/endosome to lysosome transport, intracellular transport), suggesting a group of proteins involved in pigment production linked to vesicle trafficking. A few terms appear unrelated (DNA integration, hyaluronan regulation), likely representing noise or multifunctionality, but the dominant signal ties pigmentation to vesicle transport.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":2},{"id":"GO:0006727","count":1},{"id":"GO:0099022","count":1},{"id":"GO:0006886","count":1},{"id":"GO:0006904","count":1}]},{"hash":"1350127336976062309","title":"Ion transport and homeostasis","description":"Most terms describe ion movement across membranes (sodium/potassium import/export, proton transport) and cellular ion/homeostasis (potassium ion homeostasis, cell volume regulation, salt-stress response). This coherence points to a membrane transport and ion balance function as the cluster\u2019s core, with one outlier signaling term that doesn\u2019t override the main theme.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098719","count":1},{"id":"GO:0097623","count":1},{"id":"GO:0031547","count":1},{"id":"GO:1903281","count":1},{"id":"GO:0009651","count":1}]},{"hash":"1202051080361248561","title":"Unknown","description":"The GO terms are diverse (transport, metabolism, ribosome assembly, transcription, proteolysis, antibiotic response) with no clear, single functional theme linking the proteins, so a cohesive label isn\u2019t supported.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902358","count":2},{"id":"GO:0006067","count":1},{"id":"GO:0061668","count":1},{"id":"GO:0009088","count":1},{"id":"GO:0016310","count":1}]},{"hash":"742434013117542910","title":"Ubiquitin-Proteasome Proteolysis in Neurons","description":"This cluster is dominated by GO terms for ubiquitin-dependent proteolysis and SCF-dependent proteasomal degradation, indicating a core theme of protein catabolism via the ubiquitin-proteasome system. The presence of neuron-related terms such as synapse assembly, plus stress-response terms (metal exposure, circadian regulation, oxidative stress\u2013induced apoptotic signaling), suggests the proteolytic activity is particularly relevant in neuronal contexts and stress conditions. Therefore, a concise label focusing on ubiquitin-mediated protein degradation in neurons captures the central function of the cluster.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":7},{"id":"GO:0031571","count":6},{"id":"GO:0042787","count":6},{"id":"GO:0060386","count":6},{"id":"GO:1903378","count":6}]},{"hash":"1956440771562903486","title":"Unknown","description":"The proteins map to highly diverse GO terms, including plant ABA signaling and seed dormancy, mitotic chromatid segregation, mitochondrial inner membrane protein insertion, apoptosis regulation, NF-kappaB signaling, ubiquitination, inner dynein arm assembly, and left-right developmental patterning. There is no clear, single functional theme across the cluster; the terms span stress signaling, cell division, organelle function, and development, making a unified label unreliable.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000070","count":2},{"id":"GO:0009738","count":1},{"id":"GO:0010231","count":1},{"id":"GO:0009789","count":1},{"id":"GO:0045039","count":1}]},{"hash":"973196489227574742","title":"Unknown","description":"The top GO terms span metabolism (TCA cycle), translation initiation and its regulation, oligodendrocyte development, and multiple stress and signaling responses (ethylene, nitric oxide, GTPase regulation), with no clear, shared function linking all proteins. This cluster therefore lacks a cohesive theme to label confidently.","confidence":"","size":17,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":4},{"id":"GO:0002183","count":3},{"id":"GO:0014003","count":3},{"id":"GO:0071369","count":3},{"id":"GO:0019509","count":3}]},{"hash":"85322742209336133","title":"Unknown","description":"The GO terms are spread across detoxification/metabolic processes (insecticide metabolism, organofluorine metabolism, coumarin catabolism, fatty acid omega-oxidation), immune regulation (negative regulation of macrophage chemotaxis and chronic inflammatory response), and diverse developmental/regulatory processes (hepatocyte differentiation, endothelial adhesion, uterus development, aldosterone-regulated blood volume). There isn't a single cohesive theme that ties these functions together, so a clear, specific cluster name isn\u2019t supported.","confidence":"","size":17,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0017143","count":17},{"id":"GO:0010760","count":17},{"id":"GO:0070365","count":17},{"id":"GO:0090350","count":17},{"id":"GO:0071603","count":17}]},{"hash":"1894345921100049801","title":"Xenobiotic Detox and Fatty Acid Metabolism","description":"The top GO terms are heavily weighted toward catabolic and metabolic processes for xenobiotics (camphor, coumarin, insecticide, organofluorine) and fatty acid omega-oxidation, which points to a detoxification and lipid-processing theme. While some terms touch on inflammation regulation or development, the dominant signal is xenobiotic metabolism coupled with fatty acid oxidation, suggesting a liver/endothelial-associated detox/metabolic cluster.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019383","count":17},{"id":"GO:0017143","count":16},{"id":"GO:0010760","count":16},{"id":"GO:0070365","count":16},{"id":"GO:0090350","count":16}]},{"hash":"1552694704017955671","title":"Detox metabolism and vascular inflammatory regulation","description":"The top GO terms cluster around detoxification/metabolism (insecticide metabolic process, coumarin catabolic process, organofluorine metabolism, fatty acid omega-oxidation) and vascular/immune regulation (endothelial cell\u2013cell adhesion, negative regulation of inflammatory responses and macrophage chemotaxis). Developmental terms like uterus development and hepatocyte differentiation are present but less central. Overall, the cluster seems to reflect a mix of metabolic detox pathways with regulatory roles in vascular/inflammatory contexts, hence this label. ","confidence":"Medium","size":17,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0060065","count":11},{"id":"GO:0017143","count":10},{"id":"GO:0010760","count":10},{"id":"GO:0070365","count":10},{"id":"GO:0090350","count":10}]},{"hash":"288390906465844931","title":"Lipid metabolism and redox signaling","description":"This cluster shows enrichment in lipid-related processes (prostaglandin biosynthesis, triglyceride metabolism, ergosterol biosynthesis regulation) and oxidative stress / redox responses (cellular oxidant detoxification, nitric oxide biosynthesis, ozone response). The presence of tissue-related lipid functions such as sebaceous gland differentiation and myelin maintenance supports a broader theme of lipid signaling and membrane biology. Overall, these terms suggest a cohesive theme around lipid metabolism coupled with redox signaling and environmental stress responses.","confidence":"Medium","size":17,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":4},{"id":"GO:0010193","count":3},{"id":"GO:0032094","count":3},{"id":"GO:0006641","count":3},{"id":"GO:0098869","count":3}]},{"hash":"1343119076135692976","title":"Unknown","description":"The proteins show a highly diverse set of GO terms, ranging from metabolic processes (glycogen and very long-chain fatty acid biosynthesis), transport (zinc and cadmium), transcription regulation, and various responses (antibiotic, methotrexate), with no single dominant theme. There are no edges or coherent groupings to tie them to one function, so a specific, representative label cannot be determined.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0005978","count":2},{"id":"GO:0071577","count":2},{"id":"GO:0070574","count":2}]},{"hash":"680304968893300324","title":"Mitochondrial metabolism and innate immune regulation","description":"The cluster includes mitochondrial translation and the TCA cycle, plus ribosome assembly, pointing to core energy metabolism and protein synthesis. It also shows links to innate immune signaling (RIG-I/MDA-5) and complement regulation, suggesting a link between metabolic state and immune pathway modulation.","confidence":"Medium","size":17,"edges":134,"triangles":651,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0070131","count":2},{"id":"GO:0055114","count":1},{"id":"GO:0006099","count":1},{"id":"GO:0030449","count":1},{"id":"GO:0051897","count":1}]},{"hash":"429201801215109547","title":"Ribosome Biogenesis and Cell Cycle","description":"The terms show strong enrichment for ribosome biogenesis and ribosomal export/translation, alongside cell-cycle related processes (cell cycle, cell division, septum assembly). This points to a module where ribosome assembly and protein synthesis are coordinated with cell-cycle progression, hence the combined label. ","confidence":"High","size":17,"edges":18,"triangles":2,"max_degree":16,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0007049","count":14},{"id":"GO:0051301","count":14},{"id":"GO:0000055","count":12},{"id":"GO:0042254","count":12},{"id":"GO:0090529","count":12}]},{"hash":"2037649576940684684","title":"Mitochondrial Energy Metabolism","description":"This cluster is dominated by GO terms tied to mitochondria and energy production: mitochondrial respiratory chain complex IV assembly, aerobic respiration, cytochrome complex assembly, mitochondrial electron transport (succinate to ubiquinone), and the TCA cycle. Together these indicate proteins involved in oxidative phosphorylation and central carbon metabolism. A few terms about cell wall biogenesis and chitin-based cuticle development appear, but they are few and likely reflect annotation noise or multifunctionality rather than a cohesive alternate function. Overall, the dominant theme is mitochondrial energy metabolism.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":2},{"id":"GO:0009060","count":1},{"id":"GO:0017004","count":1},{"id":"GO:0006121","count":1},{"id":"GO:0006099","count":1}]},{"hash":"1602986808521565992","title":"Pentose Phosphate Pathway and Nucleotide Salvage","description":"The top GO terms cluster around the pentose-phosphate shunt (oxidative branch) and related nucleotide salvage/biosynthesis processes (AMP salvage, purine nucleoside interconversion, FAD biosynthesis, and NAD-related catabolic processes), suggesting a metabolism-focused module centered on redox balance and nucleotide pool maintenance. A few terms like phosphorylation and cell cycle appear, but the dominant signal is PPP and nucleotide salvage.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":2},{"id":"GO:0006098","count":2},{"id":"GO:0009051","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0006747","count":2}]},{"hash":"2072911914837405383","title":"DNA Damage Response and Inflammatory Cell Death","description":"The proteins here are enriched for ubiquitination, DNA replication stress (SOS), apoptosis, and pyroptosis/inflammasome-related innate immunity, pointing to a shared role in coordinating cell-cycle checkpoints with inflammatory cell fate.","confidence":"Medium","size":17,"edges":18,"triangles":1,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0016567","count":10},{"id":"GO:0090307","count":10},{"id":"GO:0006915","count":10},{"id":"GO:0045087","count":10},{"id":"GO:1990001","count":10}]},{"hash":"110724888650187719","title":"Chromatin Regulation and Oxidative Stress Response","description":"The top GO terms cluster around heterochromatin formation/maintenance and rDNA heterochromatin, indicating chromatin organization, and alongside them are oxidative stress/detoxification terms (cellular oxidant detoxification, hydrogen peroxide\u2013mediated programmed cell death) plus metabolic regulation terms. This suggests a cohesive group of proteins involved in chromatin-based regulation coupled with cellular stress responses rather than a single pathway.","confidence":"Medium","size":17,"edges":24,"triangles":5,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060766","count":4},{"id":"GO:0045668","count":4},{"id":"GO:0098869","count":4},{"id":"GO:0030466","count":3},{"id":"GO:0006344","count":3}]},{"hash":"1695323166319287913","title":"Proteolysis and Protein Processing","description":"Based on the top terms, the strongest signal is proteolysis and protein processing: proteolysis, protein catabolic process, autoprocessing, and ERAD-related degradation. Additional terms like digestion and APP biosynthetic regulation align with protein processing pathways, while others (drinking behavior, xylan catabolism, aldosterone regulation) are broader physiological associations that may reflect distant links or annotation noise. Overall, the cluster is best described by a proteolysis/processing theme.","confidence":"High","size":17,"edges":40,"triangles":22,"max_degree":11,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0002803","count":4},{"id":"GO:0016540","count":4},{"id":"GO:0042756","count":4},{"id":"GO:0006508","count":4}]},{"hash":"1206390930519816403","title":"Posttranscriptional mRNA processing and translation control","description":"These proteins strongly feature GO terms for spliceosome-mediated splicing, splice site recognition, and regulation of alternative splicing, along with mRNA export and poly(A) tail regulation. They also include translation initiation/reinitiation steps and ncRNA-mediated silencing, indicating a cluster centered on posttranscriptional mRNA maturation and control of gene expression at the level of RNA processing and translation. The blastocyst formation term is less central but may reflect developmental contexts of these processes.","confidence":"High","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002188","count":1},{"id":"GO:0006376","count":1},{"id":"GO:0060211","count":1},{"id":"GO:0000380","count":1},{"id":"GO:0001825","count":1}]},{"hash":"1795347324320324872","title":"eIF5A-dependent Translation","description":"The top GO terms center on translation processes (initiation, elongation, termination, frameshifting) and peptidyl-hypusine biosynthesis, which is the modification required for eIF5A function in facilitating translation, especially on polyproline motifs. While there are minor terms for copper homeostasis and lipid acyl-chain remodeling, the dominant signal is translation machinery and its hypusination-dependent regulation, justifying the label focused on eIF5A-driven translation.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006878","count":2},{"id":"GO:1903272","count":1},{"id":"GO:0034050","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0045905","count":1}]},{"hash":"1084517711192918488","title":"Transcription Regulation and Kinase Signaling","description":"Top GO terms point to regulation of transcription (DNA-templated transcription; positive regulation of transcription by RNA polymerase II) and regulation of phosphorylation/kinase activity (positive regulation of peptidyl-serine phosphorylation; negative regulation of protein kinase activity), with additional hints of developmental and metabolic regulatory roles. This suggests a cohesive theme around controlling gene expression and signaling pathways, rather than a single enzymatic activity.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0045944","count":2},{"id":"GO:0033138","count":2},{"id":"GO:0044397","count":2},{"id":"GO:0035774","count":2}]},{"hash":"1163658600967061231","title":"Ubiquitin-Dependent Chromatin Regulation","description":"This cluster is dominated by GO terms related to ubiquitin signaling, especially deubiquitination of histones and regulation of ubiquitin ligase activity, as well as regulation of transcription and histone methylation. Although a single term hints at spliceosome assembly and CNS morphogenesis, the strongest common theme across the terms is ubiquitin-mediated control of chromatin state and transcription, with multiple entries pointing to deubiquitination and histone modification.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904667","count":2},{"id":"GO:0051569","count":2},{"id":"GO:0070537","count":1},{"id":"GO:0000245","count":1},{"id":"GO:0035520","count":1}]},{"hash":"1319465409814093646","title":"Unknown","description":"The listed GO terms cover development, transport, signaling, RNA processing, translation, and nuclear communication, with several obsolete annotations, and do not converge on a single cohesive function. This suggests the proteins participate in diverse roles or the terms reflect heterogeneous annotations, so no clear cluster-level function can be assigned.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021510","count":2},{"id":"GO:1904659","count":2},{"id":"GO:0007200","count":1},{"id":"GO:0000466","count":1},{"id":"GO:0006888","count":1}]},{"hash":"1884605056458155770","title":"Histone modification and chromatin regulation","description":"The top GO terms center on histone modification (H4-K16 acetylation, H3-K4 methylation) and nucleoplasm localization, pointing to a cluster of chromatin-regulating proteins. Development-related terms appear but are more ancillary; the dominant theme is chromatin modification and regulation of gene expression in the nucleus. Confidence: Medium.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043984","count":1},{"id":"GO:0001541","count":1},{"id":"GO:0040010","count":1},{"id":"GO:0048823","count":1},{"id":"GO:0080182","count":1}]},{"hash":"78794838284391900","title":"Chaperone-Mediated Protein Folding and QC","description":"The cluster is dominated by protein-folding and quality-control themes, with terms for protein folding (GO:0006457), cytoplasmic ubiquitin-proteasome\u2013mediated quality control (GO:0071629), and chaperone-mediated complex assembly (GO:0051131). Additional terms point to tubulin/microtubule assembly, suggesting a link between protein homeostasis and cytoskeletal maintenance, while transcription-related terms may reflect broader roles in gene-expression machinery. Overall, the core signal is chaperone-assisted protein folding and proteostasis with supporting cytoskeletal interactions.","confidence":"High","size":17,"edges":16,"triangles":1,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":2},{"id":"GO:0071280","count":2},{"id":"GO:0006457","count":2},{"id":"GO:0071629","count":2},{"id":"GO:0032968","count":2}]},{"hash":"71725430403590684","title":"Cell Cycle and Gene Expression Regulation","description":"The top GO terms cluster around mitotic processes (mitotic spindle checkpoint, mitotic cell cycle) and core gene expression control (DNA-templated transcription, mRNA processing), with supporting signals from ubiquitin ligase regulation and post-translational modification. This points to a cohesive theme of coordinating cell growth/division with transcriptional regulation; peripheral terms like amino acid starvation response and uterine gland development are less central but do not override the main pattern.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":2},{"id":"GO:0007094","count":2},{"id":"GO:0000278","count":2},{"id":"GO:1904667","count":2},{"id":"GO:0034198","count":2}]},{"hash":"524497160427965261","title":"Intracellular trafficking and transcription regulation","description":"The terms point to both vesicle transport between the ER and Golgi (secretory pathway) and multiple transcription-related processes (RNA polymerase II and I transcription, initiation, and nucleolus organization). This suggests a cluster spanning intracellular trafficking and gene expression regulation, though no single dominant function emerges. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0006366","count":2},{"id":"GO:2000142","count":1},{"id":"GO:0007000","count":1}]},{"hash":"1889130605918570681","title":"Ubiquitin-Proteasome\u2013Mediated Proteolysis Under Stress","description":"The cluster is dominated by GO terms for ubiquitin-dependent protein catabolic processes (SCF-dependent proteasomal degradation and polyubiquitination), indicating a proteostasis/ proteolysis focus. Additional terms point to stress responses to metals (cadmium, methylmercury) and DNA damage signaling, supporting a theme of proteasome-driven turnover linked to cellular stress, with some neuronal and circadian context as ancillary associations.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031571","count":6},{"id":"GO:1902916","count":6},{"id":"GO:0071276","count":6},{"id":"GO:0031146","count":6},{"id":"GO:0042787","count":5}]},{"hash":"2175369951056315272","title":"Cellular stress response and DNA repair","description":"The top GO terms cluster around cellular stress responses (amyloid-beta response, heat shock effects, oxidant detoxification) and genome maintenance (single-strand break repair, mtDNA replication regulation), suggesting a group of proteins involved in protecting cells from proteotoxic/oxidative stress and preserving DNA integrity. Despite no visible interactions in the data, the functional themes point to stress response and DNA repair as the core linkage.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904646","count":1},{"id":"GO:0090298","count":1},{"id":"GO:0006288","count":1},{"id":"GO:0008069","count":1},{"id":"GO:0035080","count":1}]},{"hash":"925002572698283020","title":"Viral entry, integration, and proviral latency","description":"This cluster's top GO terms cluster around viral infection processes: viral penetration into host nucleus, DNA integration, and establishment of integrated proviral latency, plus host-symbiont interaction terms like symbiont entry and symbiont-mediated activation of host apoptosis. A couple of terms about mitochondrial localization/fusion and vacuole targeting are less central but may reflect host trafficking contexts. Overall, the dominant theme is viral entry, genome integration, and latent proviral states.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006623","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0075732","count":2},{"id":"GO:0015074","count":2},{"id":"GO:0046718","count":2}]},{"hash":"438027230063185776","title":"Meiotic Chromosome Condensation and Segregation","description":"The top GO terms point to meiosis and chromosome dynamics, including meiotic cell cycle, meiotic chromosome condensation, and nuclear chromosome segregation, along with DNA replication and regulation of meiotic DSB formation. A few terms are obsolete or peripheral, but the dominant theme is meiotic chromosome maintenance and replication. The lack of network edges doesn\u2019t negate a cohesive functional group centered on meiotic chromosome structure and segregation.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990414","count":1},{"id":"GO:0051321","count":1},{"id":"GO:0061780","count":1},{"id":"GO:0010032","count":1},{"id":"GO:0070058","count":1}]},{"hash":"1631729974277889077","title":"Oxidative stress and vascular remodeling","description":"This cluster is dominated by redox-related terms (cellular oxidant detoxification, redox homeostasis) and by processes tied to vascular and tissue remodeling (negative regulation of vascular smooth muscle proliferation, negative regulation of fibroblast proliferation, animal organ regeneration), with additional calcium signaling (regulation of SR Ca2+ release) and related metabolic pathways (linoleic acid, nitrobenzene metabolism). The combination suggests a core theme around oxidative stress response coupled to remodeling and regeneration contexts in vascular/tissue settings, hence the label.","confidence":"Medium","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":12},{"id":"GO:0070527","count":11},{"id":"GO:0045454","count":11},{"id":"GO:2000255","count":11},{"id":"GO:0010880","count":10}]},{"hash":"50697169159801350","title":"Carbohydrate catabolism and sugar biosynthesis","description":"The top GO terms are all related to processing and transforming various carbohydrates and sugar-derived molecules, including tagatose-6-phosphate and lactose catabolism, ribose and fructose-related responses, adenosine salvage, and multiple sugar-nucleotide biosynthesis pathways (e.g., ADP-L-glycero-beta-D-manno-heptose, myo-inositol hexakisphosphate). This suggests a cohesive theme of carbohydrate metabolism spanning both catabolic and biosynthetic steps, rather than a single specific pathway. ","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006175","count":3},{"id":"GO:2001059","count":3},{"id":"GO:0009750","count":3},{"id":"GO:0006169","count":3},{"id":"GO:0010264","count":3}]},{"hash":"439870906719633043","title":"Ribosome biogenesis and mitotic regulation","description":"This cluster is enriched for ribosome biogenesis and translation terms (ribosome biogenesis, ribosomal small subunit biogenesis, translation, positive regulation of translation) alongside centrosome cycle and kinetochore localization, suggesting a link between ribosome production and cell cycle/mitotic machinery. The presence of transcription-related terms (DNA-templated transcription, transcription regulation by RNA Pol II) indicates concurrent nuclear gene expression control, which often accompanies cell cycle progression. Overall, the proteins likely participate in ribosome assembly and coordination with mitosis.","confidence":"High","size":16,"edges":32,"triangles":11,"max_degree":11,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0007098","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0045727","count":3},{"id":"GO:0006977","count":3}]},{"hash":"53703988045342581","title":"ER-Golgi vesicle trafficking and GTPase signaling","description":"The top GO terms point to ER-to-Golgi and Golgi-to-ER transport, endocytic recycling, and regulation of GTPase activity, with Rap signaling and TORC1-related growth cues. Together these suggest a cohesive cluster of proteins coordinating vesicle trafficking and GTPase-driven signaling that influences cell growth and mitotic progression. Subtelomeric heterochromatin formation appears as a less central motif, but does not override the trafficking/signaling theme.","confidence":"High","size":16,"edges":23,"triangles":7,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0006348","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0043547","count":2},{"id":"GO:1904263","count":2}]},{"hash":"1056812531408879769","title":"Mitochondrial Translation and PPP Metabolism","description":"The top GO terms cluster around mitochondrial tRNA aminoacylation (tRNA charging for tryptophan, tyrosine, valine) and both branches of the pentose phosphate shunt, suggesting a cohesive theme of mitochondrial protein synthesis linked to carbohydrate metabolism. Some terms on angiogenesis/vasculogenesis and an obsolete aging term seem unrelated to the core cluster and may reflect noise. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006098","count":3},{"id":"GO:0001525","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0070183","count":2},{"id":"GO:0070184","count":2}]},{"hash":"1307204032358198490","title":"Gene Expression and RNA Processing","description":"This cluster is dominated by GO terms tied to gene expression and RNA processing, including DNA-templated transcription, mRNA splicing, and rRNA maturation. The presence of histone methylation terms (chromatin modification) reinforces a nuclear, transcription-regulatory theme. A few terms such as translation reinitiation and ER-to-Golgi transport point to broader protein synthesis/trafficking roles, but the core signals are transcription, RNA maturation, and chromatin regulation, suggesting a cohesive theme around gene expression machinery.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0000398","count":4},{"id":"GO:0051568","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0034729","count":4}]},{"hash":"1764263946889245245","title":"Unknown","description":"The top GO terms are scattered across different developmental contexts (intestinal epithelium, seed, distal tubule morphogenesis, analia development) and membrane-related processes (ER\u2192Golgi transport, phospholipid translocation, GPI anchor biosynthesis) with one metabolic note (glutathione import). There is no clear, shared function tying these terms together, so a single cohesive label cannot be confidently assigned.","confidence":"","size":16,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0060576","count":1},{"id":"GO:0060628","count":1},{"id":"GO:0051515","count":1},{"id":"GO:0098709","count":1},{"id":"GO:0048316","count":1}]},{"hash":"2062439683759801179","title":"Developmental signaling and differentiation","description":"The proteins center on broad developmental processes, with enrichment in transcription (DNA-templated), mitosis, apoptosis, and signaling (notably Wnt), alongside tissue-specific differentiation events (neuronal/visual, muscle via myoblast fusion, skin via keratinocyte differentiation). This points to a general developmental regulatory program rather than a single, narrow function.","confidence":"Medium","size":16,"edges":117,"triangles":518,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0034351","count":7},{"id":"GO:0000278","count":6},{"id":"GO:0007601","count":6},{"id":"GO:0090263","count":6}]},{"hash":"1384352156561188830","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":105,"triangles":455,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000462","count":5},{"id":"GO:0000466","count":4},{"id":"GO:0000398","count":4},{"id":"GO:0000480","count":4},{"id":"GO:0042273","count":4}]},{"hash":"2286777242657753478","title":"Transcription Regulation and Development","description":"This cluster centers on transcriptional control (DNA-templated transcription; transcription regulation) intertwined with developmental and differentiation processes (neuronal maturation regulation, organ regeneration, cell-matrix adhesion, spindle-kinetochore dynamics). While some terms are obsolete, the prevailing theme is gene expression control linked to development and cell fate, with adjacent notes of cell-cycle and stress/ apoptosis pathways. ","confidence":"Medium","size":16,"edges":93,"triangles":286,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0014043","count":16},{"id":"GO:0007070","count":16},{"id":"GO:2000686","count":16},{"id":"GO:0060968","count":16},{"id":"GO:0051316","count":16}]},{"hash":"1397334842819657572","title":"Membrane Trafficking and Signaling Regulation","description":"The cluster centers on membrane transport and vesicle-related processes (proton transmembrane transport, vacuolar acidification, Cvt vesicle assembly, ERAD-related pathway) and on regulatory signaling and adhesion (Wnt signaling regulation, adherens junction assembly, cardiac action potential regulation), with developmental notes (medulla oblongata development). This suggests a cohesive theme of membrane trafficking coupled with signaling control affecting cell architecture and development.","confidence":"Medium","size":15,"edges":101,"triangles":406,"max_degree":14,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0015991","count":7},{"id":"GO:0007050","count":6},{"id":"GO:0007035","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0090090","count":5}]},{"hash":"474704603661578255","title":"N-terminal peptidyl methyltransferases","description":"These proteins are enriched for GO terms describing N-terminal peptidyl methylation (trimethylation/dimethylation) events on alanine, serine, and glycine, indicating a core function as N-terminal methyltransferases. While additional biosynthetic process terms appear, the dominant signal is specific methylation activity at the N-terminus, justifying this label.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018012","count":5},{"id":"GO:0035573","count":5},{"id":"GO:0035572","count":5},{"id":"GO:0018013","count":5},{"id":"GO:0017000","count":4}]},{"hash":"893229453515370027","title":"Nuclear transcriptional regulation and development","description":"Top terms emphasize nuclear transcription and regulation of nuclear export, with developmental signals (neuron maturation, organ regeneration) and mitotic spindle/kinetochore activity, suggesting the cluster represents nuclear gene expression control intertwined with development and cell division.","confidence":"Medium","size":15,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0034198","count":4},{"id":"GO:0046826","count":4},{"id":"GO:0014043","count":3},{"id":"GO:0007070","count":3}]},{"hash":"95351105312074350","title":"Cell Cycle Control and Autophagy with Modifications","description":"The cluster centers on cell cycle regulation (endomitotic cell cycle, regulation of cell cycle) and autophagy (mitophagy/autophagy), with supporting roles for post-translational modifications (sumoylation, lipidation) and transcription regulation, suggesting a coordinated cellular maintenance program linking division control with protein turnover and remodeling. Peripheral terms like defense responses and vitamin biosynthesis are less central but do not override the main theme.","confidence":"Medium","size":15,"edges":27,"triangles":18,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0007113","count":3},{"id":"GO:0051726","count":3},{"id":"GO:0002143","count":3},{"id":"GO:0050832","count":3},{"id":"GO:0045892","count":3}]},{"hash":"188718507316551607","title":"Viral genome integration and proviral latency","description":"This cluster is centered on processes of viral life cycle involving reverse transcription, DNA synthesis, integration into the host genome, and establishment of proviral latency (e.g., RNA-templated DNA synthesis, DNA integration, proviral latency, viral entry into the nucleus). Additional terms about host apoptosis and symbiont entry support a broader viral-host interaction theme. Together these point to retroviral-like integration and latency mechanisms.","confidence":"High","size":15,"edges":56,"triangles":97,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0006310","count":5},{"id":"GO:0075732","count":4},{"id":"GO:0015074","count":4},{"id":"GO:0046718","count":4}]},{"hash":"464271012052679225","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":2},{"id":"GO:0009116","count":1},{"id":"GO:0052704","count":1},{"id":"GO:0009113","count":1},{"id":"GO:0006048","count":1}]},{"hash":"1556794704497819327","title":"Unknown","description":"The top GO terms span unrelated processes (ERAD, GPCR signaling, rRNA maturation, ER-Golgi transport, translation reinitiation, splicing, chromatin methylation, mitochondria-nucleus signaling, and fertilization), with several terms obsolete, giving no single coherent theme. Therefore, a concise, representative label cannot be assigned.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0007200","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0002188","count":3}]},{"hash":"1911923687461035048","title":"Yeast filamentous growth and osmosensing","description":"The cluster centers on fungal morphogenesis and stress response: pseudohyphal/budding growth, cell polarity, multicellular development, and Sho1-mediated osmosensory signaling, which together drive filamentous/invasive growth under nutrient limitation and related membrane remodeling. Despite one outlier term (cocaine response), the core theme is yeast-like filamentous growth and osmotic sensing.","confidence":"High","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0061246","count":2},{"id":"GO:0007118","count":2},{"id":"GO:0001402","count":2},{"id":"GO:0048148","count":2}]},{"hash":"327294476983763075","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":4,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0090307","count":7},{"id":"GO:0016567","count":6},{"id":"GO:0006915","count":6},{"id":"GO:0045087","count":6},{"id":"GO:1990001","count":6}]},{"hash":"432327260886244099","title":"Unknown","description":"The top terms span multiple unrelated biological areas (respiratory system process, circadian gene regulation, renal sodium absorption, ureteric bud branching, pregnancy, aging, cell cycle progression, cell polarity, centrosome localization, and centromere clustering), with no clear shared function or pathway tying the proteins together. There are also no edges connecting proteins, supporting the lack of a cohesive theme. Therefore, there is no confident, representative label beyond Unknown.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003016","count":1},{"id":"GO:0032922","count":1},{"id":"GO:0070294","count":1},{"id":"GO:0090190","count":1},{"id":"GO:0007565","count":1}]},{"hash":"1491081607827061178","title":"Membrane Transporters: Ions and Sugars","description":"This cluster\u2019s GO terms cluster around transmembrane transport activities for ions (e.g., potassium, phosphate) and a range of sugars (sialic acid, arabinose, galactose, fucose), plus vesicle-associated neurotransmitter loading, suggesting a cohesive theme of membrane transport across substrates, despite no observed network connectivity. The mitochondrial translation term appears as an outlier, but the transport theme is dominant.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070124","count":1},{"id":"GO:0015739","count":1},{"id":"GO:0071805","count":1},{"id":"GO:0042128","count":1},{"id":"GO:0015751","count":1}]},{"hash":"1901666413583561107","title":"RNA Pol II Transcription Regulation","description":"This cluster is driven by terms centered on regulating transcription by RNA polymerase II, including regulation of transcription initiation and promoter activity, with additional hints of chromatin-related processes (histone acetylation, nucleosome remodeling). Some terms are obsolete or peripheral (e.g., some stress-related and respiration-associated terms), but the dominant theme is Pol II transcription control.","confidence":"High","size":15,"edges":21,"triangles":9,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0043457","count":5},{"id":"GO:1900446","count":4},{"id":"GO:0042766","count":4},{"id":"GO:0043966","count":4},{"id":"GO:0000436","count":4}]},{"hash":"1873219413784045084","title":"Transmembrane Transporters (ions and sugars)","description":"The top GO terms are dominated by various transmembrane transport processes for ions and small molecules (sialic acid, potassium, galactose, arabinose, fucose, vitamins, phosphate, 4-hydroxyphenylacetate) along with a term related to neurotransmitter loading into synaptic vesicles. This points to a cohesive theme of membrane transport proteins handling diverse substrates, with a possible vesicle-associated transport aspect. Despite no network edges, the functional signal is clear and cohesive around transport across membranes.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0015751","count":2},{"id":"GO:0098700","count":2}]},{"hash":"1979658148476983325","title":"Sodium/Potassium Ion Transport and Homeostasis","description":"The top GO terms cluster around ions moving across membranes and maintaining ionic balance, especially Na+ and K+ import/export and intracellular K+ homeostasis, plus related cell volume regulation and salt-stress responses. A neuronal signaling term (BDNF receptor signaling) is present but the dominant signal is membrane ion transport, justifying a sodium/potassium transport focus.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098719","count":1},{"id":"GO:0097623","count":1},{"id":"GO:0031547","count":1},{"id":"GO:1903281","count":1},{"id":"GO:0009651","count":1}]},{"hash":"1451914847985146279","title":"Ribosome Biogenesis and RNA Processing","description":"The top GO terms cluster around ribosome biogenesis, ribosomal subunit export, tRNA modification, and mRNA splicing, plus cell cycle/division processes, which together point to proteins involved in core RNA processing and ribosome assembly machinery as well as coordination with cell proliferation. The presence of a brain development term may reflect broader roles of RNA processing factors in development, rather than a brain-specific function, keeping the central theme anchored in fundamental gene-expression and ribosome-related activities.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0000747","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0007420","count":2}]},{"hash":"2035901064409493760","title":"Transcription and Nucleotide Biosynthesis","description":"The top terms are dominated by DNA-templated transcription and RNA (guanine-N7)-methylation, with several terms related to nucleotide and cofactor biosynthesis, suggesting a cluster centered on transcriptional regulation coupled with nucleotide metabolism. A retina development term appears as an outlier and may reflect cross-species annotation quirks rather than a shared function. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0036265","count":3},{"id":"GO:0035948","count":3},{"id":"GO:0060041","count":3},{"id":"GO:0017000","count":3}]},{"hash":"2042956121662190291","title":"Neuronal Stress and Ubiquitin Signaling","description":"The terms cluster around neuronal stress responses (heavy metal and oxidative stress, neuronal apoptotic signaling, synapse assembly) and proteostasis via ubiquitination (ubiquitin-dependent catabolic processes and protein polyubiquitination). While there is a broader cell cycle/DNA damage signaling component, the strongest and most cohesive theme ties neuronal stress pathways to ubiquitin-mediated protein regulation, suggesting cells coordinating survival, turnover, and synaptic maintenance under stress.","confidence":"Medium","size":15,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0031571","count":6},{"id":"GO:0042787","count":6},{"id":"GO:0060386","count":6},{"id":"GO:1903378","count":6},{"id":"GO:0000083","count":6}]},{"hash":"1455934651429732691","title":"Chromatin cohesin regulation in mitosis","description":"The GO terms predominantly point to regulation of cohesin loading/unloading, chromosome condensation, and protein localization to chromatin, indicating a focus on chromatin dynamics during mitosis. There is also a link to DNA repair via homologous recombination, suggesting a chromatin-DNA repair context. Overall, the proteins appear to regulate cohesin-mediated chromatin organization in cell division, with related chromatin-binding activities.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1905168","count":1},{"id":"GO:0048146","count":1},{"id":"GO:2000719","count":1},{"id":"GO:1905411","count":1},{"id":"GO:0071923","count":1}]},{"hash":"2066941137447812130","title":"Central metabolism and biosynthesis","description":"The top GO terms point to core energy and carbon-flow pathways (glycolysis, TCA cycle, gluconeogenesis, pyruvate-to-acetyl-CoA) plus biosynthetic processes (fatty acids, leucine catabolism, malonyl-CoA, antibiotic biosynthesis) and even cell wall organization, suggesting a cluster of proteins involved in central metabolism and biosynthetic capabilities. ","confidence":"High","size":14,"edges":90,"triangles":352,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":8},{"id":"GO:0006096","count":5},{"id":"GO:0006552","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0006086","count":4}]},{"hash":"687256692564066301","title":"Dopamine metabolism and xenobiotic stress response","description":"The cluster is enriched for dopamine metabolic and catabolic processes, alongside responses to xenobiotic stimuli, ethanol, LPS, and corticosterone, indicating a link between neurotransmitter turnover and chemical or hormonal stress pathways. Although a few terms are obsolete, the dominant GO terms point to dopamine-related metabolism and external-stimulus responses.","confidence":"Medium","size":14,"edges":58,"triangles":165,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":7},{"id":"GO:0055114","count":7},{"id":"GO:0045964","count":6},{"id":"GO:0043046","count":6},{"id":"GO:0042420","count":6}]},{"hash":"1210302709882605161","title":"Developmental signaling and cytoskeletal regulation","description":"This cluster combines GO terms centered on developmental processes (heart and skeletal system development, pseudohyphal growth) with molecular pathways governing cytoskeletal dynamics (Rho signaling, spindle microtubule attachment) and cell-cycle related events (neuronal maturation regulation, apoptotic clearance). The mix suggests a broad theme of developmental signaling intertwined with cytoskeletal and cell division regulation, rather than a single specific function.","confidence":"Medium","size":14,"edges":22,"triangles":6,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007507","count":5},{"id":"GO:0007124","count":5},{"id":"GO:0007266","count":5},{"id":"GO:0001501","count":5},{"id":"GO:0014043","count":4}]},{"hash":"1831488918616132364","title":"Mitochondrial protein import and ATP synthesis","description":"Most terms point to mitochondrial processes: mitochondrial translation, protein import into the mitochondrial matrix, and proton motive force-driven ATP synthesis. These indicate a cluster of proteins involved in mitochondrial energy metabolism and protein trafficking. Some terms like brain development and photosynthesis appear unrelated and may reflect annotation noise, but the dominant signal supports a mitochondrial energy metabolism theme.","confidence":"Medium","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006212","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0019684","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0030150","count":2}]},{"hash":"1532997033368099527","title":"Multisubstrate membrane transporters","description":"This cluster is dominated by transmembrane transport terms for a variety of substrates (nitrate, various sugars, ions, xenobiotics) and includes neurotransmitter loading into synaptic vesicles, implying proteins primarily function as membrane transporters with broad substrate specificity.","confidence":"High","size":14,"edges":10,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":12},{"id":"GO:0015739","count":11},{"id":"GO:0035435","count":11},{"id":"GO:0006004","count":11},{"id":"GO:0006855","count":11}]},{"hash":"1254402554917046703","title":"Mitotic spindle and ER-Golgi trafficking","description":"This cluster centers on mitosis-related processes (mitotic spindle assembly, cell division, nuclear migration in conjugation) and vesicle trafficking between the ER and Golgi (anterograde and retrograde transport). The co-occurrence suggests a coordinated role of cell cycle progression with membrane trafficking and growth signaling (TORC1). Some terms are less specific (skeletal development), but the dominant pattern points to mitosis coupled with vesicle transport.","confidence":"Medium","size":14,"edges":15,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":3},{"id":"GO:0070208","count":3},{"id":"GO:0000743","count":2},{"id":"GO:0006888","count":2},{"id":"GO:1904263","count":2}]},{"hash":"1622683995433790565","title":"Diverse Sugar Catabolism","description":"The terms point to multiple sugar-specific catabolic processes (glycerol, rhamnose, arabinose, xylose, fucose, xylulose, gluconate, glucuronate) and carbohydrate phosphorylation, indicating a cluster of proteins involved in diverse sugar utilization. Quorum sensing appears but does not define a single pathway, so the core theme is broad sugar catabolism.","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019563","count":1},{"id":"GO:0009372","count":1},{"id":"GO:0019301","count":1},{"id":"GO:0019569","count":1},{"id":"GO:0019640","count":1}]},{"hash":"11362620356099415","title":"mRNA processing and translation initiation control","description":"The cluster shows strong enrichment for mRNA processing steps (splicing via spliceosome, alternative splicing, splicing site recognition, polyadenylation regulation) and initiation of translation (formation of the translation preinitiation complex, translation reinitiation), with regulatory ncRNA-mediated gene silencing indicating post-transcriptional control. Together these terms point to coordinated RNA maturation and control of protein synthesis, with development-related terms being incidental. ","confidence":"High","size":14,"edges":86,"triangles":310,"max_degree":13,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":8},{"id":"GO:0045292","count":8},{"id":"GO:0006378","count":7},{"id":"GO:0002188","count":6},{"id":"GO:0006376","count":6}]},{"hash":"693794584473296578","title":"Retrotransposon activity and DNA integration","description":"The top GO terms are retrotransposition and DNA integration, each with 11 proteins, which strongly points to genome mobility and transposition-related processes as the core theme of this cluster. The other terms are fewer and more heterogeneous (e.g., chondrocyte differentiation, neuron maturation, cell polarity), suggesting they are peripheral associations or annotation noise rather than defining features. Therefore, a concise, representative label is \u201cRetrotransposon activity and DNA integration.\u201d ","confidence":"Medium","size":14,"edges":24,"triangles":27,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0032197","count":11},{"id":"GO:0015074","count":11},{"id":"GO:0002062","count":3},{"id":"GO:0007095","count":3},{"id":"GO:0014043","count":3}]},{"hash":"1304994907121683783","title":"Mitotic cell cycle and chromosome segregation","description":"This cluster is dominated by mitosis-related terms: mitotic cell cycle (GO:0000278), mitotic sister chromatid biorientation (GO:1990758), DNA replication (GO:0006260), and G1/S transition of the mitotic cell cycle (GO:0000082). Together these terms point to proteins involved in DNA replication preceding mitosis and in spindle assembly and chromosome segregation, including kinetochore-microtubule attachment (GO:0051316). Some terms look unrelated or obsolete, but the prevailing signal centers on cell-division machinery.","confidence":"High","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:1990758","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0000082","count":4},{"id":"GO:0014043","count":3}]},{"hash":"856516180687140076","title":"Amino acid and porphyrin/heme biosynthesis with lipid metabolism","description":"Top GO terms cluster around several biosynthetic pathways (histidine, aspartate, porphyrinogen/heme) and fatty acid metabolism/transport, suggesting a metabolic module tied to synthesis and handling of amino-acid\u2013derived and lipid-containing molecules. The transcription term is broad and likely contextual, so the label focuses on biosynthesis/metabolism.","confidence":"Medium","size":13,"edges":14,"triangles":2,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000105","count":2},{"id":"GO:0055089","count":2},{"id":"GO:0006533","count":2},{"id":"GO:0006782","count":2}]},{"hash":"694910626658465337","title":"Ubiquitin-Dependent Cell Death and Innate Immunity","description":"The cluster centers on ubiquitination with strong ties to apoptotic and pyroptotic pathways, plus innate immune responses, suggesting a theme of ubiquitin-regulated cell death within immune defense. The presence of mitotic spindle assembly hints at shared ubiquitin-regulated processes but is less central to the primary theme of death and immunity.","confidence":"Medium","size":13,"edges":30,"triangles":24,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":7},{"id":"GO:0090307","count":7},{"id":"GO:0006915","count":7},{"id":"GO:0045087","count":7},{"id":"GO:1990001","count":7}]},{"hash":"1509108407138177702","title":"Excitatory synapse assembly and presynaptic organization","description":"Most top GO terms cluster around the formation and organization of excitatory synapses and presynaptic terminals (excitatory synapse assembly, neurexin clustering at presynaptic membrane, synapse organization, terminal button organization, regulation of terminal button organization, cytoskeletal matrix at active zone, AMPA receptor activity). A few terms about IL-4/Th2 differentiation appear but do not dominate the cluster\u2019s theme. This makes excitatory synaptic assembly/presynaptic organization the best representative label.","confidence":"High","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0045064","count":3},{"id":"GO:0071353","count":3},{"id":"GO:2000969","count":3},{"id":"GO:0048789","count":3},{"id":"GO:0097115","count":3}]},{"hash":"2071579972304179660","title":"Golgi-Mediated Vesicle Trafficking and SNARE Assembly","description":"The cluster is dominated by GO terms for ER-to-Golgi and intra-Golgi vesicle transport, Golgi-to-vacuole transport, vesicle fusion with the Golgi, and SNARE complex assembly, plus exocytic delivery of neurotransmitter receptors and synaptic potentiation. This points to a cohesive role in Golgi-directed vesicle trafficking and SNARE-mediated fusion, including neuronal receptor trafficking and synaptic plasticity.","confidence":"High","size":13,"edges":28,"triangles":11,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0006891","count":4},{"id":"GO:0048280","count":4},{"id":"GO:0090161","count":4},{"id":"GO:0006896","count":3}]},{"hash":"1899923234302542320","title":"Mitotic Chromatin Assembly and Cytoskeleton Dynamics","description":"This cluster is enriched for centromeric chromatin assembly (CENP-A), microtubule severing, and cell division terms, plus vesicle trafficking (ER to Golgi) and GTPase activity regulation, indicating a module linking chromatin maintenance during mitosis with cytoskeletal remodeling and intracellular transport.","confidence":"Medium","size":13,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0061641","count":3},{"id":"GO:0043588","count":3},{"id":"GO:0051013","count":3}]},{"hash":"1629964782560910921","title":"Ribosome biogenesis and DNA replication","description":"This cluster is dominated by GO terms for ribosome biogenesis and ribosomal subunit assembly, along with DNA-templated transcription and DNA replication, pointing to core growth machinery. While there are additional terms related to development and stress responses, the strongest signal is ribosome and replication-related processes, justifying the name.","confidence":"High","size":13,"edges":29,"triangles":19,"max_degree":9,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0046677","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0070059","count":2}]},{"hash":"149201942989691191","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019068","count":1},{"id":"GO:0015074","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0030260","count":1},{"id":"GO:0075713","count":1}]},{"hash":"708083511934667339","title":"Plasma Membrane Amino Acid Transporters","description":"Most terms describe import of various amino acids across the plasma membrane (D-alanine, D-serine, L-ornithine, L-arginine, L-lysine, methionine, etc.), indicating a membrane transporter module. The nitric oxide production term reflects a downstream link via arginine metabolism during inflammatory responses, which can be connected to arginine import. Overall, the cluster centers on amino acid transporters at the plasma membrane with an arginine-NO signaling tie.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042941","count":4},{"id":"GO:0042942","count":4},{"id":"GO:0097640","count":4},{"id":"GO:0006527","count":4},{"id":"GO:0097639","count":4}]},{"hash":"314990741292282194","title":"Cell migration and membrane remodeling","description":"The top terms point to cell movement and guidance (regulation of cell migration, lamellipodium morphogenesis, chemotaxis) complemented by membrane-related processes (GPI anchor biosynthesis, phosphatidylcholine catabolism), suggesting a cohesive theme around motility and membrane remodeling. Some terms reference broader developmental processes, but the recurring motif is migration-associated signaling and membrane dynamics.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045719","count":1},{"id":"GO:2000394","count":1},{"id":"GO:0030334","count":1},{"id":"GO:0048714","count":1},{"id":"GO:0034638","count":1}]},{"hash":"1461985581265531840","title":"Ubiquitin-dependent proteolysis in neuronal stress","description":"Most frequent terms point to ubiquitin tagging and proteasomal degradation (ubiquitin-dependent protein catabolic process and protein polyubiquitination), with neural-context terms like synapse assembly in innervation and neuron-specific stress responses (oxidative stress-induced apoptotic signaling, cadmium/methylmercury responses). This suggests a theme of ubiquitin-mediated turnover linked to neuronal stress and related regulatory processes, including circadian rhythm aspects. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031571","count":6},{"id":"GO:0042787","count":6},{"id":"GO:0060386","count":6},{"id":"GO:1903378","count":6},{"id":"GO:0000083","count":6}]},{"hash":"2169118614488500670","title":"Intracellular organelle trafficking and localization","description":"This cluster centers on GO terms for vesicle trafficking between organelles (ER to Golgi, intra-Golgi, endosome to vacuole) and for mitochondrial outer membrane targeting/assembly, pointing to a general theme of intracellular transport and organelle localization. A single term (box C/D snoRNP assembly) is less clearly connected, but does not override the predominant trafficking/localization signal.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006901","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0015031","count":1},{"id":"GO:0006891","count":1},{"id":"GO:0000492","count":1}]},{"hash":"1657591422138709924","title":"Unknown","description":"This set shows mostly diverse metabolic processes (methanol/methane, glycine betaine from choline, cholesterol, beta-alanine) along with a few unrelated developmental terms (cerebral cortex development, sperm capacitation, cell size regulation). There is no single cohesive function linking all proteins, so I label it Unknown.","confidence":"","size":12,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":11},{"id":"GO:0019285","count":9},{"id":"GO:0046188","count":9},{"id":"GO:0008203","count":9},{"id":"GO:0015945","count":9}]},{"hash":"1491260549418712251","title":"Mitochondrial energy metabolism and translation","description":"The top GO terms point to mitochondrial processes: fatty acid catabolic process and mitochondrial translation are both prominent, suggesting energy metabolism linked to protein synthesis within mitochondria. There is also an item on endoplasmic reticulum organization and a transamidation step for glutaminyl-tRNA, which can reflect broader organelle-associated maintenance and translation. Some terms are unrelated or obsolete (e.g., nylon catabolic, obsolete diaminopimelate biosynthesis), indicating noise, yet the core signal centers on mitochondria-related metabolism and protein production.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009062","count":4},{"id":"GO:0007029","count":4},{"id":"GO:0032543","count":4},{"id":"GO:0070681","count":4},{"id":"GO:0019876","count":4}]},{"hash":"1533307114050276045","title":"Lipid Metabolism and Xenobiotic Detoxification","description":"The top GO terms cluster around lipid-derived signaling and detoxification of xenobiotics, including prostaglandin biosynthesis and omega-oxidation of fatty acids, plus metabolism of coumarin and organofluorines (insecticide metabolism). While there are also terms for immune modulation and development-related processes, the dominant pattern points to lipid metabolism and xenobiotic processing as the core function of this cluster.","confidence":"Medium","size":12,"edges":36,"triangles":47,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":7},{"id":"GO:0017143","count":6},{"id":"GO:0010760","count":6},{"id":"GO:0070365","count":6},{"id":"GO:0090350","count":6}]},{"hash":"112260368079298775","title":"Steroid and long-chain fatty acid metabolism","description":"The cluster is rich in steroid-related and long-chain lipid biosynthesis/catabolic terms, including steroid catabolic process, C21-steroid hormone metabolism, 3-keto-sphinganine metabolic process, very long-chain fatty acid biosynthesis, and mycolic acid biosynthesis, suggesting a cohesive lipid metabolism program. A peripheral term about transcription regulation and the obsolete oxidation-reduction term are less informative but do not contradict the lipid theme.","confidence":"Medium","size":12,"edges":18,"triangles":11,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006710","count":2},{"id":"GO:0006666","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0006706","count":2}]},{"hash":"1639758318046856625","title":"Steroid and lipid metabolism","description":"The main terms point to lipid and steroid pathways (triglyceride, sterol, testosterone, androgen biosynthesis), suggesting this cluster centers on lipid/steroid metabolism. A few outliers (glutamine metabolism, PHB biosynthesis, ozone response, vascular development) may reflect annotation noise or unrelated functions.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006541","count":2},{"id":"GO:0042619","count":2},{"id":"GO:0010193","count":2},{"id":"GO:0006641","count":2}]},{"hash":"1593373627768615085","title":"Mitochondrial energy production and redox homeostasis","description":"The core terms cluster around mitochondrial oxidative phosphorylation (ETC NADH to ubiquinone), ATP metabolism regulation, and redox balance (redox homeostasis, heme biosynthesis in mitochondria). Translation appears but is less central, suggesting the dominant theme is mitochondrial energy metabolism rather than general protein synthesis. Overall, it points to mitochondrial function and energy regulation.","confidence":"High","size":12,"edges":64,"triangles":201,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0045454","count":2},{"id":"GO:0006120","count":2},{"id":"GO:1903578","count":1},{"id":"GO:0030218","count":1}]},{"hash":"1383822846949924035","title":"RNA Processing and Translation Machinery","description":"These proteins cluster around RNA metabolism, with strong signals for translation (cytoplasmic and mitochondrial) and spliceosome assembly/generation of catalytic spliceosome steps, indicating a core role in RNA processing and protein synthesis. Some differentiation and signaling terms may reflect broader regulatory links, but the dominant theme is RNA processing and translation.","confidence":"High","size":12,"edges":52,"triangles":118,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0006415","count":5},{"id":"GO:0046677","count":5},{"id":"GO:0032543","count":5},{"id":"GO:0002244","count":4}]},{"hash":"167216763708588689","title":"Unknown","description":"The Top Terms cover a wide range of processes\u2014from histone ubiquitination and DNA replication regulation to vesicle transport, NF-kappaB signaling, neural tissue structure, and cholangiocyte proliferation\u2014across different contexts. There isn't a single cohesive function or pathway that clearly ties these terms together, so a concise, representative label cannot be confidently assigned.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070535","count":4},{"id":"GO:1990705","count":2},{"id":"GO:1905150","count":2},{"id":"GO:0044810","count":2},{"id":"GO:0021693","count":2}]},{"hash":"1000821957875713575","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006369","count":10},{"id":"GO:0000464","count":9},{"id":"GO:0000184","count":8},{"id":"GO:0000466","count":8},{"id":"GO:1990120","count":8}]},{"hash":"552146762872184763","title":"Muscle contraction and calcium signaling regulation","description":"Top terms here largely converge on muscle biology and excitation\u2013contraction coupling: regulation of heart contraction, muscle cell fate specification, response to muscle activity, and regulation of calcium release from the sarcoplasmic reticulum. Together with negative regulation of protein kinase activity, these terms suggest a cluster focused on muscle function and signaling control. Some outlier terms (dendrite morphogenesis, phosphatidylcholine biosynthesis, transcription factor activity) appear peripheral and do not negate the core muscle-focused theme.","confidence":"Medium","size":12,"edges":19,"triangles":9,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006469","count":5},{"id":"GO:0042694","count":3},{"id":"GO:0045917","count":3},{"id":"GO:0008016","count":3},{"id":"GO:0014850","count":3}]},{"hash":"972786849841364208","title":"Nucleosome Assembly and Chromatin Organization","description":"This cluster is dominated by GO terms tied to chromatin structure and nucleosome biology, including nucleosome assembly and heterochromatin organization, as well as histone modification-related terms tied to chromatin. While a few outlier terms exist (miscellaneous metabolism), the strongest signal points to chromatin packaging and organization functions.","confidence":"High","size":12,"edges":20,"triangles":9,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0071169","count":3},{"id":"GO:0097298","count":2},{"id":"GO:0006334","count":2},{"id":"GO:0016584","count":2},{"id":"GO:0098532","count":2}]},{"hash":"605383222839926957","title":"Unknown","description":"The top terms are highly diverse, spanning developmental processes (labyrinthine layer development, placenta development, sensory organ precursor division), core cell cycle events (mitotic spindle assembly, chromosome segregation, meiotic chromosome alignment, DNA-templated transcription), and regulatory processes (inflammatory response, insulin secretion, antibacterial peptide biosynthesis). There is no clear, single theme that ties these functions together, and there are no interactions indicated between proteins, so a specific, representative label isn\u2019t justifiable.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060711","count":1},{"id":"GO:0090307","count":1},{"id":"GO:0050727","count":1},{"id":"GO:0001890","count":1},{"id":"GO:0045035","count":1}]},{"hash":"723491247358190833","title":"Unknown","description":"There are no edges or triangles among the proteins (Max Degree 0) and no top GO terms to guide labeling, so there is no shared functional signal to define a specific cluster. The lack of connections means the cluster cannot be meaningfully named beyond Unknown.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1959683935538373121","title":"Unknown","description":"The top terms are very diverse, spanning aging, GTPase signaling, retrotransposition, DNA integration, neural differentiation, macrophage differentiation regulation, chemokine production, growth, MIP-1 alpha production, and NOD1 signaling, with no clear shared function or pathway. There are no edges connecting proteins, so a coherent functional label cannot be assigned.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0032197","count":1},{"id":"GO:0015074","count":1},{"id":"GO:0021707","count":1}]},{"hash":"1678712336607368776","title":"Membrane Transporters for Diverse Substrates","description":"This cluster centers on transmembrane transport GO terms across a range of substrates\u2014ions (sodium, potassium), sugars (arabinose, fucose, sialic acid), vitamins, xenobiotics, and even neurotransmitter loading into vesicles\u2014pointing to a group of membrane transporter proteins with broad substrate specificity.","confidence":"High","size":12,"edges":11,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":11},{"id":"GO:0035461","count":11},{"id":"GO:0015739","count":8},{"id":"GO:0035435","count":8},{"id":"GO:0006004","count":8}]},{"hash":"132179964547579174","title":"Diverse Transmembrane Transporters","description":"The top GO terms point to transmembrane transport of a wide range of substrates (xenobiotics, vitamins, sugars, sialic acid, ions, nitrate, phosphates, and even neurotransmitter loading into vesicles). This suggests the proteins function broadly as membrane transporters/carriers rather than a single substrate-specific role, explaining the diverse transport annotations. ","confidence":"High","size":12,"edges":11,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":12},{"id":"GO:0035461","count":12},{"id":"GO:0015739","count":11},{"id":"GO:0071805","count":11},{"id":"GO:0042128","count":11}]},{"hash":"283733281515556565","title":"Inositol phosphate and phosphatidylinositol signaling","description":"This cluster shows enrichment for inositol phosphate biosynthetic processes and phosphatidylinositol phosphate biosynthesis, plus regulation of these pathways, pointing to a shared role in phosphoinositide metabolism and signaling. While a few terms touch on neuronal or immune contexts, the clear common thread is PI/inositol signaling, suggesting this as the core function of the group.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097062","count":2},{"id":"GO:0001841","count":1},{"id":"GO:0002262","count":1},{"id":"GO:0006525","count":1},{"id":"GO:0046854","count":1}]},{"hash":"1608870502313586131","title":"Carbohydrate Metabolism and Glycolysis Regulation","description":"The cluster centers on carbohydrate metabolism, including fructose processing, glycolysis regulation, gluconeogenesis, and lactate metabolism, indicating a shared energy-generation theme. Brain development and viral process terms appear incidental; with no edges, the label emphasizes metabolic function rather than interaction networks.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0045730","count":1},{"id":"GO:0006000","count":1},{"id":"GO:0006003","count":1},{"id":"GO:0045820","count":1}]},{"hash":"1151329685523805998","title":"Hormone signaling and oxidative stress response","description":"These proteins are enriched for cellular responses to multiple hormones (thyroid hormone, norepinephrine, prostaglandin D, retinoic acid) and to oxidative stress (hydrogen peroxide, redox processes). They also show links to pro-survival signaling (positive regulation of PI3K/AKT) and anti-apoptotic regulation, suggesting a cohesive theme of hormone-driven signaling coupled with redox-stress responses that promote cell survival.","confidence":"Medium","size":11,"edges":49,"triangles":122,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":10},{"id":"GO:0070301","count":10},{"id":"GO:0051897","count":9},{"id":"GO:1901653","count":9},{"id":"GO:0042415","count":9}]},{"hash":"1187077149477595870","title":"Neural development and interneuron migration","description":"The cluster\u2019s top GO terms point to brain development (substantia nigra, hippocampus), interneuron migration to the cortex, axon guidance, and synaptic transmission regulation, with supporting roles from tubulin assembly and endosomal trafficking\u2014collectively indicating neural development and neural connectivity. ","confidence":"High","size":11,"edges":10,"triangles":1,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0021762","count":6},{"id":"GO:0046677","count":5},{"id":"GO:0033138","count":5},{"id":"GO:0021766","count":5},{"id":"GO:0008283","count":5}]},{"hash":"272224401273497747","title":"Ubiquitin-Regulated DNA Damage Response and Apoptosis","description":"The cluster is dominated by ubiquitination-related proteins and DNA damage/repair processes (DNA replication, DSB repair via sister chromatids, repair pathways), along with mitotic spindle assembly and cell death signals (apoptosis and pyroptosis) and innate immune response. This suggests a cohesive module where ubiquitin signaling coordinates DDR during replication stress and mitosis, leading to repair, checkpoint control, and programmed cell death, with inflammatory signaling as a possible downstream effect.","confidence":"High","size":11,"edges":35,"triangles":50,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":9},{"id":"GO:0090307","count":9},{"id":"GO:0006915","count":9},{"id":"GO:0045087","count":9},{"id":"GO:1990001","count":9}]},{"hash":"251117092754972811","title":"Translational initiation and preinitiation complex formation","description":"This cluster is driven by GO terms focused on regulation of translational initiation and the formation of the translation preinitiation complex (GO:0006446, GO:0001731), with additional signals from cytoplasmic translation and translation reinitiation. While a few terms touch on broader RNA processing, the strongest and most frequent signals point to initiation control of protein synthesis.","confidence":"High","size":11,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006446","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0090603","count":1},{"id":"GO:0008292","count":1},{"id":"GO:0061526","count":1}]},{"hash":"344464750726686019","title":"Transposon and Proviral Latency","description":"This cluster centers on mobile genetic element activity and virus-like genome integration: retrotransposition and DNA integration are prominent, with DNA transposition also represented, and proviral latency establishment plus viral entry terms suggesting latent, nucleus-targeted elements. The presence of translation and RNA processing terms appears ancillary, likely related to host cellular context rather than core function. Overall, the proteins likely function in transposon/retroelement dynamics and proviral latency within host cells.","confidence":"Medium","size":11,"edges":8,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0032197","count":2},{"id":"GO:0015074","count":2},{"id":"GO:0033119","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0006407","count":1}]},{"hash":"904880745569890360","title":"Mitochondrial Metabolite Transporters","description":"This cluster is driven by diverse mitochondrial metabolite transport terms, covering transmembrane movement of substrates such as thiosulfate, pyridoxal phosphate, thiamine pyrophosphate, citrate, alpha-ketoglutarate, deoxynucleotides, manganese, and phosphate, along with regulation of mitochondrial membrane potential and a response to superoxide. Together, these points indicate a cohesive group of mitochondrial transporter proteins involved in metabolite exchange and membrane potential maintenance.","confidence":"High","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051881","count":6},{"id":"GO:0015709","count":6},{"id":"GO:0031921","count":6},{"id":"GO:0006843","count":6},{"id":"GO:0000303","count":6}]},{"hash":"323313304444458088","title":"Chromatin regulation and transcription control","description":"This cluster\u2019s terms cluster around nucleosome assembly, histone modification, and regulation of transcription (including antisense RNA). Although there are tissue-specific terms (uterine gland development, liver regeneration), the common thread is regulation of chromatin state and gene expression rather than a single pathway, suggesting a broad chromatin- and transcription-focused theme.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006334","count":2},{"id":"GO:1903709","count":1},{"id":"GO:0006469","count":1},{"id":"GO:2000134","count":1},{"id":"GO:0036333","count":1}]},{"hash":"1906574533772734781","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006096","count":1},{"id":"GO:0009073","count":1},{"id":"GO:2001059","count":1},{"id":"GO:0046386","count":1},{"id":"GO:0019512","count":1}]},{"hash":"2105189860128910951","title":"Actin Cytoskeleton Remodeling and Synaptic Clustering","description":"This cluster is dominated by actin-related processes: barbed-end actin filament capping, lamellipodium assembly, and general actin cytoskeleton organization, pointing to dynamic cytoskeletal remodeling. The inclusion of AMPA glutamate receptor clustering suggests a link to synaptic organization where actin dynamics facilitate receptor localization. While a few terms touch on immune signaling or growth/fate specification, the core signal is actin-driven structural rearrangement and membrane protein clustering, compatible with motility and synaptic architecture roles.","confidence":"High","size":11,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051016","count":2},{"id":"GO:0030032","count":2},{"id":"GO:0097113","count":2},{"id":"GO:0030036","count":2},{"id":"GO:0060124","count":1}]},{"hash":"1674442036028663725","title":"Cell Wall Biosynthesis and Glycoprotein Processing","description":"These proteins cluster around processes involved in cell wall biosynthesis and remodeling (plant-type cell wall modification, xyloglucan metabolism, fungal-type wall organization). They also include glycoprotein processing events (mannose trimming in the ER and ERAD-related glycosylation steps), suggesting a link between cell wall assembly/modification and glycoprotein maturation/quality control.","confidence":"Medium","size":11,"edges":16,"triangles":5,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0009831","count":1},{"id":"GO:0031505","count":1},{"id":"GO:0006037","count":1},{"id":"GO:0010411","count":1},{"id":"GO:0042546","count":1}]},{"hash":"1200925499230276142","title":"Plant Hormone Signaling and Nitrate Transport","description":"This cluster centers on plant-specific processes: auxin-activated signaling, gibberellic acid homeostasis, response to nitrate, and nitrate assimilation, plus multiple transmembrane and transporter activities for peptides and nutrients. While there are a few general cell-cycle terms, the strongest recurring theme is plant hormone signaling coupled with nutrient and nitrate transport, suggesting a role in plant growth regulation and nutrient uptake.","confidence":"Medium","size":11,"edges":10,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:1904780","count":1},{"id":"GO:0042916","count":1},{"id":"GO:0055085","count":1},{"id":"GO:0000022","count":1},{"id":"GO:0044339","count":1}]},{"hash":"1519694885945336694","title":"Unknown","description":"The GO terms span immune signaling (NOD1 pathway, MIP-1\u03b1 and CXCL5 production), developmental/differentiation processes (Notch signaling in heart field, cerebellar granule cell differentiation), and even sporulation-related activity, with no clear shared function linking these proteins. With no edges and diverse terms, there isn\u2019t a coherent theme to name the cluster beyond Unknown. ","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042243","count":1},{"id":"GO:0031028","count":1},{"id":"GO:0021707","count":1},{"id":"GO:0010745","count":1},{"id":"GO:0071651","count":1}]},{"hash":"688888904127646701","title":"Unknown","description":"This cluster has no cohesive functional theme: GO terms cover nitrogen metabolism, organ development (lung/kidney), translation regulation, catabolic steps, salt response, and some obsolete entries, with no shared process and no interactions (edges 0). Therefore no meaningful label beyond Unknown.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019740","count":1},{"id":"GO:0030324","count":1},{"id":"GO:0017148","count":1},{"id":"GO:0009097","count":1},{"id":"GO:0050680","count":1}]},{"hash":"416704944478548780","title":"Retina rod cell development and innate immunity proteins","description":"Top GO terms point to both retina-specific development (retinal rod cell development, protein localization to photoreceptor outer segment) and general immune responses (defense response to virus, innate immune response). Although many terms are obsolete and the connections are weak, the common thread appears to be proteins involved in photoreceptor biology with potential roles in immune defense. Given the mixed signals, the label reflects a retina- and immunity-associated cluster rather than a single core function.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051607","count":1},{"id":"GO:0070389","count":1},{"id":"GO:2000531","count":1},{"id":"GO:0051291","count":1},{"id":"GO:1903546","count":1}]},{"hash":"17460515947208408","title":"Unknown","description":"The GO terms are diverse and lack a unifying function: multiple catabolic processes (xylan, cellulose, uracil), nitrogen utilization, phytochelatin biosynthesis, proteolysis, and regulatory processes. With no edges connecting the proteins, there is no cohesive theme to label the cluster.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045493","count":1},{"id":"GO:0030245","count":1},{"id":"GO:0006212","count":1},{"id":"GO:0019740","count":1},{"id":"GO:0055114","count":1}]},{"hash":"1581073513914696162","title":"Mitochondrial metabolite transporters","description":"This cluster is dominated by GO terms describing transport of various metabolites and cofactors across mitochondrial membranes (e.g., citrate, alpha-ketoglutarate, thiamine pyrophosphate, pyridoxal phosphate, deoxynucleotides, phosphate, manganese, thiosulfate), plus regulation of mitochondrial membrane potential and a response to superoxide. The common thread is carrier proteins that shuttle diverse substrates across the mitochondrial inner membrane, consistent with mitochondrial metabolite transporters. ","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051881","count":3},{"id":"GO:0015709","count":3},{"id":"GO:0031921","count":3},{"id":"GO:0006843","count":3},{"id":"GO:0000303","count":3}]},{"hash":"1012356026403099164","title":"Nitrogen metabolism and starvation response","description":"The cluster\u2019s top GO terms cluster around ammonia assimilation, nitrogen fixation, and cellular response to nitrogen starvation, indicating a core theme of nitrogen metabolism and adaptation to nitrogen availability. While other terms hint at regulatory or signaling roles, the nitrogen-related terms dominate, supporting a specific label focused on nitrogen metabolism.","confidence":"High","size":10,"edges":13,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0019676","count":2},{"id":"GO:0006995","count":2},{"id":"GO:0044044","count":2},{"id":"GO:1904797","count":2},{"id":"GO:0050679","count":2}]},{"hash":"1375984973473012129","title":"Diverse carbon substrate catabolism","description":"This cluster is enriched for multiple substrate-specific catabolic GO terms (propanediol, glycerol, 3-chlorocatechol, L-fucose, methanol, 1-butanol, glycol) and for carbon utilization, indicating proteins involved in breaking down a variety of organic carbon sources to feed metabolism. The common theme is broad substrate-dependent catabolic activity rather than a single pathway, hence a label reflecting diverse carbon-source degradation. ","confidence":"Medium","size":10,"edges":27,"triangles":36,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0051143","count":2},{"id":"GO:0015976","count":2},{"id":"GO:0019564","count":2},{"id":"GO:1901168","count":2},{"id":"GO:0071271","count":2}]},{"hash":"2235155555109740849","title":"Small-molecule Biosynthesis","description":"Most terms cluster around biosynthetic and metabolic processes for diverse small molecules (biotin biosynthesis, antibiotic biosynthesis, galactose and sorbitol biosynthesis, and inositol metabolism), with a couple regulatory or obsolete terms that do not define the core theme. The shared thread is production of small metabolites rather than a single pathway or complex, so a label like \u201cSmall-molecule biosynthesis\u201d captures the main function across the cluster.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0009102","count":2},{"id":"GO:0006012","count":1},{"id":"GO:0043433","count":1}]},{"hash":"1019512890983567471","title":"DNA replication and ribosome biogenesis","description":"This cluster centers on nucleic acid metabolism and ribosome assembly. Strong signals include DNA replication and DNA repair terms (GO:0006260, GO:0045003) along with rRNA maturation and mitochondrial large ribosomal subunit assembly (GO:0000466, GO:1902775), plus mRNP processing (GO:1990120, GO:1990416). While some terms relate to stress signaling (cellular response to cold; BDNF stimulus), the dominant theme ties to genome maintenance and ribosome biogenesis.","confidence":"Medium","size":10,"edges":10,"triangles":5,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0019079","count":9},{"id":"GO:0006260","count":9},{"id":"GO:0070417","count":7},{"id":"GO:0045003","count":7},{"id":"GO:0000184","count":7}]},{"hash":"994929604507302326","title":"Ubiquitin-Proteasome\u2013Mediated Proteolysis and Cell Cycle","description":"This cluster is dominated by GO terms describing ubiquitin-dependent protein degradation (including SCF-dependent proteasomal pathways) and regulation of ubiquitination, plus mitotic G1 DNA damage checkpoint signaling and G1/S transition regulation. These link proteolysis to cell cycle control and DNA damage responses, with additional hints of stress-related proteostasis (cadmium/methylmercury) and circadian regulation, which often involve ubiquitin pathways. The overall theme is the ubiquitin-proteasome system coordinating cell cycle and stress responses.","confidence":"High","size":10,"edges":2,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0042787","count":6},{"id":"GO:0000083","count":5},{"id":"GO:0071276","count":5},{"id":"GO:0031146","count":5},{"id":"GO:0031571","count":4}]},{"hash":"1015733550044512723","title":"Unknown","description":"The top terms center on basic cellular processes like translation and DNA-templated transcription, with only a few terms related to metal ion transport, and there are no edges linking the proteins. This mix does not suggest a single coherent function for the cluster, so a specific, representative label isn\u2019t well supported. ","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006260","count":2},{"id":"GO:0006353","count":2},{"id":"GO:0031564","count":2},{"id":"GO:0071577","count":1}]},{"hash":"1301568072345048798","title":"T Cell Differentiation and MAPK Signaling","description":"Our cluster shows multiple immune and T cell\u2013focused terms (T cell homeostasis, T follicular helper cell differentiation, regulation of germinal center formation) alongside signaling pathways (p38MAPK cascade, cellular response to PMA). This pattern suggests a theme of T cell differentiation and regulation via MAPK signaling, with related immune signaling and regulatory processes.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0038066","count":1},{"id":"GO:1904628","count":1},{"id":"GO:0002635","count":1},{"id":"GO:1904246","count":1},{"id":"GO:0045647","count":1}]},{"hash":"613559040184183799","title":"Gene Expression and RNA Processing","description":"Top GO terms center on transcription, RNA splicing, rRNA maturation, translation initiation, and ER-Golgi transport, which together point to gene expression regulation and RNA processing. A few terms (sarcomere organization, xylan biosynthesis, GPCR signaling) seem less connected and may reflect broader cellular context or annotation noise, but they do not override the core theme.","confidence":"Medium","size":10,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0035948","count":2},{"id":"GO:0045214","count":2},{"id":"GO:0045492","count":1},{"id":"GO:0007200","count":1}]},{"hash":"1794980989033359496","title":"Unknown","description":"Top terms span meiosis, DNA replication, transcription regulation, mRNA processing, protein autophosphorylation, and hypoxia sensing, without a dominant shared theme. There are no interactions (Edges 0), so a coherent cluster-level function cannot be inferred. Therefore Unknown, None.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007144","count":1},{"id":"GO:0016446","count":1},{"id":"GO:0018298","count":1},{"id":"GO:0000713","count":1},{"id":"GO:0006261","count":1}]},{"hash":"822213441540868958","title":"Fungal oxidative stress, autophagy, and sporulation","description":"The GO terms cluster around autophagosome assembly and ER protein folding (core cellular quality control), oxidative stress response, and sporulation-related processes (meiosis I, ascospore formation), with supporting lipid biosynthesis in fungi. These point to a fungal cell stress/development program emphasizing autophagy and sporulation, despite some metabolic/outlier terms. Therefore the label centers on fungus-specific stress and development pathways.","confidence":"Medium","size":10,"edges":10,"triangles":1,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0000045","count":1},{"id":"GO:0034975","count":1},{"id":"GO:0042952","count":1},{"id":"GO:0098869","count":1},{"id":"GO:0006979","count":1}]},{"hash":"445166910040516846","title":"Unknown","description":"Insufficient functional signal: there are 0 edges/triangles and no top GO terms, so no common biological theme is detectable among the proteins. Without a shared function, this cluster should be labeled Unknown.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"525252226296552943","title":"Peroxisomal fatty acid oxidation","description":"The cluster's top GO terms cluster around fatty acid beta-oxidation, acetyl-CoA and propionyl-CoA catabolic processes, and ketone body breakdown, with glyoxysome organization hinting at peroxisomal metabolism. This points to a shared role in lipid catabolism and energy generation, more than to signaling or development.","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006635","count":4},{"id":"GO:0046356","count":4},{"id":"GO:0006550","count":4},{"id":"GO:1902860","count":4},{"id":"GO:0010111","count":4}]},{"hash":"112050305349511658","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0018027","count":4},{"id":"GO:0031167","count":4},{"id":"GO:0018013","count":4},{"id":"GO:0014075","count":3},{"id":"GO:0000183","count":3}]},{"hash":"2205125824052910536","title":"Diverse membrane transporters","description":"These terms collectively describe transmembrane transport of various substrates (sialic acid, arabinose, fucose, phosphate ions, sodium/potassium ions, xenobiotics, nitrate assimilation) and vesicular neurotransmitter loading, pointing to a cluster of transporter proteins with diverse substrates rather than a single pathway. ","confidence":"High","size":9,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":9},{"id":"GO:0035435","count":9},{"id":"GO:0006004","count":9},{"id":"GO:0006855","count":9},{"id":"GO:0071805","count":9}]},{"hash":"1457310175518802029","title":"Unknown","description":"The term set mixes plant metabolism (stilbene catabolic process), bacterial lipopolysaccharide biosynthesis, steroid response, and several metal ion transport and calcium homeostasis processes, with no consistent common function linking all proteins. Because the GO terms are highly diverse and show no single dominant biological theme, there is no reliable label beyond Unknown.","confidence":"","size":9,"edges":10,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0046272","count":4},{"id":"GO:0046839","count":4},{"id":"GO:0016311","count":4},{"id":"GO:0009103","count":4},{"id":"GO:0097755","count":4}]},{"hash":"1645050827493788072","title":"Mitochondrial Protein Import and Localization","description":"The set of GO terms points strongly to mitochondrial trafficking and membrane integration: import into the mitochondrial matrix and inner membrane, establishment of mitochondrial localization, and mitochondrial fusion. A chloroplast import term appears but the mitochondrial-related terms dominate, suggesting a cohesive cluster centered on mitochondrial protein import/localization, with some potential dual-targeting signals. ","confidence":"High","size":9,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":3},{"id":"GO:0045037","count":2},{"id":"GO:0045039","count":2},{"id":"GO:0032094","count":2},{"id":"GO:0030150","count":2}]},{"hash":"867273820581044818","title":"Mitochondrial dynamics and ER-Golgi transport","description":"This cluster shows strong enrichment for mitochondrial fission and mitochondrial membrane organization, together with vesicle trafficking between the endoplasmic reticulum and Golgi apparatus (ER-Golgi transport), and related protein targeting terms. The co-occurrence of these organelle dynamics and trafficking functions suggests a shared theme of intracellular transport and organelle biogenesis, rather than a single signaling pathway. While a few terms point to neuronal signaling or development, the dominant pattern centers on mitochondria and the secretory pathway, supporting the chosen label.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0007049","count":6},{"id":"GO:0000266","count":4},{"id":"GO:0006623","count":4},{"id":"GO:0007006","count":4}]},{"hash":"1654625056553259177","title":"Neuronal migration and MT dynamics","description":"This cluster centers on neural development processes (interneuron migration, axon guidance, EGFR signaling) and microtubule-dependent transport/trafficking (tubulin complex assembly, spindle attachments, endosome/ER transport), along with mitochondria distribution, suggesting coordinated MT-based movement and connectivity in neurons.","confidence":"Medium","size":9,"edges":10,"triangles":1,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0048312","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0007411","count":3},{"id":"GO:0051966","count":3},{"id":"GO:0048227","count":3}]},{"hash":"1384759074931889348","title":"Ribosome biogenesis and translation","description":"The cluster is enriched for translation-related GO terms (translation, ribosome biogenesis, SSU-rRNA maturation, small subunit assembly) and fidelity maintenance, indicating proteins involved in ribosome production and accurate protein synthesis, with some antibiotic-response signals reflecting stress on ribosome function.","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0000462","count":5},{"id":"GO:0042254","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0000028","count":1}]},{"hash":"1958075010970710548","title":"Dopamine metabolism and xenobiotic stress response","description":"The cluster is driven by dopamine-related GO terms (dopamine catabolic process and positive regulation of dopamine metabolic process) along with a strong signal for response to xenobiotic stimulus. Additional terms point to broader metabolic stress responses (ethanol, corticosterone, LPS) and redox/glycolytic processes, suggesting a theme of dopamine-associated metabolism under chemical and environmental stress.","confidence":"Medium","size":9,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":3},{"id":"GO:0045964","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0043046","count":2},{"id":"GO:0042420","count":2}]},{"hash":"439365175758639793","title":"Transcriptional Regulation and Developmental Signaling","description":"These proteins show strong enrichment for transcription-related GO terms (negative regulation of transcription by RNA polymerase II; DNA-templated transcription) and development-related terms in airway tissues (lung smooth muscle, bronchus and trachea cartilage), along with signaling responses (interleukin-4, calcium). Together, they suggest a group of transcriptional regulators involved in developmental and signaling processes rather than a single specific pathway.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0071864","count":2},{"id":"GO:0061145","count":2},{"id":"GO:0060532","count":2}]},{"hash":"601077467316965000","title":"Spliceosome-Mediated mRNA Processing","description":"The cluster is dominated by GO terms centered on mRNA splicing and regulation via the spliceosome (cis splicing, alternative splicing regulation, snRNP assembly) and includes related post-transcriptional steps such as mRNA export and regulation of translation initiation, indicating a cohesive module of proteins involved in mRNA maturation and processing rather than transcriptional control.","confidence":"High","size":9,"edges":34,"triangles":71,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":5},{"id":"GO:0031047","count":3},{"id":"GO:0006406","count":3},{"id":"GO:0000381","count":3},{"id":"GO:0048025","count":3}]},{"hash":"614682510976343867","title":"Retrotransposons and Proviral Latency","description":"The top GO terms cluster around retrotransposition, DNA integration, and DNA transposition, with additional signals of viral entry and proviral latency, indicating elements derived from retroviruses and integrated proviral genomes rather than standard housekeeping functions. This supports a cohesive theme of transposable/viral genomic elements and their latent integration.","confidence":"High","size":9,"edges":12,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0032197","count":5},{"id":"GO:0015074","count":5},{"id":"GO:0006313","count":4},{"id":"GO:0075732","count":4},{"id":"GO:0046718","count":4}]},{"hash":"1768117292999060224","title":"ER protein folding and quality control","description":"The cluster is dominated by GO terms for ER-associated folding (protein folding in ER), ER lumen retention, and response to unfolded protein, plus redox homeostasis, which together point to an ER chaperone\u2013driven quality-control module managing protein folding and stress. Some terms like viral processes and inclusion body regulation may reflect host\u2013virus interactions with the ER, but the core signal is ER folding andUnfolded Protein Response activity.","confidence":"High","size":9,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":4},{"id":"GO:0034975","count":4},{"id":"GO:0006621","count":3},{"id":"GO:0016032","count":3},{"id":"GO:0090084","count":2}]},{"hash":"2241888391965952365","title":"Lymphocyte V(D)J recombination and differentiation","description":"The notable presence of pro-B cell differentiation and immunoglobulin/T cell receptor V(D)J recombination terms points to immune cell development and antigen receptor gene rearrangement. Additional terms on DNA replication and cell cycle align with proliferative states typical of developing lymphocytes, supporting a cohesive immune development theme despite some general cellular process terms.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901097","count":2},{"id":"GO:0051102","count":1},{"id":"GO:0090298","count":1},{"id":"GO:0006288","count":1},{"id":"GO:0002328","count":1}]},{"hash":"2122134333090937261","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning GPCR signaling, rRNA maturation, ER-Golgi transport, translation initiation, RNA splicing, chromatin modification, mitochondria-nucleus signaling, fertilization, and TGF-beta response, with no clear shared function or pathway tying the proteins together. The lack of edges/connectedness further supports the absence of a cohesive theme.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007200","count":1},{"id":"GO:0000466","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0002188","count":1},{"id":"GO:0090344","count":1}]},{"hash":"1013359536092680039","title":"Retroviral Integration and Host Antiviral Response","description":"The top GO terms cluster around DNA transposition, retrotransposition, DNA integration, viral entry into the host nucleus, and proviral latency, which together describe the retroelement life cycle and provirus establishment. The concurrent term for type I interferon response points to an antiviral host defense, reinforcing the theme. A couple of outliers (symbiont-related and hormone receptor assembly terms) appear peripheral to the core signal, but the dominant pattern is retroviral integration and host antiviral response.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006313","count":1},{"id":"GO:0075732","count":1},{"id":"GO:0032197","count":1},{"id":"GO:0015074","count":1},{"id":"GO:0046718","count":1}]},{"hash":"2258139946167991090","title":"Unknown","description":"GO terms span neural development, various immune cell differentiation processes, humoral immune response, and core cellular/metabolic processes (DNA replication, proteasomal regulation, amino acid starvation response, mitochondrial complex IV assembly). This broad, heterogeneous mix provides no single unifying function, so a specific label cannot be confidently assigned.","confidence":"","size":9,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048666","count":2},{"id":"GO:0032435","count":2},{"id":"GO:0034198","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0002455","count":1}]},{"hash":"2019194054936953692","title":"Nutrient-responsive transcriptional regulation","description":"This cluster is dominated by GO terms describing positive regulation of transcription from RNA polymerase II promoter in response to various nutrient- or carbon-source signals (oleic acid, nonfermentable carbon sources, nitrogen catabolite activation). While there are also biosynthetic regulation terms (lysine and pyrimidine biosynthesis) and respiration-related regulation, the unifying theme is transcriptional control modulated by metabolic cues. The lack of direct enzyme activity terms and the absence of interactions suggests a regulatory rather than catalytic cluster, best captured by a transcriptional response to nutrients. ","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045122","count":1},{"id":"GO:2001158","count":1},{"id":"GO:0043457","count":1},{"id":"GO:1904741","count":1},{"id":"GO:0001080","count":1}]},{"hash":"1710237054346555651","title":"Golgi-to-Plasma Membrane Trafficking and Ion Transport","description":"These proteins appear linked to Golgi-to-endosome and Golgi-to-plasma membrane trafficking, plus multiple ion transport processes across the plasma membrane (Na+, Ca2+, K+, Mn2+), and a synaptic plasticity term (long-term depression). The common theme is membrane trafficking coupled with ion homeostasis relevant to synaptic membranes, supporting a cohesive label.","confidence":"Medium","size":9,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006895","count":1},{"id":"GO:0000042","count":1},{"id":"GO:0043001","count":1},{"id":"GO:0060292","count":1},{"id":"GO:0097369","count":1}]},{"hash":"1224064552846542689","title":"Nucleotide biosynthesis and mtDNA replication","description":"This cluster is dominated by GO terms tied to nucleotide metabolism (tetrahydrofolate biosynthesis, CDP metabolism, nucleobase interconversion) and mitochondrial DNA replication, suggesting a cohesive role in supplying nucleotides and maintaining mitochondrial genome integrity. Some terms appear less directly related (renal system development, cerebral cortex development) and may reflect annotation noise or broader multifunctionality, but the core signal points to nucleotide metabolism and mtDNA maintenance.","confidence":"Medium","size":9,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046654","count":2},{"id":"GO:0006240","count":2},{"id":"GO:0055114","count":2},{"id":"GO:1902254","count":2},{"id":"GO:0046704","count":2}]},{"hash":"1836364456348985253","title":"ER protein folding and ERAD","description":"Most terms point to endoplasmic reticulum processes, including protein folding in the ER, cellular response to unfolded protein, and ER-associated degradation (ERAD) via retrograde transport to the cytosol. Developmental terms like cone/wing cell fate and neural crest development may reflect broader roles of secretory pathway components in development, but the dominant signal is ER quality control and protein processing. Therefore, the cluster is best described as an ER protein folding and degradation/quality-control module.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042676","count":1},{"id":"GO:0034620","count":1},{"id":"GO:0038005","count":1},{"id":"GO:0035311","count":1},{"id":"GO:0032815","count":1}]},{"hash":"1450003313470862644","title":"Unknown","description":"The top GO terms span a wide range of biological areas, including cell cycle regulation, DNA recombination, immune cell proliferation, heart and muscle regulation, complement activation, vesicle-mediated transport, neural dendrite processes, and synaptic vesicle maturation. This dispersion shows no single cohesive function or pathway linking the proteins, so a specific, representative label is not applicable. ","confidence":"","size":9,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1900087","count":2},{"id":"GO:0006310","count":2},{"id":"GO:0002322","count":1},{"id":"GO:0008016","count":1},{"id":"GO:0045917","count":1}]},{"hash":"1850698574065138452","title":"Unknown","description":"The Top Terms span diverse biological areas (metabolism, neural development, reproduction, chromatin modification) with no clear unifying function, and the cluster has no interactions connecting these terms, so a coherent, specific label cannot be assigned.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019483","count":1},{"id":"GO:0048240","count":1},{"id":"GO:0007568","count":1},{"id":"GO:0045793","count":1},{"id":"GO:0021987","count":1}]},{"hash":"2255638120274398746","title":"Unknown","description":"The top GO terms span very diverse areas (development, metabolism, detoxification, vascular and immune regulation) with no single shared function linking the proteins. This makes it unclear to assign a cohesive biological theme, so the cluster is labeled Unknown with no confidence. ","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060065","count":3},{"id":"GO:0017143","count":2},{"id":"GO:0010760","count":2},{"id":"GO:0070365","count":2},{"id":"GO:0090350","count":2}]},{"hash":"1839477380949302493","title":"Steroid and lipid metabolism","description":"The cluster's top GO terms are dominated by steroid- and lipid-related processes (androgen and steroid catabolism, C21-steroid hormone metabolism, very long-chain fatty acid biosynthesis, mycolic acid biosynthetic, retinol metabolism), suggesting a cohesive role in lipid and steroid processing. A few terms (regulation of DNA-templated transcription, response to methotrexate) may reflect broader regulatory or drug-response contexts but do not negate the lipid-centric theme.","confidence":"Medium","size":8,"edges":15,"triangles":14,"max_degree":6,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006710","count":8},{"id":"GO:0006666","count":8},{"id":"GO:0006355","count":8},{"id":"GO:0006706","count":8},{"id":"GO:0031427","count":8}]},{"hash":"1603955557574472989","title":"Xenobiotic Metabolism and Inflammation Regulation","description":"The cluster\u2019s GO terms are dominated by xenobiotic metabolism (insecticide metabolism, organofluorine metabolism, coumarin catabolism, and fatty acid omega-oxidation) and immune/inflammatory regulation (negative regulation of macrophage chemotaxis and chronic inflammatory response), with additional vascular and developmental terms suggesting broader pleiotropy. This makes xenobiotic detoxification with modulation of inflammatory responses the most coherent, specific theme for the group.","confidence":"Medium","size":8,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0017143","count":1},{"id":"GO:0010760","count":1},{"id":"GO:0070365","count":1},{"id":"GO:0090350","count":1},{"id":"GO:0071603","count":1}]},{"hash":"127583214572595489","title":"Xenobiotic metabolism and immune regulation","description":"The top GO terms include multiple xenobiotic/detoxification pathways (insecticide metabolism, organofluorine metabolism, coumarin catabolic process, fatty acid omega-oxidation) together with immune-regulatory processes (negative regulation of macrophage chemotaxis, negative regulation of chronic inflammatory response) and some developmental/adhesion terms. This points to a cluster with detoxification and immune-modulatory roles, though the presence of non-metabolic terms reduces the cohesiveness of a single theme. Low","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017143","count":2},{"id":"GO:0010760","count":2},{"id":"GO:0070365","count":2},{"id":"GO:0090350","count":2},{"id":"GO:0071603","count":2}]},{"hash":"2261901840555283963","title":"Immune and Growth Factor Receptor Signaling","description":"The terms cluster around receptor-mediated signaling (integrin, PDGF, insulin, TRK) with immune activation (innate immunity, T cell differentiation) and developmental signals (heart development), suggesting a unifying theme of signaling coordinating immunity and growth.","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0007229","count":2},{"id":"GO:0036120","count":2},{"id":"GO:0010863","count":2},{"id":"GO:0001865","count":2}]},{"hash":"613596732563362069","title":"Retroviral DNA integration and latency","description":"The top terms emphasize DNA-level processes, especially DNA integration, DNA recombination, and establishment of integrated proviral latency, which together point to factors involved in retroviral genome insertion and persistent latency. While some metabolic terms appear, the dominant theme is nucleic acid processing tied to viral integration. Confidence: Medium","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":2},{"id":"GO:0098789","count":2},{"id":"GO:0015074","count":2},{"id":"GO:0075713","count":2},{"id":"GO:0039651","count":2}]},{"hash":"1610392087379162535","title":"Mitotic spindle assembly and chromosome alignment","description":"The top GO terms point to mitosis-related processes: spindle assembly/elongation, metaphase chromosome alignment, centrosome separation, and microtubule polarity with plus-end directed transport along microtubules. This suggests a cluster of proteins coordinating microtubule-based spindle organization and chromosome segregation, with one outlier term on Purkinje cell layer structure that does not override the overall mitotic signal.","confidence":"High","size":8,"edges":10,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000742","count":7},{"id":"GO:0000022","count":6},{"id":"GO:0090307","count":6},{"id":"GO:0007080","count":6},{"id":"GO:1990942","count":6}]},{"hash":"757123341714808262","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":7,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0000466","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0042273","count":2}]},{"hash":"1168115902359238142","title":"Membrane Transporters for Ions, Sugars, and Xenobiotics","description":"This cluster shows GO terms centered on transmembrane transport across membranes for ions (sodium, potassium, phosphate), sugars (arabinose, fucose), and xenobiotics, plus a vesicular transport step for neurotransmitter loading. While metabolism terms appear (fucose metabolism, nitrate assimilation), the common thread is transport across membranes, suggesting a coherent group of transporter-related proteins.","confidence":"High","size":8,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":3},{"id":"GO:0035435","count":3},{"id":"GO:0006004","count":3},{"id":"GO:0006855","count":3},{"id":"GO:0071805","count":3}]},{"hash":"344243001840548448","title":"Retrotransposition and DNA Integration","description":"This cluster is enriched for retrotransposition and DNA integration terms (both 4 hits), pointing to proteins involved in mobile genetic element activity. Additional GO terms connect to RNA polymerase III transcription (including tRNA transcription) and broader transcription, suggesting these proteins may operate at the intersection of transposition-related processes and transcriptional machinery. Overall, the dominant theme is transposable element dynamics with DNA integration. ","confidence":"Medium","size":8,"edges":19,"triangles":20,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0032197","count":4},{"id":"GO:0015074","count":4},{"id":"GO:0006351","count":2},{"id":"GO:0006385","count":1},{"id":"GO:0042797","count":1}]},{"hash":"1607020868774531895","title":"Ribosome biogenesis and cell division","description":"This cluster is dominated by terms for ribosome assembly and protein synthesis (translation, ribosome biogenesis, tRNA modification, cytoplasmic translation, ribosomal export) and is supplemented by cell cycle and division processes (cell cycle, cell division, cell septum assembly), suggesting a coordinated program of growth-related translation with division machinery.","confidence":"High","size":8,"edges":19,"triangles":26,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0000055","count":3},{"id":"GO:0007049","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0090529","count":2}]},{"hash":"1204228357752681501","title":"Developmental signaling and transcriptional regulation","description":"The terms cluster around developmental processes for multiple tissues (heart, skeletal, nervous system) and include transcriptional regulation and Rho-GTPase signaling, with additional hints of calcium-dependent exocytosis and cell division. This suggests a broad developmental/regulatory module where signaling, transcription control, and cytoskeletal dynamics coordinate growth and differentiation, rather than a single, narrow pathway.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":2},{"id":"GO:0001501","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0045956","count":2},{"id":"GO:0007124","count":2}]},{"hash":"2234389221730590288","title":"RNA processing and nuclear transport","description":"These terms cluster around RNA metabolism and trafficking: spliceosome and snRNP assembly, mRNA deadenylation and decapping, P-body assembly, and import into the nucleus are key aspects of RNA processing both in the nucleus and cytoplasm. Additional terms related to cell cycle regulation and chromatin remodeling appear secondary, so the dominant theme is RNA processing and nuclear transport.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0070317","count":7},{"id":"GO:0000245","count":7},{"id":"GO:0000290","count":7},{"id":"GO:0033962","count":7},{"id":"GO:0009737","count":7}]},{"hash":"395977578858336930","title":"Chromatin remodeling and heterochromatin maintenance","description":"The cluster is strongly enriched for chromatin-related processes: regulation of centromere complex assembly, pericentric heterochromatin formation, rDNA heterochromatin formation, nucleosome mobilization, and transcription initiation-coupled chromatin remodeling. These terms point to a shared function in organizing and regulating chromatin architecture, with developmental terms like spermatid development and midbrain morphogenesis likely reflecting downstream roles of chromatin regulators. Despite some obsoleted terms, the core theme is chromatin dynamics and heterochromatin maintenance.","confidence":"High","size":8,"edges":7,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090230","count":2},{"id":"GO:0007286","count":2},{"id":"GO:0042766","count":2},{"id":"GO:0030466","count":2},{"id":"GO:0045815","count":2}]},{"hash":"1597210041083215047","title":"RNA Splicing and Translation Initiation","description":"This cluster is characterized by spliceosome-mediated splicing (including alternative splicing and splice site recognition), mRNA export, and regulation of translation initiation and reinitiation, suggesting proteins involved in RNA processing and initiation of translation. ","confidence":"High","size":8,"edges":3,"triangles":0,"max_degree":3,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0002188","count":2},{"id":"GO:0006376","count":2},{"id":"GO:0060211","count":2}]},{"hash":"610174285813346301","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0016237","count":1},{"id":"GO:2000769","count":1},{"id":"GO:0006799","count":1},{"id":"GO:0042144","count":1},{"id":"GO:0007034","count":1}]},{"hash":"2254708517147291580","title":"Chitin and peptidoglycan cell wall metabolism","description":"The dominant GO terms revolve around cell wall components and remodeling, including chitin catabolic and biosynthetic processes, peptidoglycan catabolic/biosynthetic pathways, and cell wall organization. This points to a coherent theme of cell wall metabolism and remodeling, despite one vesicle-transport term and a sporulation term present as minor notes. Confidence in this label is Medium.","confidence":"","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006890","count":2},{"id":"GO:0008360","count":1},{"id":"GO:0071323","count":1},{"id":"GO:0016998","count":1},{"id":"GO:1902083","count":1}]},{"hash":"493075554531768757","title":"T Cell Signaling and Differentiation","description":"The top GO terms cluster around adaptive immune functions: T cell homeostasis, T follicular helper cell differentiation, and responses to GM-CSF, alongside a p38 MAPK cascade link\u2014together these point to T cell signaling and differentiation. A few terms (splicing complex assembly, cell wall organization) appear unrelated or incidental, likely reflecting multifunctionality or annotation noise. Thus, the core theme is T cell signaling/differentiation.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":2},{"id":"GO:0038066","count":1},{"id":"GO:1904628","count":1},{"id":"GO:0002635","count":1},{"id":"GO:0000244","count":1}]},{"hash":"25790963675252490","title":"Chromatin Regulation and Transcription with Genome Mobility","description":"The cluster is dominated by chromatin-related processes (histone deubiquitination, histone H3 acetylation) and RNA polymerase II transcription initiation/activity, while also featuring terms tied to genome dynamics (DNA integration, retrotransposition, viral genome entry) and growth/invasive responses, suggesting a cohesive theme around transcriptional regulation linked to genome mobility and growth programs.","confidence":"Medium","size":8,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016578","count":2},{"id":"GO:0043966","count":2},{"id":"GO:0051123","count":2},{"id":"GO:0009960","count":2},{"id":"GO:0001403","count":2}]},{"hash":"153857924102390888","title":"Regulation of Cell Cycle, Apoptosis, and Signaling","description":"The GO terms point to regulatory roles across multiple critical pathways: cell cycle regulation; negative regulation of apoptotic and necroptotic processes; transcriptional regulation by RNA polymerase II; regulation of Toll-like receptor signaling; and protein polyubiquitination. The shared theme is control of cell fate and immune signaling through transcriptional and post-translational mechanisms, not core effector functions. Given the sparse one-off terms and lack of dense interactions, this label is a best-fit for a regulatory module rather than a specific process singleton.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071157","count":1},{"id":"GO:0043066","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0034121","count":1},{"id":"GO:0060544","count":1}]},{"hash":"902943407343512727","title":"Protein quality control and folding regulation","description":"In this cluster, many GO terms center on managing protein folding and stress responses: unfolded protein response, chaperone-assisted refolding, and negative regulation of inclusion body formation, along with redox homeostasis that supports proper folding. A few terms (DNA replication, tRNA import) are less clearly connected and may reflect broader cellular processes or annotation noise, but the dominant theme is protein quality control and folding regulation.","confidence":"Medium","size":8,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090084","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0032781","count":2},{"id":"GO:0045454","count":2}]},{"hash":"1014933003467688205","title":"Protein folding stress response","description":"The top GO terms converge on protein quality control under stress\u2014negative regulation of protein kinase activity, response to unfolded protein, and chaperone-related refolding\u2014along with cell redox homeostasis, suggesting a cluster of proteins managing misfolded proteins and proteostasis; a few terms like DNA replication and tRNA import are less aligned but don\u2019t override the dominant signal.","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0090084","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0032781","count":2},{"id":"GO:0045454","count":2}]},{"hash":"1433237061569147532","title":"Ribosome biogenesis and mitotic division","description":"Top GO terms include strong signals for ribosome biogenesis, LSU rRNA maturation, and ribosomal subunit export, plus mitosis-related processes like CENP-A chromatin assembly, microtubule severing, and cytokinesis. Together these point to a functional cluster centered on ribosome production and cell division machinery; other terms (e.g., ER-to-Golgi transport) appear less central.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0006888","count":2},{"id":"GO:0000747","count":2},{"id":"GO:0061641","count":2}]},{"hash":"937776641517192751","title":"Unknown","description":"The GO terms are highly heterogeneous, including redox/metabolic processes (cell redox homeostasis, ubiquinone biosynthesis, 2-oxoglutarate metabolism), RNA/chromatin regulation (transcription regulation in response to oxidative stress, positive regulation of chromatin binding), epigenetic-related activity (DNA methylation-related term, though obsolete), as well as capsule biosynthesis, dopamine catabolism, and erythrocyte differentiation. There isn\u2019t a single unifying function that clearly ties these terms together, so the cluster does not reflect one cohesive biological theme.","confidence":"","size":8,"edges":15,"triangles":7,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0036091","count":2},{"id":"GO:0006744","count":2},{"id":"GO:0002098","count":2},{"id":"GO:0045227","count":2},{"id":"GO:0045454","count":2}]},{"hash":"255735548394333985","title":"Oocyte Maturation and Meiotic Spindle Assembly","description":"The cluster centers on oocyte maturation and spindle assembly in female meiosis I, reinforced by microtubule polymerization and ubiquitin-proteasome\u2013dependent protein turnover, suggesting a module coordinating cell-cycle control and cytoskeletal dynamics during oogenesis. Some neural development terms appear but are less representative of the main signal.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":6},{"id":"GO:0021678","count":5},{"id":"GO:0051436","count":5},{"id":"GO:0021993","count":5},{"id":"GO:0008285","count":5}]},{"hash":"1501119663156247797","title":"Ubiquitin-Dependent Proteolysis & Neural Development","description":"This cluster is driven by GO terms for ubiquitin-dependent proteolysis (SCF-dependent proteasomal ubiquitin-tagged protein catabolism and polyubiquitination) and includes neural development signals (neural tube closure initiation, third ventricle development) as well as synapse assembly, suggesting a theme of protein turnover coordinating neural development. The circadian regulation term adds a regulatory dimension to this proteostasis-neural development link.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":3},{"id":"GO:0042787","count":3},{"id":"GO:0060386","count":2},{"id":"GO:0021678","count":2},{"id":"GO:0000083","count":2}]},{"hash":"2086277700975409277","title":"Genome stability and RNA processing","description":"The top GO terms cluster around genome maintenance (DNA repair, telomere maintenance and capping, mitotic checkpoint signaling) alongside RNA-related processes (tRNA wobble modification, lysyl-tRNA aminoacylation, translation, and mitochondrial tRNA aminoacylation). This suggests a functional theme centered on preserving genome integrity with linked RNA metabolism and translation activities, justifying a label that captures both genome stability and RNA processing roles. ","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0002101","count":4},{"id":"GO:0006281","count":4},{"id":"GO:0010833","count":4},{"id":"GO:0071915","count":4},{"id":"GO:0006412","count":4}]},{"hash":"2101983308140531949","title":"Central carbon metabolism and growth","description":"The cluster is dominated by glycolytic and TCA cycle terms (glycolytic process, tricarboxylic acid cycle, 2-oxoglutarate metabolism) with related metabolism like glutathione, plus growth-related terms (cell division, positive regulation of cell size) and some carbohydrate biosynthesis. This points to a unified theme of central metabolism fueling growth and biosynthesis, with some ancillary biosynthetic processes.","confidence":"Medium","size":7,"edges":9,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006096","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0006099","count":3},{"id":"GO:0006103","count":3},{"id":"GO:0045227","count":3}]},{"hash":"252475420472419825","title":"Plant jasmonate/oxylipin signaling under stress","description":"This cluster is dominated by GO terms for oxylipin and jasmonic acid biosynthesis, and stress responses (response to toxic substances, response to ozone), plus lipid metabolism (unsaturated fatty acid oxidation). The inclusion of stamen development aligns with jasmonate\u2019s known role in reproductive development, supporting a cohesive theme of plant lipid signaling and stress response pathways centered on jasmonate/oxylipin biology.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":2},{"id":"GO:0048443","count":1},{"id":"GO:0010193","count":1},{"id":"GO:0031408","count":1},{"id":"GO:0033543","count":1}]},{"hash":"297986663507660526","title":"Cellular metabolism and stress response","description":"The cluster includes several biosynthetic processes (sterol, phosphatidylcholine, polyamine synthesis) and RNA-related activities (tRNA wobble modification, ribosomal small subunit export), indicating core metabolic and translation-related functions. The presence of GO terms for redox homeostasis and cellular response to xenobiotic stimuli suggests a concurrent role in stress adaptation. Together, these terms point to a metabolism-centric cluster with supportive stress-response functions rather than a single, cohesive pathway.","confidence":"Medium","size":7,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0006972","count":2},{"id":"GO:0000056","count":2},{"id":"GO:0002098","count":2}]},{"hash":"1800688550144114521","title":"Amino acid and polyamine metabolism","description":"This cluster centers on biosynthesis and catabolism of amino acids (beta-alanine, proline, alanine, lysine-related terms) and polyamine-related pathways (putrescine, GABA), indicating a shared theme of amino acid\u2013derived metabolite turnover. Some metabolites also touch on related pathways like porphyrin biosynthesis and antibiotic biosynthesis, but the dominant signal is amino acid and polyamine metabolism. ","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0019483","count":1},{"id":"GO:0009447","count":1},{"id":"GO:0009413","count":1},{"id":"GO:0055129","count":1},{"id":"GO:0006782","count":1}]},{"hash":"1267898743424964825","title":"Membrane Solute Transporters","description":"The cluster shows a clear enrichment for transmembrane transport terms\u2014sialic acid, phosphate, potassium, organic cation/anion, and xenobiotic transport across the plasma membrane\u2014suggesting these proteins function as membrane transporters for diverse solutes. A couple of metabolic GO terms about substrates (fucose, L-ascorbic acid) may reflect transported substrates rather than core functions. Overall, the dominant theme is membrane transport activity.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":1},{"id":"GO:0070715","count":1},{"id":"GO:1904728","count":1},{"id":"GO:0097080","count":1},{"id":"GO:0035435","count":1}]},{"hash":"86119426701809453","title":"Steroid and lipid metabolism","description":"The top GO terms cluster around steroid and lipid processes, including androgen and C21-steroid hormone metabolism, various lipid biosynthesis and catabolic pathways (very long-chain fatty acids, mycolic acid, retinol, 3-keto-sphinganine), and related catabolic steps, suggesting a coherent functional theme of lipid and steroid metabolism; a few terms on transcription regulation and drug response appear as peripheral annotations but do not define the core function.","confidence":"High","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006710","count":7},{"id":"GO:0006666","count":7},{"id":"GO:0006355","count":7},{"id":"GO:0006706","count":7},{"id":"GO:0031427","count":7}]},{"hash":"2218134425018015274","title":"Xenobiotic and fatty acid metabolism","description":"This cluster is dominated by GO terms related to processing foreign compounds and lipids, such as insecticide metabolic process, organofluorine metabolism, coumarin catabolic process, and fatty acid omega-oxidation, indicating a common theme of xenobiotic and lipid metabolism. While there are also terms for immune regulation and development, the strongest signal centers on metabolic processing of xenobiotics and fatty acids. ","confidence":"Medium","size":7,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0017143","count":5},{"id":"GO:0010760","count":5},{"id":"GO:0070365","count":5},{"id":"GO:0090350","count":5},{"id":"GO:0071603","count":5}]},{"hash":"1268299266076158156","title":"Carbohydrate, amino acid, and isoprenoid metabolism","description":"The top GO terms point to multiple metabolic pathways: carbohydrate phosphorylation and galactose/glycolytic processes; threonine/homoserine and methionine biosynthesis; galactitol metabolism; GDP-L-fucose salvage; and the mevalonate pathway for isoprenoid biosynthesis. This pattern indicates a cluster of proteins involved in diverse central metabolic processes, especially carbohydrate and amino acid metabolism, with a notable link to isoprenoid biosynthesis. Confidence: Medium","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":3},{"id":"GO:0019629","count":2},{"id":"GO:0009088","count":2},{"id":"GO:0061623","count":2},{"id":"GO:0010142","count":2}]},{"hash":"1948822286587933787","title":"Nucleotide Salvage and CoA Biosynthesis","description":"This cluster centers on nucleotide salvage reactions (UMP, CMP, uracil salvage) and coenzyme A biosynthesis, indicating a core metabolic theme around nucleotide and cofactor metabolism. The additional GO terms suggest broader metabolic and regulatory connections (insulin signaling, CDK activity, fatty acid biosynthesis), but the salvage and CoA biosynthesis signals are the most cohesive through-line. ","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0015937","count":2},{"id":"GO:0046626","count":2},{"id":"GO:0045737","count":2},{"id":"GO:0045717","count":2},{"id":"GO:0044211","count":1}]},{"hash":"1895365054880623012","title":"Protein folding, assembly, and degradation","description":"This cluster gathers GO terms centered on protein homeostasis: folding/refolding and oligomerization (hexamerization, complex assembly), as well as proteasomal degradation and inclusion body formation. There are also related trafficking/organization terms (ER\u2013Golgi transport, ER polarization) and mitochondrial functions (oxidative phosphorylation, complex III assembly), suggesting a broad theme of maintaining protein integrity across compartments. However, the mix includes some less-connected terms (DNA replication, translesion synthesis), so the link is plausible but not perfectly tight.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1903862","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0070389","count":1},{"id":"GO:0070987","count":1},{"id":"GO:1901800","count":1}]},{"hash":"1368749656688721964","title":"Ion and Small Molecule Membrane Transport","description":"These proteins cluster around transmembrane transport activities, with GO terms covering various ion transport (sodium, potassium) and organic molecule transport (organic cations/anions, xenobiotics), as well as transport of sialic acid, phosphate, fucose and ascorbic acid substrates. Although a couple of metabolic GO terms appear, the dominant pattern is diverse plasma membrane transport, suggesting a transporter-centric group rather than a single substrate pathway.","confidence":"High","size":7,"edges":16,"triangles":16,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":1},{"id":"GO:0070715","count":1},{"id":"GO:1904728","count":1},{"id":"GO:0097080","count":1},{"id":"GO:0035435","count":1}]},{"hash":"1804920404504012275","title":"Unknown","description":"The top GO terms are highly diverse, spanning autophosphorylation regulation, mitosis, GPCR signaling, rRNA maturation, ER-Golgi transport, translation reinitiation, splicing, histone methylation, and mitochondria-nucleus signaling. With no edges or shared functional connections, there is no clear cohesive theme to tie these proteins together, so a specific, representative cluster label cannot be assigned.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031954","count":3},{"id":"GO:0090307","count":3},{"id":"GO:0007200","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0006888","count":2}]},{"hash":"471335140741791778","title":"Apoptosis and Innate Immune Response","description":"The top GO terms cluster around programmed cell death (apoptosis, pyroptosis) and innate immune defense (innate response, defense against Gram-positive bacteria), with additional ubiquitination activity that modulates these pathways. Together these terms point to a functional theme of inflammatory cell death and immune signaling, with some residual signals related to cell cycle/maintenance.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0016567","count":3},{"id":"GO:0090307","count":3},{"id":"GO:1990001","count":3}]},{"hash":"1095613484058911687","title":"Proteostasis and Protein Folding Stress Response","description":"This cluster\u2019s GO terms cluster around protein quality control and stress responses: unfolded protein response, chaperone-assisted/refolding processes, negative regulation of protein kinase activity in stress contexts, and redox/homeostatic maintenance. These collectively point to maintaining proteome integrity under cellular stress, with a few outliers (like DNA replication and tRNA import) that are less central to the main theme.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0090084","count":5},{"id":"GO:0006469","count":5},{"id":"GO:0070389","count":5},{"id":"GO:0032781","count":5},{"id":"GO:0045454","count":5}]},{"hash":"1027658641172675321","title":"DNA replication-dependent chromatin assembly","description":"The Top Terms are dominated by chromatin-related processes tied to DNA replication, including replication-dependent chromatin assembly, chromatin organization, and heterochromatin formation, with additional links to DNA repair and cell cycle. This suggests a cohesive group of proteins coordinating chromatin packaging and silencing during DNA replication, rather than unrelated functions.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0006335","count":1},{"id":"GO:0045899","count":1},{"id":"GO:0030466","count":1}]},{"hash":"2050101670840475301","title":"Unknown","description":"The terms span highly diverse processes (GPCR signaling, rRNA maturation, ER-Golgi transport, translation reinitiation, splicing, chromatin modification, mitochondria-to-nucleus signaling, fertilization, TGF-beta response) with no clear common function. The cluster has no edges or shared interactions (Edges: 0; Triangles: 0; Max Degree: 0), indicating a non-cohesive set rather than a single pathway, so no interpretable theme emerges.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007200","count":1},{"id":"GO:0000466","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0002188","count":1},{"id":"GO:0090344","count":1}]},{"hash":"2162567400962457261","title":"Multiorgan morphogenesis and differentiation","description":"The top GO terms cluster around developmental morphogenesis across multiple organs (bronchiole development, nephron tubule morphogenesis, cardiac septum morphogenesis) plus myoblast fate determination and integrin-mediated adhesion, indicating a shared theme of tissue formation and differentiation rather than a single pathway. The diversity of tissues involved suggests these proteins participate in general morphogenetic processes during development.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042981","count":1},{"id":"GO:0060435","count":1},{"id":"GO:0072049","count":1},{"id":"GO:0007518","count":1},{"id":"GO:0072282","count":1}]},{"hash":"934921973992592550","title":"Sodium/Potassium Ion Transport and Membrane Potential","description":"The cluster\u2019s top GO terms are dominated by sodium and potassium transport (import/export) across the plasma membrane and membrane depolarization, indicating a core function in ion homeostasis and excitability. Other terms related to cuticle development and glycosylation are present but less representative of the main theme, so the label reflects the strongest shared function among the proteins.","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0098719","count":2},{"id":"GO:0030007","count":2},{"id":"GO:0097623","count":2},{"id":"GO:0008363","count":2},{"id":"GO:0097370","count":2}]},{"hash":"1019307280515210537","title":"Unknown","description":"The cluster shows a highly heterogeneous mix of GO terms (DNA recombination and repair; post-translational modification; S-layer organization; glycoprotein processing/metabolism; transport), with only a few terms represented and several marked obsolete. There is no clear, shared biological process or function tying the proteins together, so a specific label cannot be inferred.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006310","count":2},{"id":"GO:0043687","count":1},{"id":"GO:0045232","count":1},{"id":"GO:0006516","count":1},{"id":"GO:0043686","count":1}]},{"hash":"1702506469004649371","title":"Innate immune signaling and inflammatory mediator regulation","description":"Based on the GO terms, the cluster highlights innate immune signaling and inflammatory mediator production, including NOD1 signaling (GO:0070427), positive regulation of CCL5 production (GO:0071651), and positive regulation of MIP-1 alpha production (GO:0071642), as well as macrophage-related processes (negative regulation of foam cell differentiation). Although other terms touch on neural development and general gene regulation, the set with immune signaling and chemokine regulation dominates, suggesting a cluster centered on innate immune responses and inflammatory mediator regulation.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021707","count":1},{"id":"GO:0010745","count":1},{"id":"GO:0071651","count":1},{"id":"GO:0016049","count":1},{"id":"GO:0071642","count":1}]},{"hash":"1396657874172383741","title":"Ribosome biogenesis and cell division","description":"The cluster is dominated by ribosome-related processes (ribosome biogenesis; ribosomal subunit export from the nucleus; cytoplasmic translation; tRNA modification) and cell-cycle/division activities (cell cycle; cell division; cell septum assembly). This suggests a coherent module where ribosome production and translation machinery are linked to cell cycle progression and cytokinesis, with a minor outlier term related to salt stress. ","confidence":"High","size":7,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0000055","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0090529","count":2},{"id":"GO:0051301","count":2}]},{"hash":"176709933379622013","title":"Neural and Epidermal Differentiation Signaling","description":"The terms cluster around development and differentiation across neural and skin lineages, including forebrain development, visual perception, keratinocyte differentiation, and regulatory signaling pathways (Wnt, Hippo) that govern proliferation and apoptosis. This points to a cohesive theme of developmental signaling guiding cell fate in diverse tissues rather than a single pathway, justifying the label Neural and Epidermal Differentiation Signaling.","confidence":"High","size":7,"edges":5,"triangles":0,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0007601","count":4},{"id":"GO:0090263","count":4},{"id":"GO:0006915","count":4},{"id":"GO:0030216","count":4}]},{"hash":"2059890864269185867","title":"Viral entry and proviral latency in host","description":"Top terms such as viral penetration into host nucleus, DNA integration, and establishment of integrated proviral latency indicate a cluster centered on viral infection mechanisms and proviral latency within the host. Additional terms about symbiont entry and host apoptosis activation, along with innate immune response, support a host\u2013virus interaction theme. Therefore, the label viral entry and proviral latency in host captures the core function.","confidence":"High","size":7,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0033138","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0075732","count":2},{"id":"GO:0015074","count":2}]},{"hash":"1306559505006819329","title":"Unknown","description":"The seven proteins show a highly diverse set of GO terms, spanning GPCR signaling, rRNA processing, ER\u2013Golgi transport, translation reinitiation, mRNA splicing, histone methylation, mitochondria\u2013nucleus signaling, fertilization, and TGF-beta response, with no single dominant function or pathway emerging. The mixture (and presence of some obsolete terms) suggests no coherent common theme to label a specific function for the cluster. Therefore, there is no reliable, specific label beyond Unknown.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007200","count":1},{"id":"GO:0000466","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0002188","count":1},{"id":"GO:0090344","count":1}]},{"hash":"1736869842278348420","title":"Mitochondrial Cofactor and Ion Transport","description":"The cluster is dominated by GO terms for transport of cofactors and metabolites across membranes (thiosulfate, pyridoxal phosphate, thiamine pyrophosphate, citrate, deoxynucleotides, manganese), many of which are linked to mitochondrial function. Additional terms on mitochondrial membrane potential regulation and response to superoxide point to a focus on mitochondrial redox balance and energy metabolism. A couple of terms (microtubule anchoring at centrosome, liver regeneration) are less central to this theme, likely representing broader cellular or tissue contexts, but the core signal supports a cohesive theme of mitochondrial cofactor/ion transport and stress response. ","confidence":"High","size":7,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0097421","count":3},{"id":"GO:0034454","count":3},{"id":"GO:0051881","count":2},{"id":"GO:0015709","count":2},{"id":"GO:0031921","count":2}]},{"hash":"40709142427951000","title":"Neural development and signaling","description":"Key terms cluster around nervous system development, neurogenesis, and axon guidance (Roundabout pathway), plus related signaling; accompanying terms cover general transport and transcription regulation that occur during development.","confidence":"Medium","size":7,"edges":12,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":2},{"id":"GO:0022008","count":2},{"id":"GO:0007283","count":2},{"id":"GO:0035385","count":2},{"id":"GO:0050852","count":2}]},{"hash":"1045109111588185269","title":"ER-Golgi vesicle trafficking regulation","description":"The dominant GO terms point to vesicle transport between the ER and Golgi, including retrograde Golgi-to-ER transport and positive regulation of ER-to-Golgi transport, with ubiquitination suggesting regulatory control. Other terms (dendrite development, axon guidance, epithelial polarity, apoptosis) may reflect broader cellular roles or pleiotropy, but the core signal is ER-Golgi trafficking regulation.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006890","count":2},{"id":"GO:0033028","count":2},{"id":"GO:0071260","count":2},{"id":"GO:2000171","count":2},{"id":"GO:0097284","count":2}]},{"hash":"1591254525178934785","title":"Retroviral DNA integration and proviral latency","description":"The Top Terms cluster around steps in the retroviral life cycle: reverse transcription (RNA-templated DNA biosynthetic process), DNA integration, DNA recombination, and establishment of integrated proviral latency, plus notes on viral entry into the host nucleus and host responses. This combination suggests a cohesive theme of proviral integration and latency maintenance by retroviruses, with related host interaction processes. ","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0075732","count":3},{"id":"GO:0015074","count":3},{"id":"GO:0046718","count":3},{"id":"GO:0039651","count":3}]},{"hash":"1674201616107796153","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":2},{"id":"GO:0051591","count":1},{"id":"GO:0006546","count":1},{"id":"GO:0034516","count":1},{"id":"GO:0046724","count":1}]},{"hash":"1770745338748280639","title":"Unknown","description":"The top GO terms span xenobiotic metabolism, inflammatory regulation, endothelial adhesion, and various developmental and hormonal processes, with no clear single function tying them together. Edges are absent, so there is no cohesive network to define a specific, interpretable label. None","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017143","count":5},{"id":"GO:0010760","count":5},{"id":"GO:0070365","count":5},{"id":"GO:0090350","count":5},{"id":"GO:0071603","count":5}]},{"hash":"43186254213638718","title":"Cytochrome P450\u2013mediated xenobiotic detoxification","description":"Top GO terms point to epoxygenase P450 pathway, insecticide metabolism, and coumarin catabolic processes, indicating detoxification/metabolism of xenobiotics by cytochrome P450 enzymes. Additional terms related to methylation, inflammatory regulation, endothelial adhesion, and hepatocyte differentiation suggest broader regulatory roles but the dominant signal is P450-driven detoxification. This cluster is best described as a detox/metabolism group with P450 involvement, with some ancillary immune and differentiation associations.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900087","count":3},{"id":"GO:0032259","count":3},{"id":"GO:0019373","count":3},{"id":"GO:0017143","count":2},{"id":"GO:0010760","count":2}]},{"hash":"1325956322747163174","title":"Ribosome biogenesis and translation","description":"The cluster is strongly enriched for translation- and ribosome-related GO terms (cytoplasmic and mitochondrial translation, translational termination, ribosomal subunit assembly, and rRNA maturation), indicating a core role in ribosome biogenesis and the translation machinery; the presence of antibiotic response terms aligns with ribosome-targeting stress contexts, supporting this as a cohesive translation-focused cluster.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0032543","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0006415","count":1}]},{"hash":"1329393704222756355","title":"Diverse substrate transmembrane transport","description":"The top GO terms point to transport of a wide range of substrates across membranes, including ions (protons, potassium), sugars (arabinose, galactose, fucose), phosphate and nitrate-related transport, and vesicular neurotransmitter loading, suggesting a cluster of proteins that broadly facilitate membrane transport of diverse solutes rather than a single substrate.","confidence":"High","size":6,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1902600","count":3},{"id":"GO:0015739","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0015751","count":2}]},{"hash":"1024028469198083168","title":"DNA-Templated Transcription Regulation Complexes","description":"The dominant GO terms point to regulation of DNA-templated transcription and transcription from DNA templates, and the presence of protein heterooligomerization suggests these proteins form transcription-regulating complexes. A single innate immune term is present but not central, so the core theme is transcription regulation via multi-protein complexes.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0000746","count":1},{"id":"GO:0006627","count":1},{"id":"GO:2000531","count":1}]},{"hash":"1271686511178710656","title":"Ribosome Biogenesis and Translation","description":"Dominant GO terms center on ribosome biogenesis, translation, and ribosomal subunit export, with supporting cues from cytoplasmic translation and tRNA modification. The inclusion of cell cycle and division terms suggests a link between ribosome production and proliferation, while septum assembly and conjugation hints reflect broader growth-related processes. Overall, the cluster is best characterized by ribosome assembly and protein synthesis functions.","confidence":"High","size":6,"edges":7,"triangles":4,"max_degree":4,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0006412","count":4},{"id":"GO:0007049","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0090529","count":2}]},{"hash":"1473071340960472555","title":"Ubiquitin-regulated immune signaling","description":"The cluster centers on immune-related signaling pathways (TNF signaling, Fc-epsilon receptor signaling, antigen processing/presentation via MHC I) and ubiquitin-related processes (deubiquitination, regulation of ubiquitin ligase activity), suggesting proteins that coordinate ubiquitin-dependent control of immune signaling. ","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":6},{"id":"GO:0010043","count":5},{"id":"GO:0038095","count":5},{"id":"GO:0090090","count":5},{"id":"GO:0002479","count":5}]},{"hash":"918920836188287142","title":"Unknown","description":"The top GO terms span a mix of unrelated processes (ubiquitin-dependent ERAD, multicellular growth, genomic imprinting regulation, GPCR signaling, rRNA maturation, ER\u2013Golgi transport, translation reinitiation, splicing, histone methylation, aging). With no network connections (edges/triangles zero) and many terms labeled obsolete, there isn\u2019t a clear, unified function to label this cluster, so a confident representative name cannot be assigned.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0035264","count":3},{"id":"GO:0006349","count":3},{"id":"GO:0007200","count":2},{"id":"GO:0000466","count":2}]},{"hash":"1279322794296067035","title":"Protein catabolism and turnover","description":"The top GO terms are dominated by proteolysis and protein degradation (proteasomal ubiquitin-dependent protein catabolic process, peptide catabolic process, vacuolar proteolysis), indicating a cluster centered on protein turnover; other terms such as DNA repair and mitochondrial ATP synthesis are present but less central, suggesting them as peripheral annotations.","confidence":"High","size":6,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032435","count":1},{"id":"GO:0006281","count":1},{"id":"GO:0042775","count":1},{"id":"GO:0015774","count":1},{"id":"GO:0007039","count":1}]},{"hash":"1264498337363732091","title":"Gene Expression Regulation and Protein Ubiquitination","description":"This cluster centers on regulation of gene expression and protein modification (negative regulation of transcription by RNAP II, ncRNA-mediated silencing, regulation of mRNA splicing, and positive/overall protein ubiquitination). Additional terms touch on circadian regulation and synapse-related processes, which can tie into gene expression control. Some terms (cobalamin biosynthesis, tRNA wobble modification) are less connected but may reflect broader cellular contexts rather than a single function.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":3},{"id":"GO:0009236","count":2},{"id":"GO:0002098","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0031047","count":2}]},{"hash":"1335923748282972717","title":"RNA splicing and transcription regulation","description":"The top terms center on mRNA splicing via the spliceosome, ncRNA-mediated gene silencing, and regulation of transcription by RNA polymerases I and III, plus translation initiation, pointing to a cluster focused on RNA processing and transcription control. Some terms (DNA replication, heat response) are ancillary but do not override the core theme.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0009408","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0045292","count":2}]},{"hash":"402787074413518538","title":"RNA Pol II Transcription Regulation","description":"This cluster\u2019s top GO terms are centered on transcription controlled by RNA polymerase II, including regulation of DNA-templated transcription, transcription initiation at RNA Pol II promoters, and RNA Pol II preinitiation complex assembly, with an additional note on Notch target transcription regulation. Peripheral terms such as snoRNP assembly and chromatin-related acetylation hint at related nuclear processes, but the dominant theme is transcription regulation by RNA Pol II.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0006367","count":1},{"id":"GO:0042795","count":1},{"id":"GO:0035372","count":1},{"id":"GO:1902897","count":1}]},{"hash":"52189317566092656","title":"Mitochondrial apoptosis regulation and DNA damage response","description":"Most terms point to mitochondrial function, including assembly of respiratory chain complexes and regulation of cytochrome c release, plus p53-mediated DNA damage response and apoptosis control. A few terms on phospholipid transport reinforce mitochondrial membrane dynamics, collectively defining a mitochondrial stress-response and apoptosis-regulation module.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045332","count":1},{"id":"GO:0033108","count":1},{"id":"GO:0006626","count":1},{"id":"GO:1902166","count":1},{"id":"GO:2001140","count":1}]},{"hash":"524547431575980556","title":"Ubiquitin-Proteasome Regulation of Cell Cycle","description":"The cluster is dominated by GO terms tied to ubiquitin-dependent proteolysis, including SCF- and APC/C-mediated ubiquitination and proteasomal degradation (e.g., K11-linked ubiquitination, general ubiquitin-dependent catabolic processes) and neddylation, which regulates cullin-RING ligases. This strongly points to a coordinated ubiquitin-proteasome system underpinning cell cycle progression (cell division, mitotic checkpoints, APC/C-dependent catabolic processes) and genome maintenance (DNA damage response and nucleotide-excision repair). The presence of viral process terms may reflect viral interactions with ubiquitin pathways, but the core signal remains proteolysis-driven cell cycle regulation and repair. ","confidence":"High","size":6,"edges":8,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":5},{"id":"GO:1902916","count":4},{"id":"GO:0031571","count":4},{"id":"GO:0070979","count":3},{"id":"GO:0051301","count":3}]},{"hash":"1495665136210569239","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":11,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0042274","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0070058","count":2}]},{"hash":"1233888579777482015","title":"Lipid Biosynthesis and Fatty Acid Metabolism","description":"The top GO terms cluster around lipid metabolism and processing, including fatty acid response, monounsaturated fatty acid biosynthesis, sphinganine (a sphingolipid) metabolism, cholesterol esterification, and adipose-related differentiation. Some terms are insect- or obsolete-specific, but the dominant theme is lipid biosynthesis and lipid-related signaling/storage. Confidence: Medium","confidence":"","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0010205","count":2},{"id":"GO:0044130","count":2},{"id":"GO:0034435","count":2},{"id":"GO:0010873","count":2},{"id":"GO:1903699","count":2}]},{"hash":"1169790224956456698","title":"Unknown","description":"The six proteins have a highly diverse set of GO terms, including ribosome biogenesis, chromatin organization, UV response, ER vesicle fusion, and plant developmental terms, with no clear shared function or dominant pathway. Because no coherent theme emerges, a specific functional label cannot be reliably assigned.","confidence":"","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0042273","count":1},{"id":"GO:0035067","count":1},{"id":"GO:0010582","count":1},{"id":"GO:0002903","count":1},{"id":"GO:2001243","count":1}]},{"hash":"1897074914906253426","title":"Ubiquitin-Dependent Proteolysis and Innate Immunity","description":"This cluster is enriched for ubiquitin-mediated proteolysis (SCF-dependent and general ubiquitin-dependent protein catabolic processes) and innate immune signaling (TLR6 pathway, IL-6 production, defense against Gram-positive bacteria). Some terms touch on development or neuronal processes, but the core pattern supports a link between protein turnover and innate immune responses.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0002322","count":1},{"id":"GO:0061368","count":1},{"id":"GO:0045087","count":1}]},{"hash":"341850637051340191","title":"Proteasome-Dependent Protein Degradation","description":"The top GO terms point to ubiquitin-dependent protein catabolic processes and proteasome-mediated ubiquitin-dependent protein degradation, suggesting a proteolysis-centric cluster. The other terms (enucleate erythrocyte development, negative regulation of gluconeogenesis, and negative regulation of myeloid cell apoptosis) are less directly related, so the dominant theme is proteasome-mediated protein degradation.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048822","count":1},{"id":"GO:0042787","count":1},{"id":"GO:0045721","count":1},{"id":"GO:0043161","count":1},{"id":"GO:0033033","count":1}]},{"hash":"1275007735937149369","title":"DNA Repair and Nuclear Organization","description":"The top terms are dominated by DNA maintenance processes\u2014base-excision repair and DNA recombination\u2014paired with nuclear-related organization and transcription regulation terms, suggesting a core function in genomic maintenance within the nucleus. Some lipid metabolism and ER/nuclear-associated terms appear as minor signals, but they are not as representative of the cluster\u2019s primary function. ","confidence":"Medium","size":6,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":2},{"id":"GO:0006284","count":2},{"id":"GO:0006310","count":2},{"id":"GO:0009062","count":1},{"id":"GO:0019375","count":1}]},{"hash":"1774976254504406057","title":"Glycerolipid Catabolism and Endocannabinoid Signaling","description":"The dominant GO terms are lipid catabolic processes (diacylglycerol, monoacylglycerol, triglyceride, phosphatidylserine) and regulation of endocannabinoid signaling, pointing to a cohesive lipid metabolism and signaling theme; a few outliers (cellulose catabolic process, synapse organization, xenobiotic response) suggest broader or context-specific roles.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":3},{"id":"GO:0042493","count":2},{"id":"GO:0042136","count":2},{"id":"GO:0046340","count":2},{"id":"GO:0052651","count":2}]},{"hash":"659435022903233768","title":"Unknown","description":"No GO terms or functional hints are provided, and with only a small, unannotated set of proteins (6 proteins, 6 edges, 1 triangle) there is no clear shared function to label. Therefore, Unknown with no confidence.","confidence":"","size":6,"edges":6,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[]},{"hash":"1825258296771557090","title":"Xenobiotic Response and Fatty-Acid Metabolism","description":"This cluster shows enrichment for xenobiotic response terms (cellular response to xenobiotic stimulus; response to cocaine) and for fatty-acyl-CoA biosynthesis/catabolism (long- and medium-chain), plus related metabolic processes such as enterobactin biosynthesis and phenylacetate catabolism, pointing to a metabolic theme around xenobiotic handling and lipid substrate processing.","confidence":"Medium","size":6,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":2},{"id":"GO:0001300","count":2},{"id":"GO:0042220","count":2},{"id":"GO:0035338","count":2},{"id":"GO:0051792","count":2}]},{"hash":"2188307170383468008","title":"Vesicle-mediated protein transport","description":"Top GO terms cluster around ER-Golgi and Golgi-plasma membrane trafficking, plus retrograde ER transport and general protein transport, indicating a cohesive focus on intracellular vesicle trafficking and secretion. While there are a few small-molecule transport terms, the dominant signal is vesicle-mediated protein movement, supporting a functionally coherent cluster. ","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0043001","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0015031","count":2},{"id":"GO:0090316","count":2}]},{"hash":"414563637768049583","title":"Neuronal development and vesicle trafficking","description":"The cluster includes forebrain neuron development and acetylcholine receptor signaling, indicating neuronal function, plus strong mentions of ER-Golgi vesicle transport, protein targeting to vacuole, tubulin complex assembly, and cytoskeleton polarity. This combination points to a theme of neuronal differentiation coupled with intracellular transport and cytoskeletal dynamics that support neuron structure and signaling.","confidence":"Medium","size":6,"edges":10,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009785","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0021884","count":4},{"id":"GO:1902953","count":4},{"id":"GO:0000266","count":4}]},{"hash":"2210818348646492753","title":"Ubiquitin-mediated proteolysis and mitotic regulation","description":"This cluster is dominated by ubiquitination-related GO terms (K6- and K27-linked ubiquitination, N-end rule pathway) along with protein catabolic processes, plus mitosis-related terms (mitotic spindle elongation, chromosome segregation). The convergence of ubiquitin signaling with cell-cycle proteolysis suggests a cohesive role in regulating protein turnover during mitosis, with some overlap into DNA damage response pathways.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0000022","count":6},{"id":"GO:0030466","count":6},{"id":"GO:0085020","count":6},{"id":"GO:0070987","count":6},{"id":"GO:1903955","count":6}]},{"hash":"652837026941810766","title":"Golgi- and synaptic vesicle trafficking","description":"The GO terms point to Golgi-associated vesicle transport (ER-to-Golgi, Golgi organization, vesicle fusion with Golgi) together with synaptic vesicle handling (docking, regulation of receptor localization to synapse, and excitation of postsynaptic potential), suggesting a cohesive role in coordinating intracellular trafficking with synaptic function in neurons.","confidence":"High","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":1},{"id":"GO:1902685","count":1},{"id":"GO:1903358","count":1},{"id":"GO:0090166","count":1},{"id":"GO:1903422","count":1}]},{"hash":"1288547697919902874","title":"Redox-related proteins","description":"The Top Term points to an oxidation-reduction process, suggesting these proteins may participate in redox reactions. The GO term is obsolete (GO:0055114), which slightly lowers confidence, and only a single term is observed among 6 proteins, making the signal weak but still indicative of a redox-related cluster.","confidence":"Low","size":6,"edges":10,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":1}]},{"hash":"1574774830258192134","title":"Mitotic spindle and kinetochore regulation","description":"Based on the top GO terms, the cluster is dominated by processes related to mitosis and cell-cycle control: negative regulation of CDK activity, kinetochore localization, spindle microtubule attachment to the kinetochore, and transcriptional regulation during the mitotic cell cycle. While metabolic and neuronal maturation terms appear, the strongest signal is coordination of the spindle-kinetochore apparatus and mitotic regulation, defining a mitosis-focused cluster.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0045736","count":4},{"id":"GO:0006006","count":4},{"id":"GO:0034501","count":4},{"id":"GO:0006695","count":4},{"id":"GO:0014043","count":3}]},{"hash":"305900683709033240","title":"Virus entry and genome integration","description":"The top GO terms point toward stages of viral life cycles and virus-host interactions\u2014virion assembly, DNA integration, and establishment of integrated proviral latency\u2014along with terms about host entry by symbionts and host apoptosis activation. The metabolic terms (NADP/NAD+ metabolism, phosphorylation, and polyphosphate metabolism) may reflect general cellular processes or incidental associations rather than core cluster themes. Overall, a cohesive theme around viral entry, genome integration, and proviral latency best fits the cluster, with some noise from general metabolism terms.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006741","count":1},{"id":"GO:0016310","count":1},{"id":"GO:0006797","count":1},{"id":"GO:0019674","count":1},{"id":"GO:0019068","count":1}]},{"hash":"1351430937201794255","title":"Large subunit ribosome biogenesis and export","description":"This cluster is dominated by GO terms for maturation and assembly of the large ribosomal subunit and its nuclear export (LSU rRNA processing, preribosome assembly, LSU export). A minor outlier is tyrosine dephosphorylation, but the core signal points to LSU biogenesis.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035335","count":1},{"id":"GO:0030389","count":1},{"id":"GO:0000055","count":1},{"id":"GO:0000466","count":1},{"id":"GO:1902626","count":1}]},{"hash":"471105883877077724","title":"Bacterial glycosylation and O-antigen biosynthesis","description":"This cluster is dominated by GO terms for dolichol-linked and dolichyl diphosphate\u2013dependent glycosylation pathways (N-linked glycosylation, dolichol-linked oligosaccharide biosynthesis, dolichyl diphosphate biosynthetic process) and O-antigen/enterobacterial common antigen biosynthesis, pointing to proteins involved in cell-surface glycan assembly and envelope biosynthesis in bacteria. Additional terms related to cell wall organization and cell division suggest a link to envelope remodeling during growth. ","confidence":"High","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":1},{"id":"GO:0008360","count":1},{"id":"GO:0006489","count":1},{"id":"GO:0009243","count":1},{"id":"GO:0009246","count":1}]},{"hash":"1947200343239995202","title":"Plastid Carbohydrate and Lipid Metabolism","description":"The dominant GO terms\u2014glycolysis, gluconeogenesis, PPP, glycerol catabolic process, and triglyceride mobilization\u2014point to central carbon metabolism and lipid turnover occurring in plastids/ chloroplasts, supported by chloroplast organization. A developmental term (primary root development) is present but the overall theme centers on plastid-centered energy and lipid metabolism in plants.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019563","count":1},{"id":"GO:0006094","count":1},{"id":"GO:0006642","count":1},{"id":"GO:0080022","count":1},{"id":"GO:0032504","count":1}]},{"hash":"2260247645946914207","title":"Diverse Substrate Membrane Transporters","description":"These terms cluster around transmembrane transport of diverse substrates (ions, sugars, vitamins, and metabolites) and neurotransmitter loading into synaptic vesicles, suggesting the proteins function as membrane transporters with broad substrate specificity. The lack of edges implies no inferred interactions beyond shared transport-related annotations.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0015751","count":2},{"id":"GO:0098700","count":2}]},{"hash":"914435607629429258","title":"Glycolysis and PPP Regulation","description":"The GO terms point to regulatory control of central carbon metabolism: fructose metabolism, glycolysis, gluconeogenesis, and the pentose phosphate pathway, with links to serine biosynthesis. Negative regulation of glycolytic flux and glucose-to-lactate conversion further support a theme of balancing energy production and redox state. Some terms like respiratory burst/gaseous exchange are tangential, likely reflecting redox context rather than core metabolism.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045730","count":1},{"id":"GO:0006000","count":1},{"id":"GO:0006003","count":1},{"id":"GO:0045820","count":1},{"id":"GO:0033133","count":1}]},{"hash":"1022290210874473121","title":"Ehrlich pathway ethanol fermentation","description":"Most terms describe ethanol production via the Ehrlich pathway and related pyruvate/branched-chain amino acid catabolic routes (e.g., pyruvate fermentation to ethanol, pyruvate decarboxylation to acetyl-CoA, and aromatic amino acid catabolism to alcohol via Ehrlich pathway), indicating proteins involved in alcohol fermentation and linked carbon metabolism. The connections are coherent but focused on metabolism of pyruvate and amino acids toward alcohol, with a small number of biosynthetic terms attached. High","confidence":"","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019596","count":1},{"id":"GO:0034077","count":1},{"id":"GO:0042867","count":1},{"id":"GO:0000950","count":1},{"id":"GO:0006086","count":1}]},{"hash":"338541907748034915","title":"Transcription-Associated Processes","description":"This cluster is dominated by GO terms related to transcription across RNA polymerase II and I, including transcription initiation, elongation, termination, and transcription-coupled nucleotide-excision repair, suggesting a central theme around transcription machinery and its regulation. A few metabolic and transport terms appear as outliers, indicating the set may include some unrelated annotations, but the prevailing signal points to transcription-related functions.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009255","count":2},{"id":"GO:0009099","count":2},{"id":"GO:0009097","count":2},{"id":"GO:0006366","count":2},{"id":"GO:0006283","count":2}]},{"hash":"1359232868078512890","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044210","count":1},{"id":"GO:0010043","count":1},{"id":"GO:0000105","count":1},{"id":"GO:0070365","count":1},{"id":"GO:0006508","count":1}]},{"hash":"734255353560664740","title":"RNA Pol II Transcription Regulation and Heterochromatin","description":"The top GO terms emphasize DNA-templated transcription and transcription by RNA polymerase II, with concurrent negative regulation signals, plus heterochromatin formation/maintenance terms. This points to a cohesive cluster of factors involved in regulating transcription and chromatin state, including rDNA heterochromatin.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0060766","count":2},{"id":"GO:0045668","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0006366","count":2}]},{"hash":"977221364895176101","title":"Multi-substrate carbon catabolism","description":"The GO terms are dominated by various catabolic processes across substrates (ethanol, retinol, galactose via D-galactonate, formaldehyde, glucose, fatty acids), suggesting the proteins participate in breaking down diverse carbon sources rather than a single pathway. While the specific substrates differ, the shared theme is catabolic metabolism of small molecules and aldehydes, indicating a broad, substrate-diverse catabolic set. A few entries (e.g., response to copper ion) may relate to cellular stress responses that accompany metabolism but do not define a single pathway. Overall, it points to a cluster of enzymes involved in broad carbon-source catabolism. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":3},{"id":"GO:0006068","count":3},{"id":"GO:0007584","count":3},{"id":"GO:0006069","count":3},{"id":"GO:0033498","count":2}]},{"hash":"291399432043158792","title":"Steroid and Xenobiotic Metabolism","description":"The dominant GO terms point to steroid hormone metabolism (androgen metabolic process, testosterone biosynthetic process) and several xenobiotic/detoxification pathways (insecticide metabolism, coumarin catabolic process, organofluorine metabolism, fatty acid omega-oxidation). A few terms about inflammation regulation or cell adhesion appear, but they are not central to the cluster\u2019s main theme. This suggests the cluster mainly reflects steroid and xenobiotic metabolic functions.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008209","count":4},{"id":"GO:0061370","count":4},{"id":"GO:0017143","count":3},{"id":"GO:0010760","count":3},{"id":"GO:0070365","count":3}]},{"hash":"1522401342983710902","title":"Neuronal development and secretory trafficking","description":"The prominent terms include substantia nigra development and dendrite morphogenesis, pointing to neural development, while ER-to-Golgi vesicle transport and calcium ion detection suggest secretory trafficking and signaling in neurons. The mevalonate pathway can support membrane trafficking through isoprenylation, but several terms (meiotic cell cycle, DNA damage checkpoint, obsolete CTD dephosphorylation) are less coherent with neurons, indicating some noise. Overall, this label captures the strongest shared themes, with Moderate confidence.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0050774","count":4},{"id":"GO:0051321","count":4},{"id":"GO:0031573","count":4},{"id":"GO:0070940","count":4}]},{"hash":"1996920611824871172","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by genes involved in protein synthesis and ribosome maturation: translation (GO:0006412) is the main term, supported by ribosome biogenesis and assembly terms (ribosome biogenesis, ribosomal small subunit assembly, preribosome assembly, and nuclear export steps). The presence of positive regulation of ribosome biogenesis further reinforces a focus on ribosome production, with a few secondary terms (base-excision repair and TNF response) likely incidental. Overall, the cluster corresponds to ribosome production and protein synthesis.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0042254","count":2},{"id":"GO:0006407","count":2},{"id":"GO:0000028","count":1},{"id":"GO:1902626","count":1}]},{"hash":"533777686981871234","title":"Diverse catabolic metabolism","description":"Most terms are metabolic and catabolic, spanning several substrates (galactose, glucose, sorbitol, amino acids) and compounds (formaldehyde). While there are a few outliers (copper ion response, peptidoglycan biosynthesis, fatty acid biosynthesis), there is no clear, single pathway linking all proteins. This suggests a cluster of proteins broadly involved in diverse catabolic/metabolic roles.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033498","count":1},{"id":"GO:0000947","count":1},{"id":"GO:0019595","count":1},{"id":"GO:0046294","count":1},{"id":"GO:0046688","count":1}]},{"hash":"1954753190987566262","title":"Acetate-Glyoxylate-TCA Metabolism","description":"The GO terms point to central carbon metabolism, especially the glyoxylate cycle and the TCA cycle, with an explicit response to acetate and propionate catabolic activity, indicating adaptation to C2 carbon sources and acetyl-CoA utilization. Obsolete or minor terms do not override this core theme, so a metabolism-focused label fits well.","confidence":"High","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0010034","count":3},{"id":"GO:0006097","count":3},{"id":"GO:0019629","count":3},{"id":"GO:0032923","count":3},{"id":"GO:0006099","count":3}]},{"hash":"1780976619159510166","title":"Membrane Targeting and Fe-S Cluster Assembly","description":"The top GO terms point to SRP-dependent cotranslational and post-translational protein targeting to membranes, along with iron-sulfur cluster assembly, suggesting a combined role in protein maturation with membrane targeting and Fe-S biogenesis. Some terms are obsolete or relate to stress/proteostasis, but the recurring themes of membrane targeting and Fe-S assembly provide a cohesive, if small, functional cluster. ","confidence":"Medium","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0090084","count":3},{"id":"GO:0016226","count":3},{"id":"GO:0006616","count":3},{"id":"GO:1903751","count":3},{"id":"GO:0070389","count":3}]},{"hash":"861667356889829296","title":"Chromatin remodeling and heterochromatin formation","description":"The top GO terms are dominated by chromatin regulation (transcription initiation-coupled chromatin remodeling; pericentric and rDNA heterochromatin formation; silent mating-type cassette heterochromatin), with links to germline development such as spermatid development and centromere assembly. While a few terms point to broader developmental processes, the shared theme centers on chromatin dynamics and heterochromatin formation.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":2},{"id":"GO:0090230","count":1},{"id":"GO:0007286","count":1},{"id":"GO:0030466","count":1},{"id":"GO:0045815","count":1}]},{"hash":"2186606562390598047","title":"Endosomal trafficking and membrane remodeling","description":"The top GO terms cluster around endocytic recycling, intralumenal vesicle formation, endosome maturation, and phosphatidylinositol-mediated signaling, together with membrane remodeling activities like plasma membrane tubulation and cleavage furrow formation. While some terms touch on secretory granules or mast cell histamine release, the strongest shared theme is vesicle trafficking and endosomal dynamics, indicating a role in endocytosis, vesicle formation, and membrane remodeling. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097320","count":1},{"id":"GO:0071539","count":1},{"id":"GO:1990502","count":1},{"id":"GO:0036089","count":1},{"id":"GO:1903595","count":1}]},{"hash":"1332871639722748027","title":"Oskar mRNA localization and oocyte axis specification","description":"The terms cluster around oskar mRNA regulation and localization in the oocyte, including regulation of oskar mRNA translation, translation initiation, and pole plasm localization, along with axis specification in oocytes. This points to a cohesive module governing maternal mRNA localization and translational control that drives dorsal/ventral axis formation during oogenesis, with supportive but less central terms like spliceosome-mediated splicing and preinitiation complex formation. Confidence is high that this label reflects the cluster\u2019s core function.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0046011","count":1},{"id":"GO:0002188","count":1},{"id":"GO:0006376","count":1},{"id":"GO:0007310","count":1},{"id":"GO:0008069","count":1}]},{"hash":"268344838495820026","title":"Iron-Sulfur Cluster Biogenesis","description":"The cluster is best characterized by iron-sulfur (Fe-S) cluster biogenesis and maturation, as indicated by GO terms for 2Fe-2S cluster assembly and Fe-S cluster transfer. The sporulation-related terms (meiosis I, ascospore formation) are present but seem less central to the core function. Overall, the map points to a shared role in Fe-S cluster biosynthesis.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1903026","count":1},{"id":"GO:0044571","count":1},{"id":"GO:0051220","count":1},{"id":"GO:0034396","count":1},{"id":"GO:0036086","count":1}]},{"hash":"689228689199460281","title":"Nuclear import and nuclear pore assembly","description":"This cluster is dominated by GO terms related to import of proteins into the nucleus (NLS-bearing and ribosomal proteins) and assembly of the nuclear pore complex, pointing to a cohesive role in nuclear transport and trafficking between the cytoplasm and nucleus. Some outlier terms about GTPase regulation and desumoylation are present but do not override the core nuclear transport theme.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006607","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0060188","count":4},{"id":"GO:0006610","count":4},{"id":"GO:0051292","count":4}]},{"hash":"2089581049981506286","title":"Neuronal cytoskeleton remodeling and synaptic signaling","description":"This cluster is characterized by GO terms linking actin cytoskeleton dynamics (actin polymerization, formin-nucleated actin cables, stress fiber assembly), microtubule-related assembly (tubulin complex), and neuronal-specific processes such as axon guidance, interneuron migration, and regulation of synaptic vesicle exocytosis and glutamatergic transmission, along with vesicle trafficking between the plasma membrane and endosomes. Together these terms point to coordinated cytoskeletal remodeling driving neuronal development and synaptic function.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000300","count":3},{"id":"GO:0051496","count":3},{"id":"GO:0090338","count":3},{"id":"GO:0030838","count":3},{"id":"GO:0007411","count":2}]},{"hash":"1328958414457066055","title":"Neuronal RNA metabolism and translation","description":"The cluster\u2019s top GO terms are dominated by translation, rRNA processing, mRNA stabilization and miRNA regulation, with additional links to motor neuron development (hypoglossal nerve morphogenesis, motor behavior, motor neuron apoptotic process). This points to a cohesive role in neuronal RNA metabolism and protein synthesis supporting neuron development and function, despite a few broader terms appearing. ","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006364","count":3},{"id":"GO:0045087","count":2},{"id":"GO:0070934","count":2},{"id":"GO:0061744","count":2}]},{"hash":"455836590672028400","title":"V-ATPase-driven vacuolar transport","description":"The top GO terms center on vacuolar acidification and assembly of the V-type ATPase complex, suggesting a focus on proton pumping and vacuolar function. Several terms indicate membrane transport across various substrates (sialic acid, organic cations, phosphate, selenite, fucose). A couple of terms (ribosome biogenesis, activation of protein kinase activity) are less clearly connected to transport, so the overall signal appears to be membrane/ion transport with a vacuolar emphasis, plus some noise. ","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032147","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0007035","count":1},{"id":"GO:0070072","count":1},{"id":"GO:0015739","count":1}]},{"hash":"2101329232364209241","title":"Ribosome Biogenesis and SRP-Targeting","description":"This cluster centers on core translation components: ribosome biogenesis (GO:0042254), ribosomal small subunit assembly (GO:0000028), and SRP-dependent cotranslational protein targeting to membrane (GO:0006614), suggesting a cohesive theme around ribosome assembly and targeting newly synthesized proteins to membranes. The presence of activation of protein kinase activity hints at associated signaling linked to translation, and cellular response to amino acid starvation aligns with translational regulation. Some terms like hemidesmosome assembly and shoot meristem initiation appear less related and may reflect broader or context-specific annotations. Overall, the dominant signals point to translation machinery and protein targeting as the core of this cluster.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032147","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0031581","count":1},{"id":"GO:0006407","count":1},{"id":"GO:0000028","count":1}]},{"hash":"447411892996919908","title":"Polysaccharide biosynthesis and cell wall assembly","description":"The cluster\u2019s top GO terms mainly point to synthesis and organization of cell wall components and polysaccharides (cell wall polysaccharide biosynthetic process, chitin biosynthetic process, capsule polysaccharide biosynthetic process, cell wall organization). This suggests a shared role in building or remodeling the extracellular matrix rather than a single protein complex function. A few terms seem tangential (e.g., insect visual primordium formation, formation of infection structure), but the dominant theme is polysaccharide production and cell wall construction, including chitin and capsule pathways, with related cytokinesis-associated processes reflecting structural assembly.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000916","count":1},{"id":"GO:0034217","count":1},{"id":"GO:0001744","count":1},{"id":"GO:0070592","count":1},{"id":"GO:0000920","count":1}]},{"hash":"975074922509187998","title":"Protein quality control and ER-Golgi trafficking","description":"The GO terms show chaperone-assisted protein refolding, ER to Golgi vesicle transport, ER polarization, proteasomal protein catabolic regulation, and inclusion body assembly, all pointing to maintenance of proteostasis and proper protein trafficking. Additional terms about protein hexamerization and mitochondrial complex III assembly reflect assembly/organization of protein complexes and metabolic regulation that can intersect stress responses. A few terms such as DNA replication and error-free translesion synthesis appear less central, so the label focuses on the dominant theme of proteostasis and secretory pathway function.","confidence":"Medium","size":5,"edges":5,"triangles":1,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:1903862","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0070987","count":2}]},{"hash":"957075322669693852","title":"Unknown","description":"The GO terms are diverse (RNA methylation, rRNA maturation, translation reinitiation, ER-Golgi transport, growth hormone response, proliferation, proteolysis, cellulose catabolism) with no clear shared function or connectivity among the proteins. There isn't a cohesive theme tying these terms together, so a specific, representative label isn\u2019t evident.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036265","count":2},{"id":"GO:0060416","count":2},{"id":"GO:0008284","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0030245","count":2}]},{"hash":"149387361398555195","title":"Mitosis and DNA damage tolerance with ubiquitination","description":"The top terms center on mitosis (mitotic spindle elongation, chromosome segregation) and DNA damage tolerance (translesion synthesis), with several ubiquitin-related processes (K6-/K27-linked ubiquitination, N-end rule proteolysis) suggesting regulated protein turnover during the cell cycle. While some terms relate to chromatin silencing or ER-stress responses, they appear ancillary to the core cell-division/ubiquitin theme. ","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0000022","count":5},{"id":"GO:0030466","count":5},{"id":"GO:0085020","count":5},{"id":"GO:0070987","count":5},{"id":"GO:1903955","count":5}]},{"hash":"1225720357906025700","title":"Unknown","description":"The top GO terms cover lignin catabolism, nitrate assimilation/denitrification, copper/iron/arsenate ion transport, FtsZ-dependent cytokinesis, sporulation, antibiotic biosynthesis, and redox processes\u2014essentially a broad mix of metabolic, transport, and developmental functions with no single unifying theme. This spread suggests there is no coherent functional label for the cluster. ","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046274","count":3},{"id":"GO:0042128","count":3},{"id":"GO:0043093","count":3},{"id":"GO:0006825","count":3},{"id":"GO:0030435","count":3}]},{"hash":"2022247609775280461","title":"Ribosome Biogenesis and Cell Division","description":"This cluster centers on ribosome assembly and function (ribosome biogenesis, cytoplasmic translation, tRNA modification, ribosomal subunit biogenesis and export) and ties in cell cycle and division processes (cell cycle, cell division, septum assembly). The co-occurrence of these GO terms suggests a functional module where ribosome production and protein synthesis are linked to cell growth and division, with some signaling related to amino acid availability. Confidence: High","confidence":"","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:1903833","count":3},{"id":"GO:0007049","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0090529","count":3},{"id":"GO:0051301","count":3}]},{"hash":"1280361342075626279","title":"Apoptosis and Regeneration","description":"These proteins appear linked to stress-induced cell fate decisions, including apoptosis and tissue repair. Key terms like intrinsic apoptotic signaling in response to ER stress, apoptotic cell clearance, and animal organ regeneration point to a role in controlled cell death and subsequent tissue remodeling. The presence of more general terms (transcription, cell-matrix adhesion, spindle-kinetochore interactions) alongside several obsolete GO terms suggests a broad, loosely connected set of functions, and the overall connectivity in the cluster is weak, so the label remains tentative.","confidence":"Low","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0014043","count":2},{"id":"GO:0007070","count":2},{"id":"GO:2000686","count":2},{"id":"GO:0060968","count":2},{"id":"GO:0051316","count":2}]},{"hash":"1465996957878894157","title":"Unknown","description":"Top Terms are not provided (no GO terms listed), so there is no evident shared function to label the cluster. With 5 proteins and 7 edges (3 triangles, max degree 4), the connectivity alone does not reveal a coherent biological theme.","confidence":"","size":5,"edges":7,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[]},{"hash":"1024755949321902740","title":"Bacterial envelope biosynthesis and biofilm formation","description":"The cluster contains GO terms related to biosynthesis of cell-surface components such as lipid A and lipopolysaccharide, as well as spore wall assembly and biofilm formation, indicating a common theme around cell envelope synthesis and surface-associated structures; a few outlier terms (e.g., allantoin/xylan metabolism) may reflect annotation noise or broader context, but the envelope-focused terms drive the overall interpretation.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0036108","count":1},{"id":"GO:0019428","count":1},{"id":"GO:0045493","count":1},{"id":"GO:0009245","count":1},{"id":"GO:0034232","count":1}]},{"hash":"1719939606850129567","title":"Triglyceride catabolism and lipid remodeling","description":"Proteins in this cluster are enriched for triglyceride mobilization and catabolic processes, including triglyceride acyl-chain remodeling and phospholipid (phosphatidylethanolamine/phosphatidylcholine) catabolism, indicating a lipid metabolism-focused group. While there is a hint of signaling regulation (negative regulation of PKA activity), the dominant pattern is lipid breakdown and remodeling, especially triglyceride catabolism.","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006642","count":2},{"id":"GO:0046338","count":2},{"id":"GO:0019433","count":2},{"id":"GO:0010898","count":2},{"id":"GO:0034638","count":2}]},{"hash":"512539377628023022","title":"Unknown","description":"The top GO terms are a mix of RNA-related functions (regulatory ncRNA-mediated gene silencing and positive regulation of mRNA splicing) and several disparate catabolic/metabolic processes, with only a single edge and no clear cohesive theme. This lack of a shared, interpretable function makes a cohesive cluster label untenable.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0008203","count":1},{"id":"GO:0015945","count":1},{"id":"GO:0019285","count":1}]},{"hash":"2243824733820656208","title":"Unknown","description":"This cluster contains widely varying GO terms (innate immune response, retinal rod cell development, striatum development, microtubule centrosome anchoring, development, and general regulatory processes) with no clear common function or protein interactions (edges/triangles are zero), making a cohesive, specific label inappropriate.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051291","count":2},{"id":"GO:0045087","count":2},{"id":"GO:2001162","count":2},{"id":"GO:0051348","count":2},{"id":"GO:0046548","count":2}]},{"hash":"1684882628253702944","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning xenobiotic and alkaloid responses, neurotransmitter and taurine biosynthesis, calcium signaling, differentiation, pigmentation, and aging, with no clear shared function tying the cluster together. ","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":1},{"id":"GO:0048085","count":1},{"id":"GO:0006587","count":1},{"id":"GO:0071312","count":1},{"id":"GO:0071363","count":1}]},{"hash":"252947340543789323","title":"RNA processing and translation","description":"The top terms center on RNA-related processes: GO:0000466 maturation of 5.8S rRNA, GO:0000398 mRNA splicing via spliceosome, and GO:0002188 translation reinitiation, suggesting a shared theme around RNA processing and protein synthesis; additional terms (GPCR signaling, ER-to-Golgi transport, etc.) appear more peripheral, likely reflecting noisy or multifunctional annotations in a small cluster.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0007200","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0090344","count":3}]},{"hash":"1900240501779555085","title":"Broad Metabolism and Immune Response","description":"The top GO terms span diverse metabolic processes (fatty acid oxidation/biosynthesis, retinol and prostaglandin metabolism, amino acid and sugar catabolism) as well as an immune-related response (response to lipopolysaccharide). This mix suggests no single cohesive pathway but a cluster of proteins involved in general metabolism with an added stress/immune facet, justifying a broad label rather than a more specific one.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0032496","count":3},{"id":"GO:0000947","count":2},{"id":"GO:0046294","count":2},{"id":"GO:0046688","count":2}]},{"hash":"339520102853930627","title":"Steroid and lipid metabolism","description":"The top GO terms cluster around breakdown and processing of steroids and lipids, including androgen and steroid catabolic processes, C21-steroid hormone metabolism, very long-chain fatty acid biosynthesis, retinol metabolism, and mycolic acid biosynthesis, with additional lipid-related metabolism like 3-keto-sphinganine. This suggests a cohesive theme of lipid/steroid metabolic functions, though a few terms (e.g., transcription regulation, methotrexate response) are more distant. Overall, the dominant signal points to steroid and lipid metabolism.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006710","count":4},{"id":"GO:0006666","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0006706","count":4},{"id":"GO:0031427","count":4}]},{"hash":"1298456603199652093","title":"Nucleotide Biosynthesis and DNA Replication Initiation","description":"The dominant terms point to nucleotide metabolism and phosphorylation (GTP, ITP, ADP, CDP, AMP salvage) along with DNA replication initiation, suggesting the proteins work together to supply nucleotides for DNA synthesis and the start of replication. The liver/brain development terms appear incidental rather than central. Therefore, this label captures the core functional theme.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046039","count":2},{"id":"GO:0046041","count":2},{"id":"GO:0006270","count":2},{"id":"GO:0006172","count":2},{"id":"GO:0046705","count":2}]},{"hash":"863534112750044823","title":"DNA replication and cell cycle regulation","description":"This cluster is dominated by GO terms tied to DNA replication and DNA-templated transcription, core processes of the cell cycle. The presence of a spindle-kinetochore attachment term further supports a mitotic context, while the apoptotic-related terms may reflect cell fate decisions linked to cell cycle stress. Some terms are development- or obsolete-related, but the strongest signal centers on replication and cell-cycle control.","confidence":"Medium","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0014043","count":2},{"id":"GO:0007070","count":2},{"id":"GO:2000686","count":2},{"id":"GO:0060968","count":2}]},{"hash":"507937305264941884","title":"Motor neuron development and RNA metabolism","description":"The presence of motor-related GO terms (hypoglossal nerve morphogenesis, motor behavior, motor neuron apoptotic process) alongside RNA processing and regulation terms (rRNA processing, CRD-mediated mRNA stabilization, regulation of miRNA metabolism) suggests a theme around neural development with post-transcriptional RNA control. Innate immune response appears but is less central, so the core function is neural development linked to RNA metabolism.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:0070934","count":3},{"id":"GO:0061744","count":3},{"id":"GO:0090502","count":3},{"id":"GO:0044387","count":3}]},{"hash":"1575313030827916862","title":"Unknown","description":"The top GO terms are a mix of plant secondary metabolism (lariciresinol/ secoisolariciresinol biosynthesis), carbohydrate metabolism (galactose), bacterial biosynthesis (lipopolysaccharide core region, poly-hydroxybutyrate), antibiotic response, and general transcription. There is no clear, cohesive functional theme tying these four proteins together, and the lack of edges supports a non-specific or mixed set of roles.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0042619","count":2},{"id":"GO:0046677","count":2},{"id":"GO:1902135","count":1},{"id":"GO:1902128","count":1}]},{"hash":"2046827174693685290","title":"Unknown","description":"The terms cover mitochondria, telomeres, protein turnover, and various cellular processes (mitosis, vesicle transport, osteoblast activity) with little overlap, so there is no single cohesive function to label the cluster. ","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0072670","count":1},{"id":"GO:0000722","count":1},{"id":"GO:0046944","count":1},{"id":"GO:0006508","count":1},{"id":"GO:0006888","count":1}]},{"hash":"1957749714026174588","title":"DNA replication and repair machinery","description":"This small cluster shows enrichment for DNA replication (GO:0006260) and nucleotide-excision repair (GO:0006289), as well as depurination and DNA damage response terms, indicating involvement in genome maintenance and repair. A xenobiotic stimulus response term (GO:0042493) suggests stress-related regulation, possibly reflecting chemical-induced DNA damage, and the presence of protein homooligomerization supports assembly of repair complexes. Overall, the cluster appears to represent core DNA replication/repair machinery under stress.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":3},{"id":"GO:0006260","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0071897","count":2},{"id":"GO:0033158","count":2}]},{"hash":"489283852999677865","title":"Transmembrane solute transporters","description":"The terms predominantly reflect transmembrane transport of diverse solutes (sialic acid, organic cations, xenobiotics, ions, phosphate, and metabolic substrates), pointing to a function as membrane transporters; the single \"replicative senescence\" term likely represents noise or broad annotation.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":1},{"id":"GO:0070715","count":1},{"id":"GO:1904728","count":1},{"id":"GO:0097080","count":1},{"id":"GO:0035435","count":1}]},{"hash":"985868274963329021","title":"Keratinocyte differentiation and DNA damage response","description":"The cluster shows terms centered on keratinocyte differentiation, DNA replication, and DNA damage checkpoint signaling, together with apoptosis and apoptotic clearance. This points to an epidermal (keratinocyte) context where cells balance proliferation and differentiation while monitoring DNA integrity and removing damaged cells. The lack of edges suggests these proteins share related roles in these processes rather than forming a single cohesive complex.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900087","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0071375","count":2},{"id":"GO:0043277","count":2},{"id":"GO:0030216","count":2}]},{"hash":"1753302605318288595","title":"Mitochondrial energy production and proteostasis","description":"The top terms cluster around mitochondrial oxidative phosphorylation and respiratory complex assembly, alongside proteostasis processes (chaperone-assisted refolding and proteasomal degradation). While there are a few ER-related trafficking terms, the strongest shared function appears to be mitochondrial energy production linked to protein quality control and folding, justifying a label focused on mitochondria and proteostasis.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1903862","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0070389","count":4},{"id":"GO:0070987","count":4},{"id":"GO:1901800","count":4}]},{"hash":"1327471837367567396","title":"Aminoacyl-tRNA Synthetase\u2013Translation","description":"This cluster centers on translation and tRNA charging, with GO terms for translation and specific aminoacyl-tRNA synthetase activities (Ile, Met, Leu, Val) and regulation of translational fidelity, indicating a cohesive set of proteins involved in protein synthesis. A few atypical terms (neural development, histone methylation) appear incidental here.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006450","count":2},{"id":"GO:0006428","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006431","count":2},{"id":"GO:0006429","count":2}]},{"hash":"877627784571980836","title":"Unknown","description":"TheTopTerms are highly diverse and largely unrelated (RNA polymerase II transcription termination, beta-alanine biosynthesis, sperm capacitation, aging, cortex development, actin depolymerization, histone methylation, porphyrin biosynthesis, dopamine metabolism, etc.), with no clear shared biological process or pathway. Several terms are labeled obsolete, and there are no edges connecting proteins, suggesting this cluster reflects random, unconnected annotations rather than a cohesive functional group. Therefore, Unknown with None confidence.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006369","count":2},{"id":"GO:0019483","count":1},{"id":"GO:0048240","count":1},{"id":"GO:0007568","count":1},{"id":"GO:0045793","count":1}]},{"hash":"79502516082332499","title":"Nucleic acid replication and ribosome biogenesis","description":"This cluster includes GO terms for DNA replication and viral genome replication, plus rRNA maturation, mitochondrial ribosomal subunit assembly, and mRNA catabolic processes, suggesting a broad theme of nucleic acid metabolism and ribosome biogenesis rather than a single cohesive function.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0019079","count":2},{"id":"GO:0070417","count":1},{"id":"GO:0045003","count":1},{"id":"GO:0042766","count":1}]},{"hash":"1376114014192861871","title":"Golgi- and synaptic vesicle trafficking","description":"The GO terms emphasize ER-to-Golgi transport, Golgi organization, vesicle docking and fusion, Ca2+-dependent exocytosis, and synaptic vesicle localization, all aligning on vesicle trafficking through the Golgi and at synapses, including regulatory steps for exocytosis and membrane targeting. This suggests a coherent cluster centered on Golgi-associated vesicle trafficking and synaptic vesicle exocytosis.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":1},{"id":"GO:1902685","count":1},{"id":"GO:1903358","count":1},{"id":"GO:0045956","count":1},{"id":"GO:0090166","count":1}]},{"hash":"1114742858929962764","title":"Immune cell adhesion and cytoskeletal remodeling","description":"The terms include innate immune response, integrin signaling, and cytoskeletal structures such as podosomes and microspikes, suggesting a shared function in immune cell adhesion and actin remodeling. While other terms touch on growth hormone secretion or Ras signaling, the strongest signals point to immune cell\u2013mediated adhesion and cytoskeletal dynamics.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060124","count":1},{"id":"GO:0050894","count":1},{"id":"GO:0035156","count":1},{"id":"GO:0045087","count":1},{"id":"GO:0071560","count":1}]},{"hash":"1022198039204294557","title":"Unknown","description":"The GO terms span metabolite biosynthesis (beta-alanine, glycine betaine, porphyrin), brain development and dopamine metabolism, aging and histone methylation, sperm capacitation, cell size regulation, and capsule biosynthesis, with no single unifying function. Thus no coherent label can be assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019483","count":1},{"id":"GO:0048240","count":1},{"id":"GO:0007568","count":1},{"id":"GO:0045793","count":1},{"id":"GO:0021987","count":1}]},{"hash":"551384090390243519","title":"Neuronal ubiquitin-mediated proteostasis and stress response","description":"The top GO terms point to ubiquitin-dependent proteolysis and polyubiquitination, indicating a central role in protein turnover. Additional terms reflect neuronal context (synapse assembly, neuron-specific apoptotic signaling) and stress responses to metals (cadmium, methylmercury) and oxidative stress, suggesting a cluster centered on ubiquitin-regulated proteostasis in neurons under stress. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031571","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0060386","count":2},{"id":"GO:1903378","count":2},{"id":"GO:0000083","count":2}]},{"hash":"1581833025812193886","title":"Developmental transcriptional regulation and morphogenesis","description":"This cluster\u2019s GO terms are dominated by embryonic development and organ formation, including heart morphogenesis, endoderm and placenta development, stem cell maintenance, and regulation of transcription with chromatin remodeling, suggesting a cohesive theme of developmental gene control.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":1},{"id":"GO:0035019","count":1},{"id":"GO:0043486","count":1},{"id":"GO:0001892","count":1},{"id":"GO:0003007","count":1}]},{"hash":"549334960303570696","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006223","count":3},{"id":"GO:0043103","count":2},{"id":"GO:0009116","count":2},{"id":"GO:0006168","count":2},{"id":"GO:0016310","count":2}]},{"hash":"405235976880648236","title":"Vesicle trafficking and organelle assembly","description":"The terms cluster around intracellular transport-related processes: vesicle docking in exocytosis, plasma membrane-to-endosome transport, and melanosome assembly, with supporting connections to axon guidance and mitochondrial inheritance that depend on cellular trafficking. However, several terms (complement-dependent cytotoxicity, neuron fate determination, sprouting angiogenesis, hyperosmotic response) are less clearly tied to this theme, indicating only a weak overall coherence. ","confidence":"Low","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048664","count":1},{"id":"GO:0097278","count":1},{"id":"GO:1903232","count":1},{"id":"GO:0051291","count":1},{"id":"GO:0007411","count":1}]},{"hash":"87118071654536497","title":"Quinone and chlorophyll biosynthesis","description":"The top GO terms center on biosynthetic pathways for multiple quinones (phylloquinone, plastoquinone, menaquinone, ubiquinone) and chlorophyll, suggesting a cohesive theme around isoprenoid-derived cofactors and pigments produced in plastids or membranes. Additional terms like dolichol and GPI anchor biosynthesis point to broader lipid/isoprenoid biosynthesis within the same cellular context, supporting a unified label for this cluster.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042372","count":1},{"id":"GO:0042371","count":1},{"id":"GO:0048034","count":1},{"id":"GO:0010236","count":1},{"id":"GO:0032194","count":1}]},{"hash":"2286482466099168047","title":"Copper Ion Homeostasis and Transport","description":"The cluster is dominated by GO terms related to copper ion handling and movement across membranes (intracellular copper ion homeostasis, regulation of copper ion transmembrane transport, copper ion import across plasma membrane), with an additional link to cisplatin response, which is often connected to metal transport pathways. The presence of xenobiotic transmembrane transport and glycosylation terms may reflect broader membrane-associated functions, but the copper/metal transport theme is the strongest signal, justifying a label focused on copper homeostasis and transport.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006878","count":1},{"id":"GO:0072719","count":1},{"id":"GO:0015680","count":1},{"id":"GO:1902311","count":1},{"id":"GO:0098705","count":1}]},{"hash":"1701625731670529956","title":"Neuronal axon guidance and microtubule dynamics","description":"Top GO terms reveal axon guidance, interneuron migration, tubulin complex assembly, and vesicle transport, indicating cytoskeletal regulation and intracellular trafficking in developing neurons; despite some unrelated terms like division septum assembly, the dominant pattern is neuronal development and microtubule-based transport.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007411","count":2},{"id":"GO:0051966","count":2},{"id":"GO:0048227","count":2},{"id":"GO:0007021","count":2},{"id":"GO:0021830","count":2}]},{"hash":"1419616919718205880","title":"Unknown","description":"The terms span metabolism, organelle structure, RNA processing, and DNA repair with no single cohesive function linking them; the cluster shows no edges or clear shared pathway, so a concise, representative label cannot be assigned. ","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009062","count":1},{"id":"GO:0007029","count":1},{"id":"GO:0032543","count":1},{"id":"GO:0070681","count":1},{"id":"GO:0019876","count":1}]},{"hash":"1742888083975354316","title":"Nuclear transport and RNA export","description":"This cluster is dominated by GO terms for exporting RNA species (mRNA, tRNA, ribosomal subunits) from the nucleus and for import into the nucleus via NLS-bearing proteins, as well as nuclear pore organization. While a few terms relate to stress responses, the core pattern points to nuclear transport and RNA/protein export processes.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035080","count":3},{"id":"GO:0036228","count":3},{"id":"GO:0035392","count":3},{"id":"GO:0000055","count":3},{"id":"GO:0071390","count":3}]},{"hash":"2043099456935452014","title":"Actin Cytoskeleton Remodeling and Endocytosis","description":"Core signals point to actin cytoskeleton dynamics: Arp2/3-mediated actin nucleation, actin filament bundle assembly, and muscle thin filament assembly indicate actin polymerization and organization. Regulation of endocytosis and calcium response further connect to actin-driven membrane trafficking and signaling. A couple of unrelated terms appear, but the dominant theme is actin-based remodeling.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009825","count":3},{"id":"GO:0042766","count":3},{"id":"GO:0034314","count":3},{"id":"GO:0051592","count":3},{"id":"GO:0030100","count":3}]},{"hash":"1443316028071973452","title":"Unknown","description":"The top GO terms come from very diverse biological areas (nitric oxide biosynthesis, mitochondrial inheritance, CNS myelin maintenance, nitrate assimilation, ergosterol and sphingolipid metabolism, fatty acid biosynthesis, mandelate metabolism, and photosynthetic carbon pathways). There isn\u2019t a single unifying function or theme that ties these terms together, so a coherent, specific label isn\u2019t supported.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006809","count":3},{"id":"GO:0000001","count":3},{"id":"GO:0032286","count":3},{"id":"GO:0042128","count":3},{"id":"GO:0032443","count":3}]},{"hash":"1457614614334179055","title":"Unknown","description":"The terms span xenobiotic/insecticide metabolism, fatty acid omega-oxidation, hepatocyte and uterus development, endothelial adhesion, and inflammatory regulation with little clear overlap, making a single cohesive function hard to assign.","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0017143","count":1},{"id":"GO:0010760","count":1},{"id":"GO:0070365","count":1},{"id":"GO:0090350","count":1},{"id":"GO:0071603","count":1}]},{"hash":"1464643029979226542","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046050","count":1},{"id":"GO:0009244","count":1},{"id":"GO:0016311","count":1},{"id":"GO:0006114","count":1},{"id":"GO:0046196","count":1}]},{"hash":"505847817336809192","title":"P53-Driven Cell Cycle and Protein Homeostasis","description":"The cluster centers on p53-mediated signaling, regulation of the cell cycle, and ubiquitin-proteasome\u2013related protein stability, suggesting a coordinated stress response that links cell cycle control with protein turnover and quality control; translation and targeting to membranes hint at broader protein biogenesis maintenance under stress.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0072717","count":2},{"id":"GO:0032986","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0071157","count":2},{"id":"GO:1904667","count":2}]},{"hash":"110503065159747269","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0006915","count":1},{"id":"GO:0032543","count":1},{"id":"GO:0000184","count":1},{"id":"GO:0000466","count":1}]},{"hash":"320691350457445757","title":"Unknown","description":"There are no top GO terms or interactions to link the three proteins, and the cluster has zero edges/triangles, so no clear shared function can be inferred. The note about ReCIPE re-adding proteins does not imply a common role.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1752077224623587322","title":"B cell cytokine production and inflammatory signaling","description":"The top GO terms are centered on cytokine production (TNF, IL-6) and inflammatory response in B cells, suggesting the cluster reflects immune cytokine regulation and inflammation associated with B cell activity. A few terms about virion assembly and host-cell translocation hint at infection-related processes, but the core pattern is cytokine-mediated immune signaling in B cells.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1904469","count":3},{"id":"GO:2000778","count":3},{"id":"GO:0002368","count":3},{"id":"GO:1904871","count":3},{"id":"GO:0044053","count":3}]},{"hash":"2098752743430660675","title":"Transcription initiation and growth signaling","description":"The top GO terms are dominated by transcription-related processes (RNA polymerase II preinitiation complex assembly; DNA-templated transcription initiation) and growth-control signals (positive regulation of stem cell proliferation; regulation of Hippo signaling), suggesting a theme around transcriptional regulation linked to cell growth. Other terms like cilium assembly and protein ubiquitination are present but less represented, and there are no interactions among proteins, implying a loosely connected or multi-functional set.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000648","count":1},{"id":"GO:0051123","count":1},{"id":"GO:0006352","count":1},{"id":"GO:0060386","count":1},{"id":"GO:0035330","count":1}]},{"hash":"1770325620789714273","title":"B cell cytokine production and inflammatory response","description":"This cluster is dominated by GO terms for positive regulation of TNF and IL-6 production and B cell cytokine production, indicating a core theme of cytokine signaling and inflammatory response in immune cells. While terms about virion assembly and host cell cytoplasm translocation appear, the strongest signals center on cytokine production and inflammation.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1904469","count":3},{"id":"GO:2000778","count":3},{"id":"GO:0002368","count":3},{"id":"GO:1904871","count":3},{"id":"GO:0044053","count":3}]},{"hash":"70581843399876959","title":"Unknown","description":"The GO terms are broad and not cohesively linked (ER\u2013Golgi transport, dendrite morphogenesis, meiotic/mitotic processes, transcription factor regulation, calcium sensing, EMT, actomyosin organization, isoprenoid biosynthesis, brain development), and with only 3 proteins there is no clear unifying function. ","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0050774","count":2},{"id":"GO:0051321","count":2},{"id":"GO:0031573","count":2},{"id":"GO:0070940","count":2}]},{"hash":"1480877371775216450","title":"Chromatin regulation and nucleolar transcription","description":"Most of the terms center on chromatin biology and epigenetic regulation (histone methylation/acetylation, chromatin localization) and nucleolar transcription control (rRNA transcription by RNA Pol I and snoRNP assembly), suggesting a chromatin- and nucleolar-transcription\u2013focused cluster. A few terms (TORC1 signaling, cilium-dependent motility) are peripheral noise.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900113","count":1},{"id":"GO:1904263","count":1},{"id":"GO:0060285","count":1},{"id":"GO:2000619","count":1},{"id":"GO:2001268","count":1}]},{"hash":"32114928076928066","title":"Antiviral Innate Immunity and NF-kappaB Signaling","description":"These proteins cluster around antiviral defense and innate immunity, with links to NF-kappaB signaling (including non-canonical pathways), ubiquitination, and regulation of apoptotic and adaptive immune processes. The set emphasizes innate antiviral signaling and NF-kappaB regulation rather than germinal center-specific functions.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051607","count":1},{"id":"GO:0046597","count":1},{"id":"GO:1901224","count":1},{"id":"GO:0032897","count":1},{"id":"GO:0042981","count":1}]},{"hash":"1509257008942179801","title":"Unknown","description":"The terms split into two largely unrelated themes: transcription initiation/elongation in the nucleus and transmembrane transport of several nucleobases and related compounds. With only three proteins and two edges, there\u2019s no clear, cohesive function binding these terms, so a confident single label cannot be assigned.","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048096","count":1},{"id":"GO:0006368","count":1},{"id":"GO:0006209","count":1},{"id":"GO:0015856","count":1},{"id":"GO:0015888","count":1}]},{"hash":"1364933024327320251","title":"Spliceosome and mRNA Splicing Machinery","description":"Reason: The top GO terms are dominated by mRNA splicing and spliceosome assembly (e.g., GO:0045292, GO:0000245, GO:0000387), with supporting signals of nuclear import and RNA processing, suggesting these proteins function in pre-mRNA splicing and RNA maturation.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":3},{"id":"GO:0070317","count":2},{"id":"GO:0000245","count":2},{"id":"GO:0000290","count":2},{"id":"GO:0033962","count":2}]},{"hash":"505862145138989957","title":"Neuronal development and microtubule transport","description":"This cluster\u2019s terms emphasize neural development processes (axon guidance, interneuron migration, regulation of synaptic transmission) and cytoskeleton/trafficking functions (tubulin complex assembly, retrograde vesicle transport, plasma membrane to endosome transport), suggesting a theme around neuronal morphogenesis and intracellular transport along microtubules. While some terms are broader, the strongest shared signal is cytoskeletal dynamics linked to neurons.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007411","count":1},{"id":"GO:0051966","count":1},{"id":"GO:0048227","count":1},{"id":"GO:0007021","count":1},{"id":"GO:0021830","count":1}]},{"hash":"1786208457933012456","title":"Unknown","description":"There are no shared GO terms or interactions among the 3 proteins, so a cohesive function cluster cannot be determined. Without a unifying theme, this cluster is labeled Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2265688264757277336","title":"Xylan degradation","description":"The top GO term is GO:0045493 xylan catabolic process, indicating these proteins are involved in breaking down xylan. With this single shared function and no other enriched terms, the cluster most likely represents xylan-degrading enzymes.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045493","count":1}]},{"hash":"904928533873038899","title":"Mitotic spindle regulation via ubiquitination","description":"This cluster is dominated by mitosis-related GO terms such as mitotic spindle elongation and chromosome segregation, along with ubiquitin-related processes (K6- and K27-linked ubiquitination, ubiquitin-dependent proteolysis via the N-end rule pathway). This pattern suggests proteins that coordinate cell cycle progression and protein turnover through ubiquitin signaling. Some terms like translesion synthesis and ER-stress\u2013related apoptosis reflect broader stress responses, but the core theme remains mitotic control modulated by ubiquitination.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0000022","count":3},{"id":"GO:0030466","count":3},{"id":"GO:0085020","count":3},{"id":"GO:0070987","count":3},{"id":"GO:1903955","count":3}]},{"hash":"1727965593777725666","title":"Embryonic organ morphogenesis","description":"The top GO terms cluster around morphogenesis and development across multiple organs (bronchiole, heart/cardiac septum, muscle, nephron, etc.), with supporting processes like cell adhesion and apoptosis regulation that commonly facilitate tissue shaping. This suggests a cohesive theme of embryonic organ formation rather than a single pathway, so the label reflects the shared function well.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042981","count":1},{"id":"GO:0060435","count":1},{"id":"GO:0072049","count":1},{"id":"GO:0007518","count":1},{"id":"GO:0072282","count":1}]},{"hash":"2095349973546824838","title":"Multicellular Development and Tissue Formation","description":"This cluster's top GO terms cluster around broad developmental processes across tissues and organs, including angiogenesis, axonogenesis, Schwann cell development, heart development, myoblast fusion, and general multicellular organism development. The presence of mitotic cell cycle terms likely reflects proliferative phases during development rather than a single pathway. Taken together, the proteins appear linked to tissue and organ formation in multicellular contexts rather than a single signaling axis. Therefore, the label emphasizes development and tissue formation.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":2},{"id":"GO:0007409","count":2},{"id":"GO:0007121","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0014044","count":2}]},{"hash":"1314732390551420244","title":"Unknown","description":"Top terms span several unrelated areas: several metabolic processes (methanol, methane, cholesterol, glycine betaine biosynthesis) and various developmental or signaling roles (synaptic assembly at neuromuscular junction, locomotor rhythm, cell differentiation, osteoblast proliferation, TRAIL-apoptotic signaling). With no consistent theme or interaction linking the proteins, and no network edges, there is no coherent label to assign.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0008203","count":1},{"id":"GO:0015945","count":1},{"id":"GO:0019285","count":1},{"id":"GO:0046188","count":1}]}]