[{"hash":"262999570748101772","title":"Plant secondary metabolite metabolism and detoxification","description":"The top GO terms cluster around aromatic compound catabolism (3-phenylpropionate, stilbene, alkaloid metabolism) and xenobiotic processing, along with detoxification and a plant-development term (secondary shoot formation). This points to a cohesive set of proteins involved in plant secondary metabolism and associated detoxification pathways, even though the annotations span related but distinct processes. Therefore, the label reflects the common theme of aromatic metabolite processing and detoxification in plants.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019380","count":6},{"id":"GO:0019260","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0017000","count":5},{"id":"GO:0097755","count":5}]},{"hash":"1962148613436097126","title":"Mitochondrial Transport and Energy Metabolism with ER Stress","description":"The cluster is dominated by GO terms for mitochondrial metabolite transport (alpha-ketoglutarate, ornithine, ATP, pyrimidines) and energy metabolism, complemented by stress-responsive processes such as unfolded protein response and ER-associated degradation, plus a nod to adaptive thermogenesis. This points to a unifying theme of mitochondrial transport/energy production intertwined with cellular stress quality control.","confidence":"Medium","size":29,"edges":7,"triangles":0,"max_degree":5,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0006986","count":4},{"id":"GO:0015742","count":4},{"id":"GO:0000066","count":4}]},{"hash":"2171194998169287162","title":"Gene Expression Regulation and RNA Processing","description":"The proteins cluster around gene expression control, featuring translation, transcriptional regulation by RNA polymerase II, RNA quality control (nonsense-mediated decay), and DNA-related processes such as replication and topology, with neuronal signaling cues (BDNF response, associative learning) suggesting a broader theme of regulation of gene expression at multiple levels.","confidence":"Medium","size":29,"edges":251,"triangles":1216,"max_degree":24,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006412","count":3},{"id":"GO:0045944","count":3},{"id":"GO:0006260","count":3},{"id":"GO:1904574","count":3}]},{"hash":"927611444459032965","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":2},{"id":"GO:0075713","count":2},{"id":"GO:0046718","count":2},{"id":"GO:0000447","count":1},{"id":"GO:0042274","count":1}]},{"hash":"1019163624736627808","title":"Cardiac Development and Electrophysiology","description":"The cluster shows strong enrichment for heart development, cardiac muscle contraction, SA node action potential regulation, and calcium/phosphatidylinositol signaling, pointing to a module coordinating cardiac growth, electrical activity, and stress-responsive hypertrophy.","confidence":"High","size":29,"edges":113,"triangles":180,"max_degree":20,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007205","count":8},{"id":"GO:0043547","count":7},{"id":"GO:0060487","count":7},{"id":"GO:0032465","count":7},{"id":"GO:0007507","count":7}]},{"hash":"2228342605702215708","title":"Neural development and brain morphogenesis","description":"The GO terms are dominated by neural development processes: forebrain development, neural tube closure, embryonic cranial skeleton morphogenesis, and broad multicellular development, with accompanying DNA replication and mitotic cell cycle terms indicating proliferating neural progenitors. Some stress-related terms are present but do not define the cluster; the core signal is neural development and brain morphogenesis.","confidence":"High","size":29,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":27},{"id":"GO:0000278","count":26},{"id":"GO:0010571","count":25},{"id":"GO:0007275","count":25},{"id":"GO:0030900","count":25}]},{"hash":"1524300339228752802","title":"Unknown","description":"The GO terms span multiple unrelated biological processes (cell migration and actin organization; telomere maintenance; adipogenesis; proteasome assembly; cardiac electrophysiology), with no obvious shared function or connectivity among the 29 proteins. Because there is no cohesive theme and the graph has no edges, I cannot assign a specific, representative label beyond Unknown.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0016477","count":5},{"id":"GO:0035994","count":5},{"id":"GO:0032212","count":5},{"id":"GO:2001275","count":5},{"id":"GO:1904355","count":5}]},{"hash":"1293725639604449050","title":"Temperature Sensing and Calcium Signaling","description":"The top GO terms point strongly to temperature-related processes (thermoception, response to cold, response to capsazepine) and calcium signaling (calcium ion import across the plasma membrane), suggesting a cluster centered on temperature sensing and Ca2+-mediated signaling. While other terms like cell cycle, ubiquitination, and transcription appear, they seem less defining for this cluster, which is why the label emphasizes temperature sensing and calcium signaling rather than broader cellular processes.","confidence":"Medium","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007049","count":5},{"id":"GO:0016567","count":5},{"id":"GO:0043547","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0050955","count":4}]},{"hash":"1872288585841491282","title":"Developmental and immune signaling regulators","description":"The cluster includes terms tied to regulation of angiogenesis, inflammatory and chemokine signaling, interferon production, and development of neural and kidney tissues, plus Rho signaling and mechanotransduction. This pattern suggests proteins acting as modulators of signaling networks across diverse developmental and immune contexts rather than a single pathway, hence a label pointing to regulatory signaling roles in development and immunity.","confidence":"Medium","size":29,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016525","count":3},{"id":"GO:0071260","count":3},{"id":"GO:0048549","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0021997","count":2}]},{"hash":"884120893903816841","title":"Regulation of excitatory glutamatergic synaptic transmission","description":"Proteins in this cluster center on modulating excitatory synapses: NMDA receptor activity, excitatory postsynaptic potentials, synaptic vesicle exocytosis, receptor internalization, and active zone cytoskeletal organization, indicating a cohesive role in glutamatergic signaling and synapse structure.","confidence":"High","size":29,"edges":132,"triangles":546,"max_degree":28,"top_function":null,"top_go_terms":[{"id":"GO:0008285","count":9},{"id":"GO:0042136","count":9},{"id":"GO:0048789","count":9},{"id":"GO:0051968","count":9},{"id":"GO:0031623","count":9}]},{"hash":"1968048203846103134","title":"Metal ion transport and homeostasis","description":"This cluster is dominated by GO terms related to manganese and iron ion handling, including manganese ion transmembrane transport, cellular response to iron ion, and intracellular manganese ion homeostasis, suggesting a core function in metal ion transport and homeostasis. A few other terms (such as ethylene response and fibroblast apoptotic regulation) appear but are sparse and likely incidental, and several entries are listed as obsolete, so the central theme remains metal ion handling.","confidence":"Medium","size":29,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071421","count":1},{"id":"GO:0071281","count":1},{"id":"GO:0006880","count":1},{"id":"GO:0030026","count":1},{"id":"GO:0071369","count":1}]},{"hash":"169914910492886966","title":"Telomere maintenance and chromosome segregation","description":"This cluster is enriched for telomere-related processes (telomere maintenance via telomerase, localization to telomeric regions) and spindle/chromosome assembly activities, with ubiquitination patterns typical of cell-cycle regulation. Some terms reflect broader developmental signaling (lens morphogenesis, axonal fasciculation, Wnt signaling), but the dominant signal points to nuclear/chromosome maintenance and cell division.","confidence":"Medium","size":29,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:2000480","count":2},{"id":"GO:0032212","count":2},{"id":"GO:0070309","count":2},{"id":"GO:0070198","count":2}]},{"hash":"1405054580966652344","title":"Viral DNA replication and proviral integration","description":"Top GO terms show strong enrichment for DNA replication, DNA integration, and RNA-templated DNA biosynthesis, alongside steps in the viral life cycle such as proviral latency establishment and viral entry into the host nucleus. While a couple terms relate to host-symbiont interactions or plant development, the dominant signal points to virus-associated DNA replication and proviral integration functions, making this label representative of the cluster.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006278","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0039651","count":3},{"id":"GO:0015074","count":3},{"id":"GO:0075713","count":3}]},{"hash":"108591444746104413","title":"Intracellular Transport and Nuclear Import","description":"This cluster centers on terms involving moving molecules within the cell, including intracellular protein transport, nuclear import of NLS-bearing proteins, and mRNA transport, with supporting signals and trafficking-related terms. The shared theme is intracellular trafficking rather than a single precise process, though diverse functions are represented. ","confidence":"Medium","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030579","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0006607","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0045945","count":2}]},{"hash":"752726823608353693","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071039","count":2},{"id":"GO:0034475","count":2},{"id":"GO:0071036","count":2},{"id":"GO:0033621","count":2},{"id":"GO:0071040","count":2}]},{"hash":"1196101377674749329","title":"Signaling, transport, and stress response regulation","description":"The cluster shows a mix of signaling-related GO terms (auxin signaling, NOD2 signaling, regulation of NF-kappaB), alongside processes in trafficking and calcium transport (pinocytosis, calcium import), cell cycle and migration, and stress responses (response to cold), plus ubiquitination. This combination suggests a broad regulatory module governing signaling and cargo transport under stress, rather than a single focused function, hence the label. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009734","count":2},{"id":"GO:0032212","count":2},{"id":"GO:0048549","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0070431","count":2}]},{"hash":"1747966124801975362","title":"Unknown","description":"The top GO terms are heterogeneous, covering cardiac action potential regulation, telomere maintenance, heat/pain sensing, adipogenesis, pinocytosis, NOD1 signaling, and more. There is no single, coherent function linking all proteins in this cluster, so a specific, representative label cannot be assigned.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0098907","count":9},{"id":"GO:0007205","count":9},{"id":"GO:1904355","count":8},{"id":"GO:0009408","count":8},{"id":"GO:0045444","count":8}]},{"hash":"327922631906952799","title":"Unknown","description":"The top terms span DNA repair, RNA processing, ubiquitination, proviral latency, DNA integration, host cell entry, and various transport/secretion processes, with no edges or clear functional cohesion among proteins. Because there\u2019s no single, coherent shared function tying these proteins together, a reliable label cannot be assigned.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006289","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0075713","count":2},{"id":"GO:0015074","count":2}]},{"hash":"2045184344780431175","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":1},{"id":"GO:0034101","count":1},{"id":"GO:0008584","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0019471","count":1}]},{"hash":"61226647156738235","title":"Unknown","description":"The top GO terms cover a broad and seemingly unrelated mix of processes (telomere maintenance, pinocytosis, NOD1 signaling, temperature sensation and heat-stress responses, transcription regulation under heat, cell cycle, synaptic plasticity regulation, telomeric localization, and calcium release). There isn\u2019t a single clear biological theme binding these terms, so a coherent, specific label isn\u2019t supported.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":19},{"id":"GO:0048549","count":19},{"id":"GO:0070427","count":19},{"id":"GO:0050955","count":19},{"id":"GO:1901594","count":19}]},{"hash":"1881544356155198220","title":"Unknown","description":"The top GO terms are highly diverse (membrane transport of glucose and potassium, DNA-templated transcription, ECM organization, development, signaling, and stress response), with no dominant shared function or pathway. The lack of interactions (edges/triangles) suggests a heterogeneous set, so a single cohesive label isn\u2019t supported.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904659","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0030198","count":1},{"id":"GO:0034101","count":1}]},{"hash":"170516431351550717","title":"Chromosome maintenance and chromatin regulation","description":"The top GO terms cluster around genome integrity and chromatin dynamics, including spindle orientation, homologous recombination repair, chromosome segregation, chromatin organization, and histone modification. This points to a cohesive theme of maintaining genome stability and regulating chromatin state during cell division, with other terms present being ancillary or broader cellular processes. ","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000132","count":3},{"id":"GO:0000724","count":3},{"id":"GO:0000747","count":2},{"id":"GO:0050679","count":2},{"id":"GO:1902510","count":2}]},{"hash":"1768062473458325638","title":"Unknown","description":"The top GO terms cover very different biological themes (bacterial biosynthesis and cell wall/capsule processes) alongside animal-related processes (dopamine catabolic process, cold response, stem cell regulation), with no clear shared pathway or function connecting the proteins, and no edges between them, so there isn\u2019t a coherent cluster label to assign.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042135","count":2},{"id":"GO:0071555","count":2},{"id":"GO:2000648","count":2},{"id":"GO:0045820","count":2},{"id":"GO:0009236","count":2}]},{"hash":"857851541561141747","title":"Telomere maintenance regulators","description":"The cluster is dominated by GO terms tied to telomere maintenance via telomerase, telomeric region localization, and telomere capping, including both positive and negative regulation of telomere maintenance. While a few terms like spindle assembly and Wnt signaling appear, the core theme centers on chromosome end protection and telomere regulation, implying proteins involved in telomere maintenance pathways.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":2},{"id":"GO:0070198","count":2},{"id":"GO:0051225","count":2},{"id":"GO:1904743","count":2},{"id":"GO:0016055","count":2}]},{"hash":"547932429190692849","title":"Membrane Transporters and Redox Homeostasis","description":"The cluster shows enrichment for multiple transmembrane transport processes (sodium, xenobiotic, sialic acid, phosphate, galactose) along with detoxification and redox homeostasis terms, suggesting a group of membrane transport proteins contributing to cellular homeostasis and oxidative stress management. Some lipid metabolism signals are present, but the dominant theme is membrane transport linked to redox balance.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009395","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0042891","count":1}]},{"hash":"319465396629128959","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001843","count":2},{"id":"GO:0001403","count":2},{"id":"GO:0070317","count":2},{"id":"GO:0070651","count":1},{"id":"GO:0071032","count":1}]},{"hash":"156697482252969664","title":"Cell cycle and DNA replication","description":"Based on the top GO terms, the ensemble of proteins is enriched for DNA replication, mitotic processes, and cell-cycle transitions (G1/S), as well as related events like spindle organization and budding growth. Although a few terms (visual perception, virus response, autophagy regulation, cardiac differentiation, ion transport) appear, the strongest cohesive signal centers on cell cycle progression and genome duplication, suggesting the cluster functions primarily in DNA replication and mitosis.","confidence":"High","size":28,"edges":328,"triangles":2375,"max_degree":27,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007601","count":24},{"id":"GO:0006260","count":24},{"id":"GO:0007118","count":24},{"id":"GO:0000278","count":24},{"id":"GO:0016242","count":23}]},{"hash":"1013721426271951134","title":"Neural and neuromuscular development","description":"The top GO terms center on axonogenesis, long-term synaptic potentiation, Schwann cell development, and myoblast fusion, pointing to coordinated formation and maturation of neural circuits and peripheral support (glial and muscular) components. Although there are broader developmental terms (e.g., multicellular organism development, heart development), the dominant theme is nervous system development and synaptic function, including neuromuscular aspects. This makes a label focused on neural and neuromuscular development appropriate and representative.","confidence":"High","size":28,"edges":79,"triangles":64,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007409","count":16},{"id":"GO:0060291","count":16},{"id":"GO:0014850","count":16},{"id":"GO:0007520","count":16},{"id":"GO:0007275","count":16}]},{"hash":"1069706063163079391","title":"Mitotic spindle and microtubule transport","description":"The cluster is defined by a strong signal for mitosis-related processes\u2014centrosome separation, metaphase chromosome alignment, and nuclear migration during cell division\u2014together with plus-end-directed vesicle transport along microtubules, indicating microtubule dynamics are central. The presence of GO terms tied to cerebellar layer structure suggests broader cytoskeletal organization in neural tissue, but the dominant theme remains mitotic spindle function and microtubule traffic.","confidence":"Medium","size":28,"edges":235,"triangles":1309,"max_degree":23,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007100","count":19},{"id":"GO:0000742","count":18},{"id":"GO:0032487","count":18},{"id":"GO:0021693","count":18},{"id":"GO:0021685","count":18}]},{"hash":"1027041248725217260","title":"Cross-Pathway Signaling and Differentiation","description":"The cluster shows enrichment across multiple major signaling pathways (Hippo, Wnt, T cell receptor), processes like apoptosis and cell cycle, transcription, and differentiation in various tissues (keratinocytes, visual system). This pattern points to proteins involved in diverse signaling networks coordinating growth, immune signaling, and tissue development, rather than a single pathway. Therefore, a label emphasizing cross-pathway signaling and differentiation is appropriate.","confidence":"Medium","size":28,"edges":257,"triangles":1303,"max_degree":24,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035329","count":22},{"id":"GO:0007601","count":22},{"id":"GO:0006915","count":22},{"id":"GO:0030216","count":22},{"id":"GO:0097011","count":22}]},{"hash":"594141890022658543","title":"RNA processing and transcription regulation under stress","description":"The cluster is dominated by GO terms tied to RNA biology\u2014ncRNA-mediated gene silencing, mRNA splicing via spliceosome, mRNA stability modulation under stress, and IRES-dependent translation\u2014along with transcriptional regulation by RNA Pol II and stress granule localization. Together these indicate a cohesive role in RNA processing, transcription control, and cellular stress response, with a minor inclusion of DNA replication that is less central. ","confidence":"High","size":28,"edges":111,"triangles":32,"max_degree":20,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":4},{"id":"GO:0048026","count":4},{"id":"GO:0010610","count":3},{"id":"GO:0075522","count":3},{"id":"GO:0045944","count":3}]},{"hash":"1912360986275216504","title":"Unknown","description":"The top GO terms point to multiple organ development (brain and heart) and broad cellular processes (transcription, signaling, cell cycle) with no single unifying function evident, and there are no interactions (edges) tying the proteins into a cohesive module. Therefore a precise, representative label cannot be inferred.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021695","count":2},{"id":"GO:0021766","count":2},{"id":"GO:0043433","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0033138","count":2}]},{"hash":"1470761148264495035","title":"Heterochromatin formation and DNA replication","description":"The top terms cluster around heterochromatin assembly and maintenance (silent mating-type cassette, rDNA and subtelomeric heterochromatin, CENP-A chromatin) together with essential DNA replication and repair processes (premeiotic replication, DNA strand elongation in replication, break-induced replication). This suggests a group of proteins focused on chromatin organization within heterochromatic regions during genome replication and maintenance.","confidence":"High","size":28,"edges":63,"triangles":29,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030466","count":4},{"id":"GO:0006260","count":3},{"id":"GO:0061641","count":3},{"id":"GO:0000183","count":3},{"id":"GO:0090102","count":2}]},{"hash":"1140930238294783712","title":"Ubiquitin-Dependent Regulation of Transcription and Development","description":"The cluster is enriched for ubiquitin-related processes (ubiquitin-dependent protein catabolic process and K29-linked ubiquitination) and regulators of transcription by RNA polymerase II, with additional links to ribosome export and developmental differentiation (mesoderm morphogenesis, intestinal epithelial cell differentiation). This points to a cohesive module where ubiquitination modulates transcriptional programs and developmental cell fate, despite some obsolete terms present. ","confidence":"Medium","size":28,"edges":65,"triangles":3,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":2},{"id":"GO:0019089","count":1},{"id":"GO:0045944","count":1},{"id":"GO:0035519","count":1},{"id":"GO:2000203","count":1}]},{"hash":"1533374314392064160","title":"RNA splicing and mRNA export regulation","description":"The cluster is enriched for post-transcriptional RNA processing activities: spliceosome-mediated mRNA splicing, regulation of splicing and polyadenylation, and mRNA export, along with regulation of translational initiation and ncRNA-mediated gene silencing. These terms together suggest a coherent theme of RNA processing and export with transcriptional/post-transcriptional regulation, making the label representative. Minor terms about nitrogen utilization and iron homeostasis appear incidental.","confidence":"High","size":28,"edges":144,"triangles":405,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":2},{"id":"GO:0048026","count":2},{"id":"GO:1900363","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0006406","count":2}]},{"hash":"1522558502096914432","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":40,"triangles":10,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0000288","count":3},{"id":"GO:0045292","count":3},{"id":"GO:0006378","count":3},{"id":"GO:0000480","count":2},{"id":"GO:0048568","count":2}]},{"hash":"2134077096455046112","title":"Genome integrity and RNA processing","description":"This cluster centers on nucleic acid maintenance and RNA metabolism: nucleosome assembly and various DNA repair processes (DNA repair, DNA alkylation repair), along with RNA-centric activities (mRNA processing, tRNA wobble uridine modification, regulation of translational initiation by tRNA modification). A few terms also touch on programmed cell death and mitochondrial permeability, suggesting links to genome stability and cell fate. Overall, the core theme is genome integrity together with RNA processing.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006334","count":2},{"id":"GO:0042245","count":1},{"id":"GO:0002098","count":1},{"id":"GO:1990983","count":1},{"id":"GO:0035552","count":1}]},{"hash":"636646354156369234","title":"Transmembrane transport of small molecules and xenobiotics","description":"The top GO terms are dominated by transmembrane transport activities for various ligands\u2014ions (sodium, phosphate), sugars (galactose, arabinose), sialic acid, vitamin\u2014and xenobiotics, indicating a membrane transporter theme. The presence of neurotransmitter loading into synaptic vesicles further supports vesicular transport roles. A few terms like protein ubiquitination are secondary outliers, but the overall pattern points to membrane transporters handling diverse small molecules and xenobiotics.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0042891","count":1},{"id":"GO:0035725","count":1},{"id":"GO:0015739","count":1}]},{"hash":"266290912097172033","title":"Yeast ion transport and budding localization","description":"The cluster\u2019s top GO terms center on potassium and sodium ion transmembrane transport and protein localization to the bud neck, a hallmark of yeast cell polarity and budding. Additional terms point to transcriptional regulation and nutrient-responsive gene expression (e.g., carbon catabolite repression), suggesting a module of yeast proteins coordinating membrane transport with cell-cycle/polarity and transcriptional control. Overall, the theme points to yeast-specific processes linking transport and budding, though some terms are more peripheral.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":2},{"id":"GO:0035725","count":2},{"id":"GO:0045429","count":2},{"id":"GO:0060038","count":1},{"id":"GO:0006351","count":1}]},{"hash":"1924971065038896277","title":"Retroviral life cycle","description":"This cluster centers on viral entry, reverse transcription (RNA-templated DNA synthesis), genome integration into host DNA, and proviral latency, followed by replication and potential host apoptosis modulation\u2014hallmarks of a retroviral infection cycle. The presence of DNA recombination and integration terms supports this interpretation, giving a coherent theme around retroviral biology.","confidence":"High","size":28,"edges":9,"triangles":0,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0015074","count":5},{"id":"GO:0075713","count":5},{"id":"GO:0046718","count":5},{"id":"GO:0007049","count":3},{"id":"GO:0006278","count":3}]},{"hash":"1016456774990672224","title":"Spinal neural patterning and sensory signaling","description":"This cluster centers on embryonic neural patterning and sensory-related signaling, with terms for spinal cord dorsal/ventral patterning, Shh-smoothened pathway in motor neuron specification, left-right symmetry determination, GPCR signaling, thermoception, and responses to cold and pain. While there are a few outliers (e.g., xylan catabolic process) and a vascular development term, the dominant theme ties neural patterning to sensory perception and receptor-mediated signaling, suggesting a coherent developmental and sensory signaling module. ","confidence":"Medium","size":28,"edges":37,"triangles":1,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0021513","count":5},{"id":"GO:0060976","count":5},{"id":"GO:0009409","count":5},{"id":"GO:0048265","count":5},{"id":"GO:0045493","count":5}]},{"hash":"2140310927579577969","title":"Ribosome Biogenesis and RNA Processing","description":"The strongest signals are for maturation of rRNA (LSU/SSU and 5.8S) and ribosomal large subunit biogenesis, pointing to a core function in ribosome assembly. Additional terms for RNA processing (spliceosome) and ubiquitin-dependent quality control (polyubiquitination, ERAD) suggest a link between ribosome production and protein homeostasis. Stress-related terms like cadmium response and defense to Gram-positive bacteria may reflect broader cellular stress signaling or annotation noise, but do not overpower the ribosome/RNA-processing theme.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071276","count":5},{"id":"GO:0050830","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0000463","count":4},{"id":"GO:0000462","count":4}]},{"hash":"367371909631915414","title":"Nociception and Sensory Development","description":"This cluster is characterized by GO terms related to pain response and thermoception, along with skin and brain development terms, pointing to proteins involved in nociceptive and sensory-development pathways. A few terms (e.g., oxidation-reduction, SA node regulation) are less directly related, but the dominant signals support a nociception/sensory-development theme.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048265","count":3},{"id":"GO:0007275","count":2},{"id":"GO:0043588","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0051260","count":2}]},{"hash":"1287590453844299267","title":"Phospholipid Remodeling and Lipid Mediator Biosynthesis","description":"This cluster is enriched for GO terms related to lipid remodeling and biosynthesis, especially phospholipids and related lipid mediators (cardiolipin remodeling, phosphatidylcholine remodeling, CDP-diacylglycerol biosynthesis, ether lipids, triglycerides, and platelet activating factor biosynthesis). A couple of immune terms (IL-2 production, regulation of T cell death) may reflect lipid signaling cross-talk but do not override the lipid-centric theme.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035965","count":2},{"id":"GO:0070236","count":2},{"id":"GO:0019432","count":2},{"id":"GO:0008611","count":2},{"id":"GO:0070970","count":2}]},{"hash":"1879621708450111484","title":"ER protein processing and secretory trafficking","description":"Among the top terms, several point to the endoplasmic reticulum and secretory pathway: protein localization to ER exit sites, ER-to-Golgi vesicle transport, retrograde transport from ER to cytosol, and ER-associated ubiquitin-dependent catabolic processes. These define a coherent theme of ER protein processing and quality control. Some terms (circadian cycle, osteoblast differentiation, polycistronic mRNA processing) appear more peripheral or outdated, but the dominant ER/traf\ufb01cking signal supports this labeling.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0042747","count":2},{"id":"GO:0031426","count":2},{"id":"GO:1903071","count":1},{"id":"GO:0070973","count":1}]},{"hash":"486032674612190900","title":"Synaptic vesicle trafficking and recycling","description":"This cluster centers on GO terms related to vesicle transport and handling at synapses, including ER-to-Golgi vesicle transport, regulation of synaptic vesicle endocytosis and exocytosis, and endocytic recycling. These collectively point to a core function in managing synaptic vesicles. Some development-related terms (substantia nigra development) and macrophage differentiation appear but do not override the predominant vesicle trafficking theme.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0007224","count":2},{"id":"GO:0006919","count":2},{"id":"GO:1900242","count":2},{"id":"GO:0048873","count":2}]},{"hash":"1527473757071151797","title":"Mitochondrial metabolism and protein import","description":"The cluster centers on mitochondrial-related functions: protein import into the mitochondrial matrix, regulation of mitochondrial membrane permeability, and triglyceride biosynthesis regulation, all pointing to mitochondrial metabolism and membrane dynamics as a shared theme. Additional hints like response to hypoxia support a mitochondria-centered energy regulation context, though a few terms (memory, metamorphosis, T cell homeostasis) seem less directly connected, likely representing broader or pleiotropic annotations.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010867","count":2},{"id":"GO:2000134","count":1},{"id":"GO:0070940","count":1},{"id":"GO:0046902","count":1},{"id":"GO:1903740","count":1}]},{"hash":"904142971793851946","title":"Retroviral replication and proviral latency","description":"The Top Terms include RNA-templated DNA biosynthetic process (reverse transcription), DNA replication, DNA integration, DNA recombination, establishment of integrated proviral latency, and viral penetration into host nucleus, which collectively map to the retroviral life cycle and proviral maintenance. While some terms refer to symbiont-host interactions, the dominant theme is viral entry, reverse transcription, genome integration, and latency. Thus, the cluster most likely represents proteins involved in retroviral replication and proviral latency.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006278","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0039651","count":1},{"id":"GO:0015074","count":1},{"id":"GO:0075713","count":1}]},{"hash":"1587050096724070631","title":"Developmental differentiation and morphogenesis","description":"The cluster's terms center on tissue differentiation and organogenesis\u2014cone cell differentiation, polarized epithelial differentiation, and genitalia morphogenesis\u2014supported by signaling and regulatory processes (RNA modification, protein ADP-ribosylation) that commonly accompany development. A few plant-related terms appear, but the core theme is developmental organization.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":2},{"id":"GO:0000961","count":2},{"id":"GO:0042793","count":2},{"id":"GO:0010019","count":2},{"id":"GO:0007499","count":2}]},{"hash":"964404218751441019","title":"Cardiac rhythm and calcium signaling regulation","description":"The top GO terms cluster around regulation of heart rhythm (SA node action potential, heart rate) and calcium signaling, with kinase-mediated control (PKC pathways and serine/threonine kinase activity). This suggests a module tied to cardiac electrical activity and calcium-dependent signaling. Some terms appear less related (e.g., metanephric tubule development, bioluminescence), likely annotation noise or multifunctional proteins. ","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0098907","count":6},{"id":"GO:0007205","count":6},{"id":"GO:0002027","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0031954","count":5}]},{"hash":"2136266422389818941","title":"Plant and fungal cell wall biosynthesis and remodeling","description":"The top GO terms are dominated by plant- and fungus-specific cell wall processes (xyloglucan metabolism, chitin metabolism, cell wall biogenesis, and both plant- and fungal-type wall organization), indicating a cohesive theme of cell wall construction and modification across kingdoms. A few signaling terms are present but likely incidental to regulation. Confidence: High","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009831","count":2},{"id":"GO:0031505","count":2},{"id":"GO:0010411","count":2},{"id":"GO:0006037","count":2},{"id":"GO:0042546","count":2}]},{"hash":"1679123328679380126","title":"Unknown","description":"These proteins map to a highly heterogeneous set of processes: thiamine biosynthesis and thiamine diphosphate biosynthesis imply a metabolic role, but many other terms point to neurotransmitter catabolism, lipopolysaccharide response, cold response, and antibiotic biosynthesis. The absence of a clear, shared function across the cluster, and the presence of obsolete GO terms, prevents a confident, unified label. ","confidence":"","size":27,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0034720","count":4},{"id":"GO:0009228","count":4},{"id":"GO:0042420","count":3},{"id":"GO:0042135","count":3}]},{"hash":"498983242629363765","title":"Redox-Linked Lipid Metabolism","description":"The cluster is dominated by GO terms for redox biology (oxidation-reduction, redox homeostasis, oxidant detoxification) and lipid biosynthesis (unsaturated fatty acids, ergosterol regulation), suggesting a functional theme around coordinating redox balance with lipid metabolism and related mitochondrial processes. A few tissue-specific terms (nerve myelin maintenance, sebaceous gland differentiation) may reflect broader roles or annotation spillover, but the core signals point to redox and lipid metabolic functions.","confidence":"Medium","size":27,"edges":34,"triangles":9,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0045454","count":5},{"id":"GO:0098869","count":3},{"id":"GO:0032286","count":3},{"id":"GO:0006675","count":3}]},{"hash":"218888928139347132","title":"RNA processing and translation regulation","description":"The GO terms are dominated by translation-related processes (formation of the translation preinitiation complex, translation reinitiation, eIF4F complex assembly) plus regulation of mRNA splicing via the spliceosome and ncRNA-mediated gene silencing. This combination suggests a cohesive theme of RNA-level gene expression control, spanning both processing/splicing and initiation of translation, within the same cluster.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0001731","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0031047","count":3},{"id":"GO:0048026","count":3},{"id":"GO:1902625","count":3}]},{"hash":"714399734661067680","title":"Nucleocytoplasmic transport and mitosis","description":"The cluster is dominated by GO terms about nucleocytoplasmic trafficking\u2014NLS-bearing protein import into the nucleus, ribosomal protein import, mRNA export, and nuclear pore complex assembly\u2014as well as mitotic chromosome alignment. A concurrent term on regulation of GTPase activity (often Ran) supports a transport/cycle-regulation theme. While there are some developmental/ciliary terms, the strongest signal ties to nuclear transport machinery and cell-cycle regulation.","confidence":"High","size":27,"edges":29,"triangles":10,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0043547","count":8},{"id":"GO:0006607","count":8},{"id":"GO:0007080","count":6},{"id":"GO:0006406","count":6},{"id":"GO:0060188","count":5}]},{"hash":"535445360758973211","title":"Telomere maintenance and cell cycle regulation","description":"The top GO terms are heavily weighted toward telomere biology and cell cycle processes (positive regulation of telomere maintenance via telomerase; protein localization to chromosome, telomeric region; cell cycle), suggesting these are the core functions of the cluster. Additional terms point to stress and signaling pathways (thermoception, capsazepine response, NOD signaling, synaptic regulation, pinocytosis), indicating a broader context of cellular stress signaling, but telomere-related processes appear most representative of the cluster\u2019s characteristic function.","confidence":"Medium","size":27,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":8},{"id":"GO:0032212","count":7},{"id":"GO:0048549","count":7},{"id":"GO:0070427","count":7},{"id":"GO:0050955","count":7}]},{"hash":"2060413794792069592","title":"Ion-Driven Excitability in Neurons and Muscles","description":"The cluster is dominated by neural synaptic plasticity terms (long-term potentiation/depression), regulation of heart and skeletal muscle contraction, and ion transport (calcium and sodium) across membranes, pointing to a shared theme of ion-dependent excitability and signaling in neural and muscular contexts. Some outliers (ascospore formation, ncRNA-mediated gene silencing) may reflect annotation noise rather than core function.","confidence":"Medium","size":27,"edges":27,"triangles":5,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0060291","count":3},{"id":"GO:0098735","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0032516","count":3},{"id":"GO:0030437","count":3}]},{"hash":"2164182567706068345","title":"Transmembrane Ion and Small-Molecule Transporters","description":"The top GO terms show a cohesive theme of membrane transport for various ions and small molecules (K+, Na+, phosphate, sugars, sialic acid, vitamins) and related processes like neurotransmitter loading into vesicles, indicating a cluster of transporter proteins at membranes. ","confidence":"High","size":27,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":5},{"id":"GO:0042891","count":4},{"id":"GO:0006855","count":4},{"id":"GO:0035725","count":4},{"id":"GO:0015739","count":4}]},{"hash":"882889266096835299","title":"DNA mobility and cell-cycle stress responses","description":"This cluster is dominated by GO terms for DNA movement and genome dynamics (DNA integration, DNA transposition, proviral latency) alongside cell-cycle and chromosome segregation processes (cell cycle, chromosome segregation, cell division). Additional terms indicate stress responses (heat, antibiotic) and host-microbe interactions (symbiont entry, proviral latency), suggesting proteins linked to genome mobility and cell-cycle control under stress and host interaction contexts.","confidence":"Medium","size":27,"edges":13,"triangles":0,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":2},{"id":"GO:0015074","count":2},{"id":"GO:0006313","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0007059","count":2}]},{"hash":"1321957073172359658","title":"Unknown","description":"The top GO terms span diverse processes\u2014from endocytosis and ubiquitination to telomere maintenance, immune signaling (NOD1), sensory perception (thermoception and response to capsazepine), heat-stress transcription, and cell cycle/synaptic regulation. There isn\u2019t a single coherent function tying these terms together, so a specific, representative label isn\u2019t supported.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048549","count":8},{"id":"GO:0016567","count":8},{"id":"GO:0032212","count":7},{"id":"GO:0070427","count":7},{"id":"GO:0050955","count":7}]},{"hash":"615826533720108572","title":"Plant Organellar RNA Editing and Processing","description":"This cluster is defined by RNA metabolism in plant organelles, especially chloroplast/plastid and mitochondrial RNA processing and editing. Terms include plastid transcription, chloroplast RNA processing, chloroplast RNA modification, and cytidine-to-uridine editing, plus regulation of mitochondrial mRNA turnover. The seed dormancy term appears as a peripheral developmental context, but the core signal is organellar RNA editing/processing.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":2},{"id":"GO:0016554","count":2},{"id":"GO:0080156","count":2},{"id":"GO:0042793","count":2},{"id":"GO:0031425","count":2}]},{"hash":"1567615857534597199","title":"Environmental Sensing and Responses","description":"The terms point to processes related to sensing environmental cues (thermoception, auditory receptor differentiation, CO2 detection, startle response) and mounting physiological responses (hypoxia response, vasoconstriction), with additional developmental and autophagy-related terms that suggest broader physiological adaptation. The cluster appears to be a mix of sensory/environmental perception and downstream responses, rather than a single narrowly defined function, hence a broad label is appropriate.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042491","count":1},{"id":"GO:0042310","count":1},{"id":"GO:0001666","count":1},{"id":"GO:0003031","count":1},{"id":"GO:0001964","count":1}]},{"hash":"633078773629477247","title":"RNA Processing and Methylation","description":"This cluster is enriched for RNA modification and methylation activities, including tRNA wobble uridine modification, rRNA modification, tRNA methylation, and histone methylation, suggesting roles in RNA processing and chromatin regulation. Some terms like mesoderm formation, nodulation, and antibiotic biosynthesis appear more distant and may reflect annotation noise, but the dominant pattern centers on RNA modification and methylation processes.","confidence":"Medium","size":27,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001707","count":2},{"id":"GO:0002098","count":2},{"id":"GO:1901052","count":2},{"id":"GO:0000154","count":2},{"id":"GO:0017000","count":2}]},{"hash":"538599959322782683","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":3},{"id":"GO:0000122","count":2},{"id":"GO:0042372","count":2},{"id":"GO:0016554","count":2},{"id":"GO:0070129","count":2}]},{"hash":"175552550460195885","title":"Stress Signaling and Cytoskeletal Regulation","description":"The cluster shows a mix of GO terms centered on kinase activity and signaling (autophosphorylation, regulation, and responses to hormones/neurotrophic factors) alongside cytoskeletal remodeling (myosin II disassembly) and stress-related processes (anoxia, necroptosis), suggesting a broad signaling and structural response rather than one single function. This broad theme best captures the diverse functions represented.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016340","count":1},{"id":"GO:0031952","count":1},{"id":"GO:1990637","count":1},{"id":"GO:0071454","count":1},{"id":"GO:1990416","count":1}]},{"hash":"2116717234387713027","title":"NF-kB and cytokine signaling inhibitors","description":"The top GO terms are dominated by negative regulation of NF-kappaB activity and suppression of multiple cytokines (IL-6, IL-1\u03b2, IL-8), plus related control of ubiquitination and desumoylation, and protein turnover. This pattern suggests a cluster of proteins that function to dampen inflammatory signaling rather than a single enzymatic pathway. Confidence: Medium","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":2},{"id":"GO:0031397","count":2},{"id":"GO:0032715","count":2},{"id":"GO:0045944","count":1},{"id":"GO:0035025","count":1}]},{"hash":"916510405061244017","title":"Plant Stress Response and Defense Signaling","description":"These terms point to plant stress responses and defense signaling, with additional emphasis on transcriptional and translational control during stress (mRNA stability and cap-independent translation) and growth signaling (auxin transport). The mix suggests a broad stress/defense regulatory theme rather than a single specific function.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043488","count":1},{"id":"GO:0044829","count":1},{"id":"GO:0034052","count":1},{"id":"GO:1900363","count":1},{"id":"GO:1903679","count":1}]},{"hash":"1979583846253340340","title":"Ascosporogenesis and cell-cycle signaling","description":"The top GO terms point to sporulation-related membrane formation (ascospore-type prospore membrane) and core cell-cycle processes (mitotic cell cycle, DNA replication), with supportive signals like phosphatidylinositol signaling and GTPase regulation. However, with no edges between proteins (Edges: 0) and only a few terms at modest counts, the linkage is tentative and may reflect dispersed, non-interacting functions spanning sporulation and growth control.","confidence":"Low","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048015","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0032120","count":2},{"id":"GO:0007584","count":2}]},{"hash":"1287614984048982848","title":"Metabolic signaling and vitamin biosynthesis","description":"The cluster combines metabolic processes (phenylacetate catabolic process; L-serine and thiamine biosynthesis) with signaling components (phosphorylation/dephosphorylation) and stress/regulatory themes (respiratory burst, response to toxic substances, transcription regulation). While not pointing to a single dominant pathway, the common thread is metabolism intertwined with signaling and regulation, hence a label reflecting both aspects.","confidence":"Medium","size":27,"edges":15,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0010124","count":3},{"id":"GO:0016310","count":3},{"id":"GO:0016311","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0006564","count":2}]},{"hash":"37671914043183804","title":"Retroviral replication and proviral integration","description":"This cluster is dominated by GO terms describing reverse transcription (RNA-templated DNA biosynthetic process), DNA synthesis and recombination, and especially DNA integration and proviral latency establishment, alongside viral entry and nuclear penetration. Together these point to the retroviral life cycle: reverse transcription of viral RNA into DNA, integration into the host genome, and the establishment of latent proviruses. The additional host\u2013symbiont interaction terms likely reflect related host-cell entry and apoptosis pathways during infection, but the core signal is retroviral replication and proviral integration.","confidence":"High","size":27,"edges":32,"triangles":9,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":20},{"id":"GO:0006310","count":20},{"id":"GO:0006278","count":19},{"id":"GO:0039651","count":19},{"id":"GO:0015074","count":19}]},{"hash":"1482359077350107634","title":"Retroviral entry, genome integration, and latency","description":"The top GO terms cluster around steps of a retroviral life cycle: entry into the host cell and nucleus, reverse transcription and DNA synthesis, integration of viral DNA into the host genome, and establishment of proviral latency, along with host defense modulation and replication. This collective signal points to a viral/retron-like program rather than a cellular pathway, justifying a label focused on retroviral entry, integration, and latency.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":11},{"id":"GO:0006278","count":7},{"id":"GO:0039651","count":7},{"id":"GO:0015074","count":7},{"id":"GO:0075713","count":7}]},{"hash":"1875496737828971799","title":"DNA transposition and cell cycle progression","description":"This cluster is dominated by GO terms tied to DNA mobility and chromosomal events (DNA transposition, DNA integration, chromosome segregation, and cell cycle), suggesting a theme around genome dynamics during division. Additional terms like RNA guanine-N7-methylation, male gonad development, and cadmium response appear but are less central to the core theme.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0036265","count":2},{"id":"GO:0008584","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0015074","count":2}]},{"hash":"2266885965092115576","title":"Ubiquitin-Dependent Protein Degradation","description":"The cluster is strongly enriched for ubiquitination-related processes (autoubiquitination, ubiquitin-dependent protein catabolic process, and K48-linked ubiquitination), indicating a core theme of protein tagging for proteasomal degradation. While some terms touch chromatin or nuclear functions (histone catabolic process, V(D)J recombination, dosage compensation), these can be linked through regulation by ubiquitin signaling and turnover. Overall, the proteins appear to participate in ubiquitin-mediated protein turnover, with peripheral links to chromatin and nuclear regulation.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":8},{"id":"GO:0042787","count":8},{"id":"GO:1900095","count":7},{"id":"GO:0070936","count":7},{"id":"GO:0033151","count":7}]},{"hash":"1882443349718156582","title":"Unknown","description":"The top terms span immune regulation (T cell homeostasis, negative regulation of T cell cytotoxicity), neural/sensory processes (sound perception, dendrite morphogenesis) and broad signaling/DNA-related terms, with zero edges connecting the proteins. This breadth and lack of interactions suggest no single cohesive function for the cluster, so a meaningful specific label isn\u2019t supported.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0043029","count":5},{"id":"GO:0007605","count":5},{"id":"GO:0050774","count":4},{"id":"GO:0071315","count":4},{"id":"GO:0035234","count":4}]},{"hash":"425363277060582784","title":"Amino acid catabolism and xenobiotic detoxification","description":"This cluster\u2019s top GO terms emphasize catabolic pathways for amino acids (phenylalanine, tyrosine) and glutathione-dependent detoxification, plus xenobiotic and methylglyoxal catabolism, suggesting a metabolic/detoxification theme. Some terms (translation, transcription regulation, responses to virus/antibiotic) may reflect general stress responses, but the core signal is amino acid breakdown and detox pathways.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006749","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0019243","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0006572","count":1}]},{"hash":"252947854176094964","title":"Phosphoinositide signaling and vesicle dynamics","description":"The cluster's top terms cluster around lipid-mediated signaling (phosphatidylinositol pathways, IP3 biosynthesis) and vesicle biology (synaptic vesicle maturation, presynaptic signaling). Additionally, phosphatidylethanolamine biosynthesis and regulation of GTPase activity align with membrane trafficking. Some terms touch on broader processes like angiogenesis or B cell signaling, but the core recurring theme is lipid signaling coordinating vesicle maturation and trafficking, hence the label.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016525","count":3},{"id":"GO:0048015","count":2},{"id":"GO:0016188","count":2},{"id":"GO:0050861","count":2},{"id":"GO:0099526","count":2}]},{"hash":"1215846808333277017","title":"Unknown","description":"The GO terms span signaling and nervous-system\u2013related responses (intracellular signal transduction, response to pain, memory, GPCR signaling) alongside plant/fungal cell wall processes and plant polysaccharide catabolism, with no clear, single function linking them. The lack of a cohesive theme and zero edges among proteins suggest no common biological role for this cluster based on the provided terms. ","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":2},{"id":"GO:0048265","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0045493","count":2},{"id":"GO:0046373","count":2}]},{"hash":"1100376205162956690","title":"Broad signaling and regulatory proteins","description":"This cluster shows a mix of terms across GPCR signaling, innate immune signaling (NOD1), sensory perception (thermoception, capsazepine response), endocytosis (pinocytosis), cell cycle, telomere maintenance, and synaptic receptor localization. The common thread appears to be broad regulation of diverse signaling and cellular processes rather than a single coherent function, so the label should reflect general regulatory signaling roles rather than a specific pathway.","confidence":"Low","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007205","count":7},{"id":"GO:0098907","count":5},{"id":"GO:0032212","count":4},{"id":"GO:0048549","count":4},{"id":"GO:0070427","count":4}]},{"hash":"677473237590489176","title":"Cellular Signaling and Localization","description":"The top GO terms point to a mix of signaling pathways (NOD1 signaling, synaptic receptor localization affecting plasticity, response to capsazepine/thermoception), membrane trafficking (pinocytosis), calcium signaling (calcium release into cytosol), and subcellular localization and polarity (telomere localization, telomere maintenance, epithelial polarity). This suggests a cluster of proteins involved in broader cellular signaling and localization processes rather than a single specific function, hence the label.","confidence":"Medium","size":26,"edges":25,"triangles":0,"max_degree":25,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":2},{"id":"GO:0048549","count":2},{"id":"GO:0070427","count":2},{"id":"GO:0050955","count":2},{"id":"GO:1901594","count":2}]},{"hash":"1953738544169817125","title":"Nuclear mRNA and ribosome export","description":"The GO terms cluster around nuclear transport and processing, including mRNA export, ribosomal subunit export, and nuclear import/export of RNA-binding proteins, with supporting links to kinetochore localization and transcriptional regulation, indicating a cohesive nuclear transport/processing role.","confidence":"High","size":26,"edges":53,"triangles":45,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":5},{"id":"GO:0034501","count":4},{"id":"GO:0000122","count":3},{"id":"GO:0035048","count":3},{"id":"GO:0042493","count":3}]},{"hash":"1350055811212588793","title":"Ribosome biogenesis and translation machinery","description":"The top GO terms show a strong focus on ribosome biogenesis (including small and large subunit biogenesis), translation, and ribosomal subunit export from the nucleus, along with tRNA modification, all pointing to the protein set being primarily involved in ribosome assembly and protein synthesis. The presence of cell cycle and cell division terms suggests coordination between ribosome production and cellular proliferation, reinforcing the theme of growth-related translation machinery. A minor, non-central term about cellular conjugation appears, but does not alter the primary interpretation. ","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0007049","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0042274","count":2},{"id":"GO:0000747","count":2}]},{"hash":"903939941349202954","title":"Unknown","description":"The top GO terms are a broad mix spanning ribosome biogenesis, inflammatory response, vesicle transport/secretory processes, RNA processing, transcription regulation, and development signals. There is no single cohesive biological function that ties these terms together, so a concise, unified label isn\u2019t supported by the data.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":1},{"id":"GO:0090594","count":1},{"id":"GO:0016192","count":1},{"id":"GO:0009306","count":1},{"id":"GO:0031054","count":1}]},{"hash":"958263298704279371","title":"Nuclear Transcription Regulation and mRNA Export","description":"The top GO terms are dominated by DNA-templated transcription and its regulation, plus mRNA export from the nucleus, pointing to a nuclear gene-expression module focused on transcription control and RNA processing; several biosynthesis-related terms appear as noise, but the core function is transcriptional regulation and RNA transport.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0042619","count":4},{"id":"GO:0046677","count":4}]},{"hash":"970303028486501821","title":"Translation initiation machinery and RNA processing regulation","description":"Top GO terms indicate roles in assembling the translation preinitiation complex and eIF4F complex, pointing to translation initiation activity. The presence of regulatory hints for mRNA splicing and RNA processing suggests these proteins also influence RNA maturation. Taken together, the cluster centers on translation initiation with concurrent RNA processing regulation.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0043547","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0048026","count":2},{"id":"GO:1902625","count":2}]},{"hash":"1069750526718905011","title":"Protein acetylation and chromatin regulation","description":"The top GO terms are dominated by acetylation-related processes (histone H4 acetylation, N-terminal acetylation/propionylation, putrescine acetylation, N-acetylglucosamine metabolism) and chromatin-related functions (subtelomeric heterochromatin formation), suggesting a core theme of protein modification and chromatin regulation. Some items like angiogenesis, melatonin biosynthesis, and leaf formation regulation are less directly connected and likely secondary annotations. Overall, the acetylation/chromatin signal is the strongest unifying thread.","confidence":"Medium","size":26,"edges":32,"triangles":1,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":5},{"id":"GO:0030187","count":4},{"id":"GO:0043967","count":4},{"id":"GO:0017198","count":4},{"id":"GO:0006348","count":4}]},{"hash":"538163676259044683","title":"Nuclear transcription and chromatin regulation","description":"The top GO terms cluster around nuclear functions: DNA-templated transcription, chromatin organization, histone modification, RNA processing (mRNA branch site recognition), and chromosome segregation, suggesting a module focused on gene expression regulation and genome organization. Some terms like phagolysosome assembly and growth hormone response are less coherent with this core theme and may represent noise or multifunction annotations. Overall, the cluster appears to reflect nuclear regulatory activities rather than cytosolic pathways.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0000747","count":1},{"id":"GO:0050679","count":1},{"id":"GO:1902510","count":1},{"id":"GO:0001845","count":1}]},{"hash":"1744771718985650583","title":"Neural and cardiac development signaling","description":"The top terms cluster around development-related processes, especially neural (hippocampus development; neurotrophin TRK receptor signaling) and cardiac (heart development) contexts, along with Hippo signaling that governs organ size. There are also generic cellular processes (DNA replication, translation, apoptosis) that often accompany development. Taken together, the dominant theme is developmental signaling in neural and cardiac tissues.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021766","count":2},{"id":"GO:0051092","count":2},{"id":"GO:0035329","count":2},{"id":"GO:0045736","count":2},{"id":"GO:0007507","count":2}]},{"hash":"43051385364011209","title":"Glucocorticoid-responsive transcription in spermatogenesis","description":"The GO terms cluster around a glucocorticoid/dexamethasone response, transcriptional regulation (DNA-templated transcription and Pol II\u2013mediated transcription control), translation regulation, and male meiosis-related processes (meiotic chromosome condensation, spermatid differentiation, male meiosis cytokinesis). Taken together, they suggest a set of proteins involved in glucocorticoid-driven transcriptional programs during spermatogenesis. Confidence: Medium","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071549","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0034638","count":2},{"id":"GO:0006955","count":2},{"id":"GO:0000122","count":2}]},{"hash":"1200481946828396491","title":"Unknown","description":"The GO terms are highly diverse, including cell cycle processes, stress responses, signaling, and bacterial biosynthesis, with no clear common function tying the cluster together; therefore a specific, representative label cannot be assigned.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0051301","count":5},{"id":"GO:0007049","count":4},{"id":"GO:0097171","count":4},{"id":"GO:2000324","count":3}]},{"hash":"396608832379533534","title":"Diverse signaling and regulatory pathways","description":"This cluster shows a mix of signaling-related GO terms (GPCR signaling, NOD1 signaling), regulatory processes (ubiquitination, endocytosis), and additional regulatory or stress-related functions (telomere maintenance, thermoception, immune regulation, cardiac action potentials). The diversity suggests involvement in multiple regulatory signaling networks rather than a single, cohesive function.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007205","count":13},{"id":"GO:0098907","count":12},{"id":"GO:0016049","count":11},{"id":"GO:0010745","count":10},{"id":"GO:0016567","count":10}]},{"hash":"1982211101972900568","title":"Retroviral DNA integration and latency","description":"The top GO terms point to steps in a retroviral life cycle (reverse transcription via RNA-templated DNA synthesis, DNA recombination, DNA integration, and establishment of proviral latency) plus viral entry/penetration into the host nucleus, indicating proteins associated with proviral integration and latency as the core theme, despite some peripheral host\u2013symbiont interaction terms.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":13},{"id":"GO:0006278","count":8},{"id":"GO:0039651","count":8},{"id":"GO:0015074","count":8},{"id":"GO:0075713","count":8}]},{"hash":"1576044608519910053","title":"Retroviral integration and latency","description":"The terms cluster around retroviral life cycle processes: reverse transcription (RNA-templated DNA biosynthetic process), DNA integration, DNA recombination, DNA replication, and establishment of integrated proviral latency, plus viral penetration into the host nucleus. A few terms refer to host\u2013symbiont interactions, but the dominant signal is proviral integration/latency and entry, suggesting a retroviral-like cluster. Confidence: Medium","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":4},{"id":"GO:0006278","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0039651","count":3},{"id":"GO:0015074","count":3}]},{"hash":"1532831802022710140","title":"Stress-Response Signaling and Telomere Maintenance","description":"The terms point to a mix of stress-related signaling (thermoception, heat-stress response, capsazepine response, NOD1 pathway), cell cycle, calcium signaling, and telomere-related localization and maintenance. There isn\u2019t a single tightly connected pathway, but the common thread is cellular signaling and regulatory responses to stress, with telomere maintenance as a notable chromosomal-related process. Hence, a label around general stress-response signaling operable across multiple processes is appropriate.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0032212","count":10},{"id":"GO:0048549","count":10},{"id":"GO:0070427","count":10},{"id":"GO:0050955","count":10},{"id":"GO:1901594","count":10}]},{"hash":"2116490850430933356","title":"Carbohydrate Metabolism and Xenobiotic Response","description":"The cluster is enriched for carbohydrate-related metabolism terms: glucose metabolic process, glycolytic process, pentose-phosphate shunt, glyoxylate metabolic process, and general carbohydrate metabolic process, indicating a cohesive focus on central carbon metabolism. The presence of terms related to cellular response to xenobiotic stimulus and response to antibiotic suggests a link between metabolic activity and stress/adaptive responses. Some other terms (protein methylation, peptidyl-arginine hydroxylation) may reflect regulatory processes within these pathways. Overall, the dominant theme appears to be carbohydrate metabolism with ancillary stress-response connections.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0005975","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0006098","count":2},{"id":"GO:0006006","count":2}]},{"hash":"768832970176752409","title":"Mitochondrial Metabolite Transport and Thermogenesis","description":"The terms are dominated by mitochondrial substrate transport (alpha-ketoglutarate, ornithine, nucleotides, ATP), malate-aspartate shuttle, and mitochondrial membrane dynamics, plus adaptive thermogenesis. This points to a cohesive cluster of proteins involved in mitochondrial metabolite exchange and energy regulation, with some links to glucose-stimulated insulin response and cell stress pathways.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0097274","count":4},{"id":"GO:0015742","count":3},{"id":"GO:0000066","count":3},{"id":"GO:1990544","count":3},{"id":"GO:1990519","count":3}]},{"hash":"630190422617949287","title":"Neuronal vesicle trafficking and nuclear export regulation","description":"This cluster centers on intracellular transport processes: ER-to-Golgi vesicle trafficking, ubiquitin-dependent endocytosis, and export regulation of ribosomal subunits and mRNA from the nucleus. The appearance of brain development and dendrite extension terms suggests a neuronal context, while positive regulation of GTPase activity points to signaling that governs trafficking and cytoskeletal dynamics. Taken together, it reflects a set of proteins involved in vesicle trafficking and nucleocytoplasmic transport in neurons.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0000747","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0007420","count":2}]},{"hash":"1655159111284797148","title":"DNA replication and proviral latency","description":"This cluster is enriched for DNA-focused processes: replication, integration, and recombination, along with establishment of integrated proviral latency, suggesting genome remodeling and retroviral-like latency as the central theme. Some terms like symbiont-related and lens morphogenesis terms appear as peripheral associations, but the dominant signal favors DNA metabolism and proviral latency.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0045737","count":2},{"id":"GO:0032237","count":2},{"id":"GO:0070309","count":2},{"id":"GO:0006278","count":2}]},{"hash":"837568768946977345","title":"Rho/GTPase signaling and synaptic vesicle exocytosis","description":"This cluster is enriched for GO terms related to regulation of Rho protein signal transduction and regulation of GTPase activity, along with a strong signal for regulation of synaptic vesicle exocytosis and intracellular transport, suggesting a cohesive role in GTPase-driven signaling controlling vesicle trafficking in neurons.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0035023","count":4},{"id":"GO:0006646","count":3},{"id":"GO:0043087","count":3},{"id":"GO:0010796","count":3},{"id":"GO:0006886","count":3}]},{"hash":"56181687121517454","title":"Regulated signaling and cell proliferation","description":"The top GO terms cluster around regulation and signaling: positive regulation of GTPase activity, kinase activity, and protein autophosphorylation indicate signaling control, while mitotic cell cycle and positive regulation of cell population proliferation point to growth/division. Additional terms (development, hypoxia response, immune defense, glial apoptotic process, mRNA transport) suggest a broad set of regulatory processes rather than a single pathway. The absence of edges supports a diverse regulatory collection rather than a tightly connected module.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0050830","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0071456","count":2}]},{"hash":"316249248450181509","title":"Signaling and transcription with temperature sensing","description":"This cluster is enriched for intracellular signaling and DNA-templated transcription, suggesting coordinated regulation of signaling pathways with gene expression. Temperature-related terms (thermoception, response to capsazepine) point to heat-sensing mechanisms, while NOD1 signaling and regulation of synaptic plasticity indicate broader neuronal and immune signaling dynamics. Telomere maintenance and pinocytosis terms appear more peripheral but may reflect additional regulatory roles in signaling networks.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0032212","count":2},{"id":"GO:0048549","count":2},{"id":"GO:0070427","count":2}]},{"hash":"141675192604544246","title":"Neural development and chromatin regulation","description":"Brain development, transcription, and histone methylation terms suggest epigenetic control of gene expression in neural contexts; the cluster seems linked to chromatin modification during development, with some additional cell-cycle and lysosome-related processes.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0051568","count":3},{"id":"GO:0034729","count":3},{"id":"GO:0007064","count":3}]},{"hash":"1609739775608375111","title":"Cell cycle control and kinase signaling","description":"The prominent terms include mitotic cell cycle, regulation of cytokinesis, protein dephosphorylation, and negative regulation of protein kinase activity, along with signaling processes such as NF-kappaB and phosphatidylinositol-mediated signaling. While there are some outliers (memory and muscle development), the core set points to coordinated control of cell division and phosphorylation-driven signaling pathways, suggesting a cohesive theme of cell cycle regulation and kinase-based signaling.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0032120","count":4},{"id":"GO:0032465","count":3},{"id":"GO:0043123","count":3},{"id":"GO:0006470","count":3}]},{"hash":"1630000755831724915","title":"Transcriptional Regulation and Development","description":"Top GO terms center on DNA-templated transcription and RNA guanine-N7-methylation, indicating core involvement in transcription initiation and RNA processing. Additional terms point to developmental contexts (multicellular organism development, skin development, brain development) and cellular regulation (autophagy, regulation of Rho protein signal transduction). Together these suggest a cluster of proteins that participate in controlling gene expression during development and related cellular remodeling, with some terms being older (obsolete) annotations likely reflecting historical assignments.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0036265","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0043588","count":2}]},{"hash":"1553168875265541312","title":"Retroviral replication and genome integration","description":"The GO terms cluster around reverse transcription (RNA-templated DNA biosynthesis), DNA replication, DNA integration, recombination, proviral latency, and viral entry into the host nucleus, all hallmark steps of the retroviral life cycle. Some terms also reflect virus-host interactions such as suppression of RNA interference and host apoptosis manipulation, reinforcing the retroviral theme. ","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006278","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0039651","count":1},{"id":"GO:0015074","count":1},{"id":"GO:0075713","count":1}]},{"hash":"1071064690756827400","title":"Translation machinery and mRNA turnover","description":"This cluster is dominated by translation-related GO terms (translation, initiation, elongation, termination, cytoplasmic translation) plus selenocysteine incorporation and deadenylation-dependent mRNA decay, indicating a set of ribosome-associated factors and RNA turnover proteins. The antibiotic response term may reflect translational stress contexts. Overall, the proteins appear to function together in protein synthesis and RNA processing/regulation.","confidence":"High","size":25,"edges":284,"triangles":1977,"max_degree":24,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":12},{"id":"GO:0046677","count":8},{"id":"GO:2000767","count":7},{"id":"GO:0001514","count":7},{"id":"GO:0006413","count":7}]},{"hash":"2077067589416796804","title":"Ossification and bone remodeling","description":"Ossification and bone remodeling. The top GO terms emphasize bone resorption, intramembranous ossification, and collagen catabolic processes, pointing to skeletal development and remodeling. Other terms indicate broader development and signaling, but the core recurring theme is the formation and breakdown of bone and connective tissue, justifying this label.","confidence":"Medium","size":25,"edges":72,"triangles":178,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0010813","count":11},{"id":"GO:0060448","count":11},{"id":"GO:0045453","count":11},{"id":"GO:0050790","count":11},{"id":"GO:2000179","count":11}]},{"hash":"978329935894789514","title":"Redox Homeostasis and Detoxification","description":"The cluster is enriched for GO terms related to cellular oxidant detoxification, redox homeostasis, and glutathione metabolism, indicating a core function in protecting against oxidative stress. Nucleotide-excision repair supports damage mitigation from oxidative stress, while additional terms reflect broader metabolic and regulatory roles; overall, the dominant theme is maintaining redox balance and detox pathways.","confidence":"High","size":25,"edges":187,"triangles":815,"max_degree":23,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0098869","count":9},{"id":"GO:0045454","count":8},{"id":"GO:0060316","count":7},{"id":"GO:0006289","count":6},{"id":"GO:2000255","count":6}]},{"hash":"471626625180150930","title":"Calcium signaling and ion transport","description":"The top GO terms are dominated by calcium-related processes: release of calcium from the sarcoplasmic reticulum, calcium import across the plasma membrane, and regulation of ryanodine-sensitive calcium-release channels, plus a term on atrial action potential repolarization and vasoconstriction. Other terms reference general ion transport (manganese) and stress responses (osmotic, hypoxia) which often intersect with calcium signaling and ion homeostasis. Taken together, the cluster centers on calcium signaling and related ion transport, with some broader stress-response context.","confidence":"High","size":25,"edges":47,"triangles":42,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0014808","count":3},{"id":"GO:0098703","count":3},{"id":"GO:0006828","count":3},{"id":"GO:0050976","count":3},{"id":"GO:0098914","count":3}]},{"hash":"507885578721593020","title":"Nuclear DNA replication and transcription under stress","description":"This cluster centers on nuclear processes such as DNA replication, transcription, and mRNA export, and also on cellular stress responses (oxidative stress, apoptosis, autophagosome maturation). The combination of DNA replication, transcription-related GO terms, and nuclear transport terms, with accompanying stress-response terms, suggests a cohesive theme around nuclear gene expression and cellular stress management.","confidence":"Medium","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0034599","count":4},{"id":"GO:0046826","count":4},{"id":"GO:0071375","count":4},{"id":"GO:0006915","count":4}]},{"hash":"2218003743388217121","title":"Stress Response and RNA Metabolism","description":"This cluster centers on stress-related regulation: localization to cytoplasmic stress granules, mRNA decay, and hypoxia response point to cellular stress handling and RNA metabolism. Additional terms like mitochondrial fission and receptor internalization reflect remodeling under stress, with transcriptional and DNA-related terms suggesting broader gene-expression control. Overall, the dominant theme is stress response with RNA regulation.","confidence":"Medium","size":25,"edges":20,"triangles":1,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:1903608","count":2},{"id":"GO:0090394","count":2},{"id":"GO:0090141","count":2},{"id":"GO:0002091","count":2},{"id":"GO:0045944","count":1}]},{"hash":"192638306668186324","title":"Antiviral innate immune signaling and stress response","description":"This cluster combines innate immune and antiviral defense terms (innate immune response, defense response to virus) with cellular stress pathways (response to unfolded protein, hydrogen peroxide response, dsRNA response, mitochondrial fission regulation) and related signaling modulation (negative regulation of protein kinase activity, glucocorticoid signaling). The co-occurrence suggests proteins involved in coordinating antiviral defense with broader cellular stress responses, making a label that reflects both themes appropriate.","confidence":"Medium","size":25,"edges":70,"triangles":79,"max_degree":16,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0090141","count":4},{"id":"GO:0006469","count":4},{"id":"GO:0070301","count":4},{"id":"GO:0006986","count":4},{"id":"GO:0071360","count":3}]},{"hash":"322148057353453033","title":"Muscle and neural development and differentiation","description":"This cluster centers on developmental and differentiation processes, particularly muscle formation (myoblast fusion, heart development) and neural lineage development (Schwann cell development) alongside multicellular development and transcriptional regulation. The presence of terms related to GTPase signaling and protein phosphorylation supports coordinated signaling and gene expression control during development, suggesting a broad developmental program rather than a single metabolic function.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":6},{"id":"GO:0043547","count":5},{"id":"GO:0007275","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0007520","count":4}]},{"hash":"108614256627536623","title":"Ubiquitin-Dependent Proteolysis and Chromatin Regulation","description":"The cluster is dominated by GO terms related to ubiquitination and proteasomal degradation (ubiquitin-dependent protein catabolic process, autoubiquitination, ERAD, K6-linked ubiquitination), with additional terms pointing to histone turnover and chromatin-related regulation. While a few terms touch on immune signaling and DNA processes, the strongest shared theme is ubiquitin-mediated protein turnover and its impact on chromatin dynamics.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":13},{"id":"GO:0051865","count":13},{"id":"GO:0030433","count":12},{"id":"GO:0033151","count":10},{"id":"GO:0009048","count":10}]},{"hash":"259169949690481212","title":"Retroviral DNA Synthesis and Integration","description":"The top GO terms cluster around retroviral processes: RNA-templated DNA biosynthesis (reverse transcription), DNA replication and recombination, DNA integration, and establishment of proviral latency, plus viral entry into the host nucleus. Some terms reference host-virus interactions and regulation of RNA processing, which fits the context of viral infection and genome integration within host cells. Overall, the pattern points to steps in the retroviral life cycle and proviral maintenance.","confidence":"High","size":25,"edges":28,"triangles":38,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006278","count":10},{"id":"GO:0006260","count":10},{"id":"GO:0039651","count":10},{"id":"GO:0015074","count":10},{"id":"GO:0075713","count":10}]},{"hash":"645064203758644230","title":"Small Molecule Transmembrane Transport","description":"The terms show a strong emphasis on transmembrane transport of diverse small molecules, including vitamins, xenobiotics, sugars, and organic acids, indicating a cluster of membrane transporter proteins mediating uptake and efflux across the cell boundary; a few peripheral terms about senescence or epithelial maintenance are present but do not define the main function. ","confidence":"High","size":25,"edges":89,"triangles":62,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":21},{"id":"GO:0006855","count":21},{"id":"GO:0042891","count":19},{"id":"GO:0052106","count":15},{"id":"GO:1904659","count":15}]},{"hash":"633972982557835671","title":"Developmental gene expression and cell migration","description":"The top terms show strong enrichment for developmental processes (multicellular development, fat cell differentiation), and core gene expression activities (DNA-templated transcription, mRNA processing) along with cell movement (cell migration, response to muscle stretch). This points to a cluster of proteins involved in regulating gene expression during development and cellular mobility, with ancillary links to telomere maintenance that may reflect genome stability roles in development. ","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0016477","count":14},{"id":"GO:0035994","count":14},{"id":"GO:0006397","count":14},{"id":"GO:0032212","count":14},{"id":"GO:2001275","count":14}]},{"hash":"1860083608944272685","title":"Oxidative stress response and redox homeostasis","description":"This cluster is dominated by GO terms related to redox balance and oxidative stress (cell redox homeostasis, oxidation-reduction process, cellular oxidant detoxification, cellular response to hydrogen peroxide, cellular response to oxidative stress), indicating a coherent oxidative stress response module. A few terms (methylamine metabolism, neural crest heart migration, RNA polymerase II regulation, ion transport modulation) appear as less central or incidental annotations, but do not override the primary redox theme.","confidence":"High","size":25,"edges":162,"triangles":513,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":8},{"id":"GO:0055114","count":8},{"id":"GO:0098869","count":7},{"id":"GO:0070301","count":5},{"id":"GO:0030416","count":5}]},{"hash":"1989396376383427718","title":"RNA processing and translation regulation","description":"The top GO terms point to RNA metabolism and control of gene expression, with regulatory ncRNA-mediated gene silencing, positive regulation of mRNA splicing via the spliceosome, and assembly of the eIF4F complex\u2014all indicating RNA processing and translation initiation/ regulation as the core theme. Some terms (protein transmembrane transport, light absorption) appear as outliers and do not fit the main signal, but the RNA-centric terms dominate. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071806","count":1},{"id":"GO:0045571","count":1},{"id":"GO:0031047","count":1},{"id":"GO:0048026","count":1},{"id":"GO:0018298","count":1}]},{"hash":"224254009740766386","title":"Endomembrane trafficking and endosome organization","description":"The dominant GO terms point to endomembrane system processes\u2014endosomal transport and endosomal vesicle fusion, plus endomembrane system organization\u2014suggesting this cluster centers on vesicle trafficking and membrane dynamics. A couple of splicing-related terms appear but likely reflect annotation noise; the vesicular trafficking themes are stronger and more representative of the cluster's function.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0016197","count":1},{"id":"GO:0034058","count":1},{"id":"GO:0034141","count":1}]},{"hash":"788937859898586848","title":"Unknown","description":"The GO terms are scattered across diverse processes: mitotic cell cycle, DNA replication, cell morphogenesis, visual perception, nervous system development, skeletal and cardiac muscle development, B cell receptor signaling, and autophagy regulation. There isn't a single cohesive function or pathway that ties these terms together in this protein set. This heterogeneity suggests the cluster doesn't reflect a specific molecular role, hence the label Unknown.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0000902","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0007519","count":2},{"id":"GO:0050853","count":2}]},{"hash":"1109836895412600594","title":"Nuclear export and transcription regulation cluster","description":"Proteins in this cluster are enriched for intracellular transport (nuclear export, general protein transport) and transcriptional regulation (DNA-templated transcription, carbon catabolite repression of transcription), with related terms including localized protein transport to cellular structures and some signaling regulation. The common theme appears to be coordination between transport processes and gene expression control rather than a single pathway.","confidence":"Medium","size":25,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046580","count":3},{"id":"GO:0046827","count":3},{"id":"GO:0006886","count":2},{"id":"GO:0060038","count":2},{"id":"GO:0006351","count":2}]},{"hash":"2147158111383320348","title":"Developmental patterning and morphogenesis","description":"The top GO terms cluster around developmental processes such as head morphogenesis, dorsal/ventral axis specification, lateral inhibition, asymmetric cell division regulation, and spindle organization. These collectively point to roles in tissue patterning and organismal development, with a few terms reflecting broader differentiation or species-specific contexts. Overall, the proteins appear to be linked by a developmental/morphogenetic theme rather than a single, specific pathway.","confidence":"Medium","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035994","count":2},{"id":"GO:0009786","count":1},{"id":"GO:0048085","count":1},{"id":"GO:0010764","count":1},{"id":"GO:0007051","count":1}]},{"hash":"452136232090603101","title":"Spliceosome-Mediated mRNA Splicing Regulation","description":"This cluster is dominated by GO terms for regulation of alternative mRNA splicing via the spliceosome, with additional terms tied to positive/negative splicing regulation and mRNA processing, plus a translation initiation factor assembly term, indicating a cohesive focus on spliceosomal control of RNA processing and related translation initiation.","confidence":"High","size":25,"edges":36,"triangles":10,"max_degree":14,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000381","count":6},{"id":"GO:0031047","count":5},{"id":"GO:0048026","count":5},{"id":"GO:1902625","count":5},{"id":"GO:0075525","count":5}]},{"hash":"2057090698132324011","title":"ER Stress and Unfolded Protein Response","description":"The top terms are dominated by ER stress-related processes: response to unfolded protein, cellular response to ER stress, and regulation of translation initiation in response to ER stress, plus related protein quality control (ER-associated ubiquitin-dependent catabolism). While a few development terms appear, the strongest, cohesive signal is cellular stress response tied to the endoplasmic reticulum and protein homeostasis, suggesting this cluster centers on ER stress/UPR pathways with ancillary stress-response connections.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0090526","count":5},{"id":"GO:0070301","count":5},{"id":"GO:0036494","count":5},{"id":"GO:0006986","count":5},{"id":"GO:0003283","count":4}]},{"hash":"400707709762201278","title":"Unknown","description":"The terms span spermatid differentiation, cilium movement, nucleotide biosynthesis, chromatin/epigenetic processes, and heart development with no clear shared function. The cluster has no edges or cohesive pathway, so no coherent theme emerges beyond Unknown.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048515","count":1},{"id":"GO:0003351","count":1},{"id":"GO:0006228","count":1},{"id":"GO:0042464","count":1},{"id":"GO:0006241","count":1}]},{"hash":"1585042331774328107","title":"Chloroplast and Mitochondrial RNA Processing","description":"Top GO terms indicate organelle RNA metabolism\u2014cytidine-to-uridine editing, chloroplast RNA processing and modification, plastid transcription, and mitochondrial mRNA modification\u2014pointing to proteins involved in organellar RNA maturation and editing rather than cytosolic RNA pathways, with the seed dormancy term appearing incidental.","confidence":"High","size":25,"edges":252,"triangles":1402,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0016554","count":5},{"id":"GO:0080156","count":5},{"id":"GO:0042793","count":5},{"id":"GO:0031425","count":5},{"id":"GO:1900865","count":5}]},{"hash":"1730841018462705105","title":"Metabolic catabolism and cofactor biosynthesis","description":"The cluster is dominated by GO terms related to various catabolic and biosynthetic processes (L-kynurenine, L-alanine, glyoxylate, organic phosphonates, pyruvate) and cofactor/cluster assembly (pyridoxine biosynthesis; [2Fe-2S] cluster assembly; iron incorporation into metallo-sulfur clusters). Notch signaling appears as an outlier, but the overall pattern points to metabolic and cofactor biogenesis functions tying the proteins together.","confidence":"Medium","size":25,"edges":296,"triangles":2214,"max_degree":24,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007219","count":9},{"id":"GO:0097053","count":9},{"id":"GO:0042853","count":9},{"id":"GO:0017000","count":8},{"id":"GO:0042866","count":8}]},{"hash":"1025822661779396881","title":"Unknown","description":"The top GO terms are highly diverse, including stress and antibiotic responses, SOS response, cell division, protein catabolic regulation, and ubiquitin-dependent ERAD, plus some plant-specific processes and biosynthetic steps. There is no clear, cohesive function or pathway that ties most proteins together, and the cluster has no edges, suggesting a heterogeneous collection rather than a single biological theme. ","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0009432","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0042176","count":2},{"id":"GO:0030433","count":2}]},{"hash":"782184956388226956","title":"Presynaptic vesicle trafficking and brain development","description":"This cluster shows strong enrichment for regulation of synaptic vesicle exocytosis and endocytosis, pointing to presynaptic vesicle trafficking in neurons. Brain-related GO terms (brain development, substantia nigra development) support a neuronal theme, while other terms (mitotic exit, heart development) appear secondary. Overall, the core function is neuronal vesicle regulation.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000300","count":4},{"id":"GO:1900242","count":3},{"id":"GO:0031384","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0010458","count":3}]},{"hash":"1410909814442773640","title":"Retroviral Integration and Latency","description":"The GO terms strongly point to the retroviral life cycle: proviral DNA integration and establishment of proviral latency, viral entry/penetration into host nuclei, and RNA-templated DNA synthesis (reverse transcription). Additional terms about DNA recombination and host transcription regulation align with viral genome integration and manipulation of host transcription. This cohesive theme supports labeling the cluster as Retroviral Integration and Latency.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006278","count":2},{"id":"GO:0039651","count":2},{"id":"GO:0015074","count":2},{"id":"GO:0043137","count":2},{"id":"GO:0075713","count":2}]},{"hash":"2075089530983415470","title":"Vacuolar amino acid transport under nutrient stress","description":"The strongest signals are transport-related: multiple GO terms describe transmembrane import of specific amino acids (L-arginine, L-tyrosine, L-serine, L-glutamate) into the vacuole and regulation of amino acid transport (e.g., positive regulation of glutamine transport). Coupled with terms for cellular responses to nitrogen and potassium starvation, the cluster appears to center on vacuolar amino acid sequestration and nutrient-stress homeostasis. Some biosynthetic terms are present but are less diagnostic for this cluster\u2019s core function.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":2},{"id":"GO:0009102","count":2},{"id":"GO:1901482","count":1},{"id":"GO:0090518","count":1},{"id":"GO:0090516","count":1}]},{"hash":"325881196286127742","title":"Sensory Detection and Rapid Response","description":"This cluster centers on sensing environmental cues (vasoconstriction, hypoxia, CO2 detection, thermoception, nociceptive signaling via capsazepine) and triggering fast physiological or behavioral actions (vasoconstriction, startle, circadian-related modulation). The presence of plant-specific jasmonic acid regulation and other disparate terms suggests broader stress and signaling roles, but the dominant theme tying these proteins together is stimulus sensing leading to immediate responses. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042310","count":8},{"id":"GO:0001666","count":8},{"id":"GO:0003031","count":8},{"id":"GO:0001964","count":8},{"id":"GO:0050955","count":8}]},{"hash":"1557536699920757037","title":"Proteostasis and protein quality control","description":"The cluster\u2019s top GO terms cluster around heat response, misfolded protein handling, ubiquitin-proteasome degradation, ER-associated degradation, and nuclear quality control, pointing to a cohesive set of proteostasis regulators and proteolytic machinery. While some terms like DNA replication and mesoderm formation appear, they may reflect broader roles of proteostasis-related factors in cell cycle and development annotations. Overall, the common theme is proteostasis and quality-control of proteins.","confidence":"High","size":25,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006469","count":16},{"id":"GO:0009408","count":13},{"id":"GO:0006260","count":12},{"id":"GO:0097428","count":12},{"id":"GO:0032781","count":12}]},{"hash":"2182778216287837916","title":"Oxidative Stress and Xenobiotic Metabolism","description":"This cluster centers on redox-related processes (oxidation-reduction, cellular oxidant detoxification) and xenobiotic/chemical metabolism (carbazole and toluene catabolic processes) with responses to fatty acids and ER stress, suggesting a theme of detoxification and chemical stress response. Some terms like viral process and nonphotochemical quenching appear as outliers but may reflect broader stress-adaptation pathways; overall, the shared focus is on managing oxidative balance and processing xenobiotic compounds. ","confidence":"Medium","size":25,"edges":11,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:1902600","count":2},{"id":"GO:0046232","count":2},{"id":"GO:0070542","count":2},{"id":"GO:0098869","count":2}]},{"hash":"2262852267003972148","title":"Cellular stress response and apoptosis","description":"The cluster\u2019s top GO terms cluster around stress-related processes: apoptotic process, response to hypoxia, response to xenobiotic stimulus, and response to lipopolysaccharide, plus regulatory signaling through Rho and proliferation control. While there are a few peripheral terms (abscisic acid signaling, carnitine transport, excitatory postsynaptic potential) that might reflect broader metabolic or cross-kingdom annotations, the dominant signal is cellular stress response and programmed cell fate. This supports labeling the cluster as representing stress-related signaling and apoptosis pathways.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0001666","count":2},{"id":"GO:0009738","count":2}]},{"hash":"1805322543854502366","title":"Mitochondrial Transport and Metabolic Regulation","description":"The top GO terms cluster around transport across mitochondrial membranes (alpha-ketoglutarate, ornithine, ATP, pyrimidine import, magnesium export), the malate-aspartate shuttle, and mitochondrial dynamics (membrane fission), indicating a core role in mitochondrial metabolism and energy homeostasis. Additional terms tied to adaptive thermogenesis and regulation of necroptosis and insulin secretion further emphasize mitochondria-driven metabolic signaling and cell fate decisions. This coherent theme supports a label focused on mitochondrial transport and metabolic regulation.","confidence":"High","size":25,"edges":115,"triangles":287,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0015742","count":19},{"id":"GO:0000066","count":19},{"id":"GO:1990544","count":19},{"id":"GO:1990519","count":19},{"id":"GO:1990845","count":19}]},{"hash":"1687713209158578206","title":"Ubiquitin-Mediated Proteostasis","description":"The top GO terms are dominated by ubiquitin-related processes: autoubiquitination, K63-linked ubiquitination, and SUMOylation, as well as ubiquitin-dependent ERAD and general proteostasis. While a few plant-development terms (cytokinin signaling, root meristem growth) and aging-related terms appear, the strongest signal centers on ubiquitin- and SUMO-dependent regulation of protein stability and turnover, making proteostasis the best common thread for this cluster.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051918","count":2},{"id":"GO:0007596","count":2},{"id":"GO:0000722","count":1},{"id":"GO:0051865","count":1},{"id":"GO:0070534","count":1}]},{"hash":"1405868166449051503","title":"RNA decay and translation control","description":"This cluster centers on RNA metabolism and protein synthesis regulation, with multiple terms tied to mRNA decay pathways (no-go decay, nonsense-mediated decay), translation, ribosome disassembly, and transcription termination, suggesting a cohesive role in RNA surveillance and translation control. ","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070966","count":1},{"id":"GO:0090502","count":1},{"id":"GO:0019827","count":1},{"id":"GO:0006449","count":1},{"id":"GO:0032790","count":1}]},{"hash":"523974891078745496","title":"Unknown","description":"The terms are highly heterogeneous: smooth muscle contraction and axon regeneration imply animal signaling, while mitochondrial membrane potential regulation, mitochondrial translation, and ER-to-Golgi transport point to intracellular trafficking and organelle stress responses; plastid transcription and chloroplast RNA processing are plant-specific; the presence of an obsolete RNA phosphodiester hydrolysis term further indicates annotation noise. No unifying function emerges among the 25 proteins.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006939","count":2},{"id":"GO:0048680","count":2},{"id":"GO:0010917","count":1},{"id":"GO:0002037","count":1},{"id":"GO:0008631","count":1}]},{"hash":"326999376268585086","title":"Sugar and Ion Membrane Transport","description":"GO terms cluster around transmembrane transport of sugars, ions, vitamins, and related nutrients (glucose homeostasis, D-glucose transport, sodium ion transport, vitamin transport, plasma membrane selenite transport, nitrate assimilation). A related term on neurotransmitter loading into synaptic vesicles points to vesicular transport as well. Overall, the dominant theme is membrane transport of nutrients and ions, so 'Sugar and Ion Membrane Transport' is representative.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042593","count":2},{"id":"GO:0098700","count":1},{"id":"GO:0035461","count":1},{"id":"GO:0042128","count":1},{"id":"GO:0042891","count":1}]},{"hash":"1178367264801787118","title":"Mitosis and Cell Cycle Machinery","description":"The top terms are dominated by cell division, mitotic spindle orientation, sister chromatid cohesion, and mitotic DNA replication, indicating a primary focus on mitosis and cell cycle progression. There are a few ribosomal RNA maturation terms and protein oligomerization annotations present, but they do not redefine the cluster\u2019s main theme, which remains mitosis-related processes.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0000132","count":2},{"id":"GO:0007064","count":2},{"id":"GO:1903461","count":2},{"id":"GO:0000463","count":2}]},{"hash":"108519454443871006","title":"Unknown","description":"The top GO terms span a wide and unrelated set of functions (spermatogenesis, circadian sleep, renal development, immune signaling, metabolism, and even plant phototropism), with no clear shared biological theme or dominant process. The cluster lacks edges or cohesive functional linkage, so no specific common function can be confidently assigned.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007283","count":2},{"id":"GO:0018120","count":1},{"id":"GO:0071660","count":1},{"id":"GO:0019677","count":1},{"id":"GO:0032764","count":1}]},{"hash":"474569245904078386","title":"Mechanosensory and Thermosensory Signaling","description":"The top GO terms cluster around sensory responses: cellular response to mechanical stimulus, thermoception, and response to capsazepine, which points to TRP-channel\u2013related temperature and chemical sensing. While there are outliers (pinocytosis, NOD1 signaling, telomere maintenance, etc.), the strongest shared theme appears to be mechanosensory/thermosensory signaling with some unrelated annotations.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048549","count":3},{"id":"GO:0016477","count":3},{"id":"GO:2001275","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0071260","count":3}]},{"hash":"1550048318562796532","title":"Secreted peptide maturation and hormone processing","description":"The top GO terms cluster around processing and secretion of signaling molecules\u2014insulin processing, nerve growth factor production, renin secretion, and peptide pheromone maturation\u2014suggesting a theme of secreted peptide maturation and hormone signaling. Some terms about LDL receptor catabolic processes appear, but the dominant pattern supports the secretory peptide processing theme.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010124","count":2},{"id":"GO:0032902","count":1},{"id":"GO:0002001","count":1},{"id":"GO:0032804","count":1},{"id":"GO:0032802","count":1}]},{"hash":"1940432091467399756","title":"Sperm Axoneme Assembly and Ciliary Motility","description":"The GO terms center on cilium and flagellum biology (sperm axoneme assembly; cilium movement; epithelial cilium movement) and microtubule modifications (polyglutamylation, polyglycylation), plus regulation of Rho/GTPase signaling that modulates cytoskeletal dynamics. This combination strongly points to proteins functioning in sperm flagellum formation and ciliary motility rather than broader cytoskeletal roles, justifying a specific label.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":2},{"id":"GO:0043087","count":2},{"id":"GO:0018095","count":1},{"id":"GO:1905419","count":1},{"id":"GO:0018094","count":1}]},{"hash":"779563017119301134","title":"GPCR-driven cAMP/cGMP signaling and light sensing","description":"The top GO terms point strongly to G protein-coupled receptor signaling (adenosine, adrenergic, and guanylyl cyclase pathways) and biosynthesis of cAMP and cGMP, complemented by blue light signaling and hypoxia detection. This suggests a functional module centered on GPCR-mediated second-messenger signaling with links to light-responsive and hypoxia-related pathways, with transcription regulation as a downstream or ancillary feature.","confidence":"High","size":24,"edges":8,"triangles":2,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":5},{"id":"GO:0071880","count":4},{"id":"GO:0070483","count":4},{"id":"GO:0006182","count":4},{"id":"GO:0009785","count":4}]},{"hash":"133764870499495981","title":"Gonadal retinoid and steroid metabolism","description":"The top GO terms are dominated by retinol/retinal metabolic processes and regulation of retinoic acid receptor signaling, along with C21-steroid hormone biosynthesis and male gonad development, suggesting a cohesive theme of retinoid and steroid metabolism in gonadal development. Some sugar catabolic processes appear as ancillary metabolic activity but do not define the core function of the cluster.","confidence":"High","size":24,"edges":254,"triangles":1771,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":22},{"id":"GO:0042574","count":21},{"id":"GO:0055114","count":20},{"id":"GO:0046370","count":20},{"id":"GO:0048385","count":19}]},{"hash":"783246008893149667","title":"Translation initiation and ribosome biogenesis","description":"This cluster is dominated by GO terms on translation reinitiation, formation of translation preinitiation complex, and ribosome biogenesis, indicating a core role in protein synthesis. The presence of transcription, splicing, and ncRNA regulation terms suggests a broader link to gene expression machinery, but translation-related terms appear most representative.","confidence":"Medium","size":24,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002188","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006351","count":2}]},{"hash":"225413157227066880","title":"Metabolism and protein synthesis","description":"The cluster gathers terms tied to core metabolism (TCA cycle, glyoxylate cycle, propionate catabolic processes) and to translation-related processes (ribosome biogenesis, threonyl- and alanyl-tRNA aminoacylation), suggesting a broad grouping around metabolic activity and protein production rather than a single precise function. Some terms are less connected, but the dominant themes are metabolism and translation.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032147","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0006099","count":1},{"id":"GO:0010034","count":1},{"id":"GO:0075141","count":1}]},{"hash":"15085409666383426","title":"Ubiquitin-dependent protein degradation","description":"Top GO terms are dominated by ubiquitination (K48- and K63-linked), ubiquitin-dependent ERAD, and ubiquitin-mediated protein catabolic processes, indicating a cluster focused on tagging proteins for degradation and turnover. The presence of NF-kappaB/TNF signaling regulation terms suggests a role for ubiquitin signaling in controlling inflammatory pathways, and a peroxisomal matrix import term appears secondary. Overall, the theme is ubiquitin-mediated proteostasis.","confidence":"High","size":24,"edges":83,"triangles":123,"max_degree":19,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":14},{"id":"GO:0030433","count":14},{"id":"GO:0070936","count":12},{"id":"GO:0016558","count":11},{"id":"GO:0042787","count":9}]},{"hash":"994821354351923888","title":"RNA processing and transcriptional regulation under stress","description":"The cluster is enriched for RNA metabolism and transcriptional control (miRNA catabolic process; pre-miRNA processing; DNA-templated transcription; transcription termination/antitermination; CRD-mediated mRNA stabilization) and shows links to stress hormone signaling (glucocorticoid response) and osmotic stress-related pathways, plus kidney development signals\u2014together suggesting a coordinated role in RNA processing and transcription regulation during stress and development.","confidence":"Medium","size":24,"edges":22,"triangles":6,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0010587","count":4},{"id":"GO:0031054","count":3},{"id":"GO:0006351","count":3},{"id":"GO:1902219","count":3},{"id":"GO:0060567","count":3}]},{"hash":"934905837147781370","title":"Nuclear rRNA processing and RNA catabolism","description":"The dominant GO terms point to nuclear RNA processing and ribosomal RNA maturation/catabolism (e.g., maturation of SSU-rRNA, nuclear polyadenylation-dependent rRNA catabolic processes, CUT catabolic process, tethering of RNA Pol II genes at the nuclear periphery). A single glycogen metabolic term appears but does not define the cluster, suggesting the core theme is RNA metabolism in the nucleus rather than metabolism of glycogen. Overall, the cluster appears cohesive around RNA processing and turnover within the nucleus.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":1},{"id":"GO:0000469","count":1},{"id":"GO:0005977","count":1},{"id":"GO:0043666","count":1},{"id":"GO:0009966","count":1}]},{"hash":"313391886778876752","title":"Unknown","description":"The cluster has no GO terms or network connectivity reported (edges/triangles = 0), and most proteins are only noted as re-added by ReCIPE. Without shared functional annotations or interactions, there is no clear theme to assign a specific label.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"466795303585024956","title":"Unknown","description":"Top terms span metabolism, DNA replication, apoptosis, and multiple tissue development processes with no single cohesive theme; lack of edges suggests no unified function linking the proteins. Therefore, a specific label cannot be assigned.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0016311","count":4},{"id":"GO:0006094","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0030324","count":4},{"id":"GO:0006915","count":4}]},{"hash":"2132815830020616166","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016554","count":2},{"id":"GO:0080156","count":2},{"id":"GO:0042793","count":2},{"id":"GO:0031425","count":2},{"id":"GO:1900865","count":2}]},{"hash":"1107806460454467139","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":275,"triangles":2002,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0071318","count":1},{"id":"GO:0046196","count":1},{"id":"GO:0031247","count":1},{"id":"GO:0006470","count":1},{"id":"GO:0006114","count":1}]},{"hash":"1366540608979191466","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031426","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0016554","count":3},{"id":"GO:0080156","count":3},{"id":"GO:0042793","count":3}]},{"hash":"496632793992434168","title":"Vacuolar amino acid transport","description":"These proteins are annotated with multiple GO terms for importing various amino acids into the vacuole (proline, arginine, serine, tyrosine, histidine, glutamate/glutamine, lysine, etc.), indicating a shared function as vacuolar amino acid transporters, likely linked to nutrient/starvation responses. The collective pattern supports a cohesive label focusing on vacuolar amino acid uptake.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015824","count":3},{"id":"GO:1901482","count":2},{"id":"GO:0090518","count":2},{"id":"GO:0090516","count":2},{"id":"GO:2000487","count":2}]},{"hash":"1684198042589761309","title":"Unknown","description":"The top terms span diverse processes from cell cycle and telomere maintenance to pinocytosis, NOD1/2 signaling, thermoception, calcium signaling, foam cell regulation, and SA node action potential, with no single coherent function tying them together. Therefore no intuitive, specific label can capture the cluster\u2019s function.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":5},{"id":"GO:0032212","count":5},{"id":"GO:0048549","count":5},{"id":"GO:0070427","count":5},{"id":"GO:0050955","count":5}]},{"hash":"637878103179466723","title":"Plant hormone signaling and fruit ripening","description":"The GO terms cluster around plant hormones (gibberellin, auxin, salicylic acid) and processes tied to fruit development and regulation, plus transcriptional activity and stress-related responses (H2O2-mediated PCD). This pattern suggests a group of proteins involved in hormone-regulated ripening and defense rather than a single enzyme pathway.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0010023","count":1},{"id":"GO:0046244","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0042318","count":1}]},{"hash":"1409617740731199339","title":"Unknown","description":"The GO terms span oxidative stress responses (cellular response to hydrogen peroxide), DNA repair, and apoptosis, alongside a variety of transport and processing activities (GPI anchor biosynthesis, sodium and vitamin transport, neurotransmitter loading) and metabolism (nitrate assimilation, diadenosine tetraphosphate catabolic). There isn\u2019t a single unifying function linking these terms, indicating a heterogeneous cluster rather than a cohesive biological theme.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070301","count":2},{"id":"GO:0006506","count":2},{"id":"GO:0015967","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0006915","count":2}]},{"hash":"1043834982874729310","title":"Heat stress response and temperature sensing","description":"This cluster is dominated by GO terms related to heat and temperature perception (response to heat, thermoception, transcriptional responses to heat stress), suggesting a coherent theme around heat stress signaling and temperature sensing. Other terms (GPCR signaling, NOD1 signaling, telomere maintenance, pinocytosis, SA node regulation) appear more peripheral or reflect broader stress-response connections, but the core pattern points to heat-related cellular responses.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098907","count":6},{"id":"GO:0007205","count":6},{"id":"GO:0009408","count":5},{"id":"GO:0032212","count":4},{"id":"GO:0048549","count":4}]},{"hash":"1967765876377664758","title":"Neuromodulator signaling and locomotion","description":"Dominant terms relate to neurotransmitter metabolism (dopamine catabolic, octopamine biosynthesis) and behavioral outputs (locomotion, locomotory behavior, visual learning, pain, amphetamine response), suggesting a neuromodulatory signaling cluster governing movement and sensory processing; immune-related terms appear but are not central.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042420","count":1},{"id":"GO:0043059","count":1},{"id":"GO:0002443","count":1},{"id":"GO:0001816","count":1},{"id":"GO:0007626","count":1}]},{"hash":"1870802375933815225","title":"Muscle differentiation and cardiac hypertrophy regulation","description":"The dominant signals are negative regulation of skeletal muscle differentiation and positive regulation of cardiac muscle hypertrophy in response to stress, suggesting a muscle-development/remodeling theme. Microtubule nucleation implies cytoskeletal changes relevant to muscle cells, while ion transport and PI-mediated signaling may reflect concurrent stress responses.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001015","count":2},{"id":"GO:0043388","count":2},{"id":"GO:1903244","count":2},{"id":"GO:0007020","count":2},{"id":"GO:0071421","count":1}]},{"hash":"391703492791169912","title":"Neuronal development and synapse regulation","description":"The cluster\u2019s top GO terms cluster around neural-related processes, including regulation of neuron apoptotic processes, synapse organization, and Wnt signaling, with additional connections to cytokinesis, GTPase regulation, and cell cycle. This pattern suggests proteins involved in neural development and synaptic signaling, even though the terms are diverse and there are no observed edges linking members. ","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035307","count":1},{"id":"GO:0060393","count":1},{"id":"GO:0080182","count":1},{"id":"GO:0043525","count":1},{"id":"GO:0090263","count":1}]},{"hash":"186422366162543589","title":"P-body\u2013associated mRNA decay and silencing","description":"The cluster's top GO terms emphasize deadenylation-dependent decapping, mRNA decay, P-body assembly, and miRNA-mediated post-transcriptional silencing, pointing to proteins that regulate mRNA turnover and translation in P-bodies.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045944","count":1},{"id":"GO:0000290","count":1},{"id":"GO:0000288","count":1},{"id":"GO:0033962","count":1},{"id":"GO:0061014","count":1}]},{"hash":"2189872404867045651","title":"Retroviral replication and proviral latency","description":"Based on the dominant GO terms, the cluster centers on retroviral life cycle processes\u2014from reverse transcription (RNA-templated DNA synthesis) to DNA replication, integration, recombination, and establishing integrated proviral latency, as well as viral entry into the host nucleus. While some annotations reference symbiont interactions, the strongest signal is retrovirus-related steps, suggesting these proteins function in proviral integration and latency regulation.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0006278","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0039651","count":1},{"id":"GO:0015074","count":1}]},{"hash":"1070327698033682244","title":"Golgi\u2013ER\u2013endosome vesicle trafficking","description":"The cluster is dominated by GO terms for intracellular transport within the secretory pathway, including endosome-to-Golgi and Golgi-to-ER retrograde transport, ER-to-Golgi transport, endocytosis, and recycling, indicating a cohesive vesicle trafficking/function group; pigmentation and retina development terms likely reflect tissue-specific contexts but align with vesicle trafficking in pigmented or retinal cells.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006886","count":4},{"id":"GO:0042147","count":3},{"id":"GO:0006897","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0043473","count":2}]},{"hash":"822574952691603957","title":"RNA polymerase assembly and transcription regulation","description":"The top GO terms cluster around assembly of RNA polymerase I/II/III complexes and regulation of transcription elongation by RNA polymerase II, pointing to a unit of transcription machinery components; additional terms for protein folding and tubulin complex assembly appear peripheral but do not override the central RNA polymerase/transcription signal.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990113","count":1},{"id":"GO:0007021","count":1},{"id":"GO:0006457","count":1},{"id":"GO:0032968","count":1},{"id":"GO:0031137","count":1}]},{"hash":"61070247014376485","title":"Calcium signaling and NFAT transcription regulation","description":"The top GO terms repeatedly point to calcium-related signaling (detection of calcium ion, phosphatidylinositol-mediated signaling) and regulation of the calcineurin-NFAT pathway, which ties calcium signaling to transcriptional control. This suggests a coherent theme of calcium-dependent signaling influencing gene regulation, even though other terms show diverse developmental contexts or are more general (e.g., bioluminescence). The lack of strong connectivity (no edges) implies this cluster may be functionally loose, but the calcium/NFAT axis stands out as the most plausible unifying thread. Therefore, a label centered on calcium signaling and NFAT transcription aligns with the most representative functional signal in the set.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048235","count":1},{"id":"GO:0040015","count":1},{"id":"GO:0050873","count":1},{"id":"GO:0048015","count":1},{"id":"GO:0045944","count":1}]},{"hash":"1988262078403644982","title":"Retina neural development with immune signaling","description":"This cluster is characterized by strong signals for retina development and neural connectivity, including retina vasculature development, axonogenesis, and positive regulation of synapse assembly, suggesting a neural development focus in the eye. The presence of immune-related responses (lipopolysaccharide and GM-CSF stimulus) implies associated inflammatory signaling. While there are generic cell-cycle and transcription terms, the dominant theme appears to be retinal neural development with immune signaling.","confidence":"Medium","size":23,"edges":26,"triangles":12,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071222","count":14},{"id":"GO:0031100","count":13},{"id":"GO:0009636","count":13},{"id":"GO:0061298","count":12},{"id":"GO:0007409","count":12}]},{"hash":"178000862006469274","title":"Mitotic spindle assembly and microtubule dynamics","description":"The cluster is dominated by GO terms describing mitotic spindle assembly, spindle elongation, minus-end microtubule sliding, kinetochore attachments, and cytokinesis, all pointing to microtubule-driven chromosome segregation and cell division. Some terms touch plant chloroplast movement or specific developmental contexts, but the unifying theme is microtubule-based mitotic processes across species. ","confidence":"High","size":23,"edges":60,"triangles":40,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:1990942","count":16},{"id":"GO:0021693","count":16},{"id":"GO:0000022","count":16},{"id":"GO:0051296","count":16},{"id":"GO:0009904","count":16}]},{"hash":"1509349399510312648","title":"Unknown","description":"The Top Terms span diverse, seemingly unrelated processes (DNA repair/recombination, ribosome biogenesis and rRNA maturation, cell division, actin dynamics and neuron projection development, NAD biosynthesis, and protein translocation into host cytoplasm), with no single dominant theme tying them together. This lack of a cohesive functional motif makes it difficult to assign a precise, representative label.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0031175","count":2},{"id":"GO:0051016","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0000463","count":2}]},{"hash":"1406029703140286977","title":"RNA processing and ribosome biogenesis","description":"The terms point to multiple RNA-processing activities (ncRNA silencing, mRNA splicing via spliceosome, maturation of rRNA) and ribosome assembly (rRNA maturation, ribosomal large subunit biogenesis), with additional hints of transcription regulation by RNA polymerase II. This suggests a cluster centered on RNA metabolism and ribosome biogenesis, with some transcription-related activity.","confidence":"Medium","size":23,"edges":59,"triangles":78,"max_degree":13,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":10},{"id":"GO:0048026","count":10},{"id":"GO:0000466","count":9},{"id":"GO:0000462","count":8},{"id":"GO:0042273","count":8}]},{"hash":"1798403291260236086","title":"Core DNA replication and cell division","description":"This cluster is driven by GO terms related to DNA replication (DNA replication, DNA strand elongation) and cytokinesis, which point to core cell-cycle machinery. There are also a few unrelated or obsolete terms (translation, ubiquitination, immune-related processes), suggesting mixed signals and a less cohesive theme. Overall, the dominant signal seems to be the core processes of DNA replication and cell division, with weaker ties to other cellular housekeeping activities.","confidence":"Medium","size":23,"edges":22,"triangles":0,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0070940","count":1},{"id":"GO:0048304","count":1},{"id":"GO:1901972","count":1}]},{"hash":"499269509618404110","title":"Mitochondrial metabolism and Fe-S biogenesis","description":"The top GO terms cluster around mitochondrial-focused metabolic and biosynthetic processes: TCA cycle, amino acid catabolism (L-alanine), pyridoxine (vitamin B6) biosynthesis, organic phosphonate catabolism, and Fe-S cluster assembly/iron incorporation, plus mitochondrial tRNA thio-modification. These collectively point to mitochondrial energy metabolism and metal cofactor biogenesis. Notch signaling appears among the terms but does not define the overall theme.","confidence":"Medium","size":23,"edges":252,"triangles":1750,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0009436","count":8},{"id":"GO:0007219","count":7},{"id":"GO:0097053","count":7},{"id":"GO:0042853","count":7},{"id":"GO:0006099","count":6}]},{"hash":"293758321374535440","title":"Neuronal Ion Transport and GPCR Signaling","description":"This cluster centers on ion transport (potassium and sodium) and GPCR-mediated signaling with second-messenger responses (cAMP/cGMP), suggesting a neuronal signaling/ion homeostasis theme; protein tetramerization and chromatin localization terms may reflect broader regulatory roles, while a defense-response term likely reflects annotation noise.","confidence":"Medium","size":23,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":3},{"id":"GO:0071169","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0048681","count":2},{"id":"GO:0098719","count":2}]},{"hash":"1256738727308314584","title":"Retroviral integration and latency","description":"The top GO terms strongly point to retroviral processes: RNA-templated DNA biosynthesis (reverse transcription), DNA integration, and establishment of integrated proviral latency, along with DNA recombination. The additional terms about symbiont entry into host cells and host apoptosis modulation fit with viral infection and host manipulation, supporting a viral life cycle theme.","confidence":"High","size":23,"edges":9,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":2},{"id":"GO:2000617","count":2},{"id":"GO:0071442","count":2},{"id":"GO:0006278","count":1},{"id":"GO:0039651","count":1}]},{"hash":"1634446446432912639","title":"Regulation of gene expression and immune signaling","description":"The cluster centers on regulatory processes: regulation of transcription, dephosphorylation and protein kinase activity, and modulation of immune signaling pathways (inflammatory response and interferon production). While a couple of GO terms touch on development or neural functions, the strongest common theme across the terms is regulation of gene expression and signaling, making this a coherent label for a regulatory-function cluster.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0016311","count":1},{"id":"GO:0009056","count":1},{"id":"GO:0070100","count":1},{"id":"GO:0050729","count":1}]},{"hash":"869002851477448449","title":"Mitochondrial Fe-S cluster biogenesis and respiration","description":"Top terms point to mitochondrial Fe-S cluster assembly (2Fe-2S) and mitochondrial electron transport, suggesting a cluster centered on Fe-S biogenesis feeding the respiratory chain.","confidence":"High","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034396","count":1},{"id":"GO:0036086","count":1},{"id":"GO:0097428","count":1},{"id":"GO:0044571","count":1},{"id":"GO:1903026","count":1}]},{"hash":"282885948392347045","title":"T Cell Immunoregulation and Homeostasis","description":"Top GO terms center on T cell regulation (proliferation, homeostasis), IL-2 suppression, and germinal center regulation, with additional signals related to glucocorticoid response and growth-factor stimuli. Taken together, these imply immunomodulatory signaling that tunes T cell responses.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071385","count":2},{"id":"GO:0045085","count":2},{"id":"GO:0045647","count":2},{"id":"GO:0060710","count":2},{"id":"GO:0044344","count":2}]},{"hash":"1357045517470048478","title":"Unknown","description":"The top GO terms describe very different processes (negative regulation of MHC II biosynthesis, host-mediated activation of viral genome replication, and nuclear poly(A) tail shortening) with no connectivity among them. This dispersion provides no cohesive functional theme to label the cluster, so a specific, representative name cannot be justified.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045347","count":1},{"id":"GO:0044829","count":1},{"id":"GO:0000289","count":1}]},{"hash":"1485473153508297798","title":"Transcriptional Regulation and Epigenetic Modification","description":"The top GO terms cluster around regulation of DNA-templated transcription and epigenetic marks (DNA methylation, histone H3K9 methylation), pointing to control of gene expression via chromatin state. Additional terms reflect stress/immune responses and metabolism, suggesting these proteins operate in transcriptional regulation with epigenetic and metabolic context. Confidence is moderate due to mixed signals and some deprecated terms, but the core theme of transcriptional regulation via epigenetic mechanisms is clear.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":4},{"id":"GO:0046886","count":3},{"id":"GO:0051573","count":3},{"id":"GO:0043046","count":3},{"id":"GO:0032496","count":3}]},{"hash":"1278222128170453861","title":"Transcription Elongation & RNA Processing Machinery","description":"The cluster is enriched for GO terms tied to transcription elongation (by RNA Pol I/II), DNA-templated transcription, transcription regulation, and RNA processing (rRNA processing, mRNA localization). While a translation elongation term appears, the dominant signal points to transcriptional control and RNA processing as the shared function of the proteins.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060291","count":2},{"id":"GO:0098735","count":2},{"id":"GO:0006414","count":2},{"id":"GO:0006351","count":2},{"id":"GO:2001208","count":2}]},{"hash":"231998078279221815","title":"DNA/RNA repair and programmed cell death signaling","description":"This cluster shows enrichment for DNA repair and DNA alkylation repair, RNA processing and tRNA modification affecting translation, and signals related to programmed cell death and mitochondrial membrane permeability in cell death paths, plus Rho signaling. The common theme appears to be a stress-response module that links nucleic acid maintenance with cell fate decisions under stress, rather than a single pathway. Confidence: Medium","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":2},{"id":"GO:0042245","count":1},{"id":"GO:0002098","count":1},{"id":"GO:1990983","count":1},{"id":"GO:0035552","count":1}]},{"hash":"1111021630542297419","title":"Kinase signaling and cell cycle regulation","description":"The top GO terms point to phosphorylation- and signaling-driven control of the cell cycle (positive regulation of protein autophosphorylation and serine/threonine kinase activity, mitotic cell cycle) along with GTPase activity regulation and protein oligomerization. Additional terms reflect stress and developmental roles (hypoxia response, skeletal muscle fiber and multicellular development) and processes like mRNA transport and vacuole fusion, suggesting a core of signaling kinases coordinating growth, division, and development with auxiliary RNA and organelle dynamics. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0051260","count":6},{"id":"GO:0071456","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0031954","count":5}]},{"hash":"1877727473902476341","title":"Trehalose biosynthesis and heat-stress response","description":"The Top Terms show a strong emphasis on trehalose biosynthetic/metabolic processes and cellular response to heat, suggesting a theme of carbohydrate metabolism linked to heat/shock stress. Galactose metabolism also supports general carbohydrate processing, while a few obsolete terms and outliers indicate annotation noise. Overall, the cluster appears aligned with stress-associated carbohydrate metabolism, especially trehalose production.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0006012","count":4},{"id":"GO:0034605","count":4},{"id":"GO:0043154","count":3},{"id":"GO:0045429","count":3}]},{"hash":"1133310969816648733","title":"Unknown","description":"There are 23 proteins, but no GO terms are listed (Top Terms empty) and the network is disconnected (Edges 0, Triangles 0, Max Degree 0). Without functional terms to guide labeling, no common biological theme is evident. The note about ReCIPE re-adding proteins does not establish a shared function.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"513727640079902107","title":"Unknown","description":"The top terms span many unrelated biological processes (cell cycle, telomere maintenance, pinocytosis, NOD signaling, thermoception, calcium signaling, foam cell regulation, and cardiac electrophysiology), with no clear single theme tying the proteins together. This makes it inappropriate to assign a specific functional label, so the cluster is best described as Unknown. ","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":8},{"id":"GO:0032212","count":8},{"id":"GO:0048549","count":8},{"id":"GO:0070427","count":8},{"id":"GO:0050955","count":8}]},{"hash":"362075435958119244","title":"Nucleolar transcription and ribosome biogenesis","description":"Most GO terms cluster around transcription activity in the nucleolus and ribosome assembly (RNA Pol I/II/III\u2013driven transcription, nucleologenesis, ribosome biogenesis, RNA-templated transcription, and ncRNA-mediated heterochromatin formation). A spindle organization term is present but peripheral, suggesting the core theme is nucleolar transcription machinery and ribosome biogenesis.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042797","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0017126","count":1},{"id":"GO:0001172","count":1},{"id":"GO:0042790","count":1}]},{"hash":"1434023331991805576","title":"Auxin transport and signaling in roots","description":"The cluster is dominated by GO terms tied to auxin biology\u2014polar transport, auxin-activated signaling, and auxin export\u2014tied to adventitious root development. Additional terms on endosomal and vesicle trafficking align with transporter cycling (e.g., PINs) that moves auxin directionally, reinforcing a coherent theme of auxin transport and root development.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010197","count":1},{"id":"GO:0009734","count":1},{"id":"GO:0010252","count":1},{"id":"GO:0048830","count":1},{"id":"GO:0009926","count":1}]},{"hash":"1153928559044485622","title":"Unknown","description":"The terms span circadian rhythm, kidney tubule morphogenesis and function, skeletal muscle differentiation, germinal center formation, viral latency release, and even plant hormone signaling, with no single cohesive process linking them. Since there is no clear shared function and the proteins show no interactions, a specific label cannot be justified.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042752","count":2},{"id":"GO:0070294","count":2},{"id":"GO:0072156","count":2},{"id":"GO:0031397","count":2},{"id":"GO:0048741","count":2}]},{"hash":"1252588582328076311","title":"Transcription Regulation and ER-Golgi Trafficking","description":"This cluster centers on transcription-related processes (DNA-templated transcription and negative regulation of RNA polymerase II) and components of intracellular trafficking (ER to Golgi vesicle transport and regulation of protein export from the nucleus). The combination suggests proteins that coordinate transcription control with nuclear-cytoplasmic transport and secretory pathway logistics, with some redox-related regulation (deglutathionylation). Overall, a coherent, specific label is warranted.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0016242","count":2},{"id":"GO:0000122","count":2},{"id":"GO:1903206","count":2}]},{"hash":"2191584756324767416","title":"Diverse Metabolic Pathways","description":"These proteins touch on several biosynthetic and metabolic processes (polyamine, lipoprotein, oxaloacetate, NAD+), plus some post-translational modifications and stress-related terms. There isn't a single dominant function tying all terms together, so the label reflects a broad metabolic theme rather than a specific pathway.","confidence":"Low","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006596","count":2},{"id":"GO:0042158","count":2},{"id":"GO:0006107","count":2},{"id":"GO:0009435","count":2},{"id":"GO:0046686","count":2}]},{"hash":"1459149787585297297","title":"NF-\u03baB regulation and inflammatory cytokine production","description":"This cluster centers on regulation of NF-\u03baB signaling (both activation and inhibition) and cytokine production (IL-6, IL-1\u03b2), with supporting roles for ubiquitin-proteasome pathways and innate immune sensing (NOD2). The presence of SCF-dependent ubiquitination and proteasomal degradation links NF-\u03baB control to protein turnover, while RIP-like signaling and cytokine upregulation reflect inflammatory output; endothelial tube extension and apoptotic terms appear secondary to these core processes.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":3},{"id":"GO:0032755","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0043124","count":2},{"id":"GO:0050718","count":2}]},{"hash":"584706017065932699","title":"Mitochondrial metabolite transport and energy metabolism","description":"The cluster shows multiple transmembrane transport terms for mitochondrial substrates (phosphate, alpha-ketoglutarate, ornithine, ATP, pyrimidines) and components of the malate-aspartate shuttle, plus notes on mitochondrial membrane fission and adaptive thermogenesis, pointing to a cohesive function in mitochondrial transport and energy regulation. While some terms touch on insulin secretion and necroptosis regulation, the dominant signal is mitochondrial metabolite transport and energy metabolism.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":3},{"id":"GO:0015742","count":2},{"id":"GO:0000066","count":2},{"id":"GO:1990544","count":2},{"id":"GO:1990519","count":2}]},{"hash":"1285418413679684905","title":"Bone and Cranial Skeletal Development","description":"This cluster strongly maps to bone formation and cranial skeletal system development (bone development, osteoblast fate commitment, cranial skeletal system development). Other terms indicate related processes such as podosome assembly and adipose regulation, plus circadian rhythm and synaptic plasticity, but the dominant signal is skeletal development.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060378","count":2},{"id":"GO:0002051","count":2},{"id":"GO:1904179","count":2},{"id":"GO:0060348","count":2},{"id":"GO:1904888","count":2}]},{"hash":"1769533104450754777","title":"Calcium-regulated cytoskeleton remodeling","description":"The cluster\u2019s GO terms repeatedly point to calcium signaling (calcium-release channel regulation, release of sequestered calcium into cytosol) and cytoskeletal dynamics (regulation of cell shape, actin crosslinking, cytoskeleton-dependent transport), with additional mentions of development and secretion (retina layer formation, nephron/tubule development, insulin secretion, and synaptic potentiation). This suggests a theme where calcium signaling governs cytoskeletal remodeling and associated secretory/developmental processes across diverse tissues. Therefore, a concise label emphasizing calcium-driven cytoskeletal regulation fits the shared function.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008360","count":5},{"id":"GO:0060315","count":4},{"id":"GO:0072221","count":4},{"id":"GO:0035774","count":4},{"id":"GO:1900271","count":4}]},{"hash":"111142030803566944","title":"Ubiquitin-Mediated Protein Regulation","description":"The cluster\u2019s top GO terms point to ubiquitin-dependent processes (K63-linked ubiquitination, autoubiquitination) and protein degradation pathways (ERAD). While there are also terms for nuclear processes like mRNA processing and DNA repair, the common thread appears to be regulation of protein turnover through ubiquitination and related degradation pathways. Some additional terms related to apoptosis and stress responses may reflect broader cellular regulation but are less central to the cluster\u2019s core theme.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0030579","count":1},{"id":"GO:0008626","count":1},{"id":"GO:0030433","count":1}]},{"hash":"491400029518849955","title":"Developmental axis specification and proteolysis","description":"The top GO terms point to axis determination (dorsal/ventral identity), development/germ cell death, and general proteolysis/protein catabolic processes, with additional notes on centrosome localization and signaling regulation. This suggests a cluster involved in developmental patterning alongside regulated protein turnover, rather than a single narrow enzymatic function. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904924","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0035234","count":2},{"id":"GO:0030163","count":2},{"id":"GO:2000016","count":1}]},{"hash":"248983138570655348","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042797","count":1},{"id":"GO:0090239","count":1},{"id":"GO:0045899","count":1},{"id":"GO:0031440","count":1},{"id":"GO:0010793","count":1}]},{"hash":"1670050476071886690","title":"Cardiovascular development and endothelial differentiation","description":"Based on the top GO terms, the cluster is enriched for heart and vascular development, notably venous endothelial cell differentiation and right atrium morphogenesis, with supporting signals from actin cytoskeleton organization and calcium ion handling that facilitate morphogenesis and endothelial function. A few telomere-associated terms appear as potential noise, but the dominant signal points to cardiovascular development and endothelial differentiation.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046475","count":2},{"id":"GO:0098703","count":2},{"id":"GO:0060843","count":2},{"id":"GO:0003213","count":2},{"id":"GO:0070213","count":2}]},{"hash":"2198047076588787731","title":"Spliceosome Assembly Factors","description":"Based on the top GO terms, the strongest signals are about spliceosome formation and snRNP assembly (GO:0000349 and GO:0000387), indicating a core function in pre-mRNA splicing. Other terms touch mitochondria or cell cycle regulation, but they are less central to the cluster's main theme, so the label emphasizes RNA processing.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000349","count":1},{"id":"GO:0000387","count":1},{"id":"GO:2000134","count":1},{"id":"GO:0070940","count":1},{"id":"GO:0046902","count":1}]},{"hash":"1965535455487817278","title":"Unknown","description":"The top GO terms are scattered across telomere maintenance, cell migration, adipocyte differentiation, mRNA processing, mechanosensation, endocytosis, and immune signaling, with no single unifying function linking them. This diversity suggests no clear common theme for the cluster.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":4},{"id":"GO:0032212","count":3},{"id":"GO:2001275","count":3},{"id":"GO:1904355","count":3},{"id":"GO:0045444","count":3}]},{"hash":"216568273316167433","title":"Embryonic development and morphogenesis","description":"The terms with higher counts point to developmental and morphogenetic processes (trophoblast differentiation, EMT related to heart development, endocrine system development, and cartilage morphogenesis), suggesting the cluster is broadly linked to embryonic tissue formation and organ morphogenesis. A few redox-related terms are present but seem less representative of the main theme.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902083","count":2},{"id":"GO:0071447","count":2},{"id":"GO:1903204","count":2},{"id":"GO:0060707","count":1},{"id":"GO:0003198","count":1}]},{"hash":"2250189502087553483","title":"DNA replication and mitotic cell cycle","description":"This cluster is dominated by GO terms tied to DNA replication, DNA-templated transcription, G1/S transition, and meiotic cell cycle, plus kinase/kinetochore localization, which together point to a cohesive cell-cycle and chromosome-segregation theme. Some terms (Schwann cell development, response to cocaine) appear peripheral or reflective of broader annotation, but do not disrupt the core cell-cycle signal.","confidence":"High","size":22,"edges":163,"triangles":709,"max_degree":19,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0007100","count":8},{"id":"GO:0006351","count":7},{"id":"GO:0000742","count":7},{"id":"GO:0000082","count":6}]},{"hash":"31327380629993310","title":"Cell Cycle Regulation and Differentiation Signaling","description":"This cluster centers on proteins involved in intracellular signal transduction and regulatory processes linking cell cycle control (including negative regulation of CDK activity and cell cycle) with differentiation (notably fat cell differentiation) and telomere maintenance/capping, plus mechanical signaling and transcription-related processes (mRNA processing). The spread of terms suggests a broad theme of signaling that coordinates proliferation, differentiation, and genome stability rather than a single, tight pathway. The lack of direct interaction edges reinforces a functional, rather than physical, linkage. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035556","count":8},{"id":"GO:0016477","count":8},{"id":"GO:0035994","count":8},{"id":"GO:0045736","count":8},{"id":"GO:0006397","count":8}]},{"hash":"2197955325325977431","title":"Developmental transcription and DNA damage response","description":"This cluster shows strong emphasis on DNA-templated transcription, cell cycle progression, and organismal development, with supporting links to DNA repair and stress responses (senescence, metal and HGF-related signaling), suggesting genes coordinating developmental transcriptional programs with genome maintenance and environmental stress response.","confidence":"High","size":22,"edges":53,"triangles":139,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":11},{"id":"GO:0000278","count":9},{"id":"GO:0007275","count":8},{"id":"GO:0006281","count":8},{"id":"GO:0043552","count":8}]},{"hash":"769839271581659087","title":"DNA replication and damage response with transcription regulation","description":"This cluster is dominated by core genome maintenance processes: DNA replication, recombination, and topological changes, alongside SOS response signaling and mRNA quality control (NMD). The presence of protein targeting/import and GO term for transcriptional regulation by RNA Pol II suggests integration with nuclear protein trafficking and gene expression control. Together, these terms point to a cohesive module centered on DNA replication/repair and its coordination with transcription.","confidence":"Medium","size":22,"edges":85,"triangles":133,"max_degree":17,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0000184","count":7},{"id":"GO:0006310","count":7},{"id":"GO:0006260","count":6},{"id":"GO:0006265","count":6},{"id":"GO:0006268","count":6}]},{"hash":"1201175769656585162","title":"Actin dynamics and cell migration signaling","description":"The cluster is dominated by terms related to cell migration and actin cytoskeleton remodeling (cell migration; actin filament bundle assembly; response to muscle stretch), with supporting signaling from the p38MAPK cascade and mechanotransduction cues. While a few terms touch on telomere maintenance and fat cell differentiation, the core theme aligns with cytoskeletal dynamics driving cell movement. ","confidence":"Medium","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0016477","count":4},{"id":"GO:0035994","count":4},{"id":"GO:0032212","count":4},{"id":"GO:2001275","count":4},{"id":"GO:1904355","count":4}]},{"hash":"2005905576339922673","title":"Chromatin Regulation and Transcription","description":"The cluster centers on DNA-templated transcription, rDNA heterochromatin formation, and methylation, pointing to a core role in chromatin dynamics and gene expression. Supporting signals from cell division and stress-response terms (response to xenobiotic stimulus, response to lipopolysaccharide) suggest transcriptional regulation during the cell cycle and under stress. Some terms (cobalamin and lignin biosynthetic processes) appear outliers or annotations noise but do not override the main theme of chromatin-mediated transcription control.","confidence":"Medium","size":22,"edges":170,"triangles":825,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009236","count":5},{"id":"GO:0009809","count":5},{"id":"GO:0032496","count":4},{"id":"GO:0019518","count":4},{"id":"GO:0000183","count":4}]},{"hash":"1558620415698838573","title":"Retroviral integration and latency","description":"The top GO terms collectively point to steps in the retroviral life cycle: integration of viral DNA into the host genome (DNA integration, proviral latency), reverse transcription (RNA-templated DNA biosynthetic process), and entry into the host nucleus (symbiont entry into host cell, viral penetration into host nucleus). Supporting processes like DNA replication and recombination align with genome maintenance, while host-pathogen interactions (symbiont-mediated activation of host apoptosis, negative regulation of siRNA processing) reflect viral manipulation of host defenses. An outlier term (proline transport) is less connected to the core theme but does not undermine the overall retroviral-focused signal. Confidence reflects the strong coherence around retroviral lifecycle processes.","confidence":"High","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0015074","count":4},{"id":"GO:0075713","count":4},{"id":"GO:0046718","count":4},{"id":"GO:0006278","count":3},{"id":"GO:0006260","count":3}]},{"hash":"822956101842925200","title":"RNA Processing and Export","description":"The top GO terms center on mRNA maturation steps\u2014splicing via spliceosome, polyadenylation, and export of mRNA from the nucleus\u2014strongly suggesting a coordinated RNA-processing module. A few terms reflect stress and signaling responses, but the repeated emphasis on RNA processing indicates the cluster\u2019s core function.","confidence":"High","size":22,"edges":92,"triangles":221,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0006406","count":2},{"id":"GO:0040038","count":2},{"id":"GO:0010507","count":2}]},{"hash":"23754001962521464","title":"Unknown","description":"The terms are dispersed across mitochondrial assembly, protein targeting, DNA replication, ER stress regulation, and other unrelated processes, with several obsolete terms; there is no single cohesive function tying all proteins together, so a specific label isn\u2019t justifiable.","confidence":"","size":22,"edges":49,"triangles":29,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":2},{"id":"GO:0090084","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0006616","count":1},{"id":"GO:1900035","count":1}]},{"hash":"1191086055985028400","title":"Unknown","description":"The GO terms are scattered across very disparate functions (mammary gland epithelial cell proliferation, intracellular protein transport, transcription regulation in several contexts, autophagy regulation, glycogen metabolism, cell-cycle regulation, and even plant-specific stomatal opening), with no clear unifying theme and no network connections. This heterogeneity makes it unlikely to assign a meaningful, cohesive label beyond Unknown.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033601","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0006351","count":1},{"id":"GO:0016242","count":1},{"id":"GO:0000411","count":1}]},{"hash":"422757022110712789","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:0000447","count":1},{"id":"GO:0000472","count":1},{"id":"GO:0048254","count":1},{"id":"GO:0071166","count":1}]},{"hash":"264696381097494681","title":"Neuroimmune signaling and pain modulation","description":"This cluster blends innate immune functions (innate immune response, defense against Gram-positive bacteria, LPS signaling, dsRNA response) with neural development and pain-related processes (dopamine response, axonogenesis, synapse assembly, pain behavior). The data suggest proteins involved in neuroimmune communication that modulate synaptic signaling and pain, rather than a single, isolated pathway. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903351","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0051965","count":2},{"id":"GO:0043330","count":2}]},{"hash":"29254016297006353","title":"DNA recombination and meiotic genome maintenance","description":"The cluster is dominated by terms tied to DNA recombination and telomere maintenance (t-circle formation, telomere maintenance via recombination, DNA strand invasion) and meiotic processes (spermatid development, sister chromatid cohesion in female meiosis). While a few terms like mRNA processing and xenobiotic response appear, the core theme centers on genome stability during recombination and meiosis.","confidence":"High","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":2},{"id":"GO:0090656","count":1},{"id":"GO:0051106","count":1},{"id":"GO:0072757","count":1},{"id":"GO:0000722","count":1}]},{"hash":"1684592233922193360","title":"GTPase-regulated vesicle transport proteins","description":"Proteins in this cluster are enriched for GO terms related to GTPase activity regulation and vesicle loading/transport, including neurotransmitter loading into synaptic vesicles and various forms of transmembrane transport. The inclusion of positive regulation of GTPase activity points to Rab/Rho-family\u2013driven trafficking, while negative regulation of stress fiber assembly hints at cytoskeletal dynamics linked to vesicle movement. Taken together, the terms outline a theme of membrane transport and vesicle trafficking governed by GTPase signaling, making this a coherent label for the cluster.","confidence":"Medium","size":22,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0051497","count":2},{"id":"GO:0098700","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0042128","count":2}]},{"hash":"2119911981959279121","title":"Retroviral Integration and Latency","description":"The top terms center on the retroviral life cycle: reverse transcription (RNA-templated DNA synthesis), DNA integration, and establishment of integrated proviral latency, plus entries related to viral penetration into the host nucleus and host DNA recombination. This pattern strongly indicates processes tied to retroviral infection and provirus maintenance, with a few general host interaction terms that do not override the core theme.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0090502","count":4},{"id":"GO:0042493","count":4},{"id":"GO:0039651","count":4},{"id":"GO:0075732","count":4},{"id":"GO:0046718","count":4}]},{"hash":"1525191843660105565","title":"Xenobiotic catabolism and toxic response","description":"The cluster shows multiple catabolic/metabolic GO terms related to xenobiotic compounds (1,2-dichloroethane, stilbene, prostaglandin catabolic processes) and a general response to toxic substances, along with related biosynthetic/metabolic processes (alkaloid, poly-hydroxybutyrate biosynthesis). The shared theme appears to be handling and breaking down external or toxic compounds, rather than a single, narrow pathway, suggesting a xenobiotic/degradation-focused cluster.","confidence":"Medium","size":22,"edges":42,"triangles":8,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0019260","count":1},{"id":"GO:0017000","count":1},{"id":"GO:0097755","count":1}]},{"hash":"1247374899432553304","title":"Ribosome biogenesis and transcription-related processes","description":"The cluster is enriched for rRNA maturation (5.8S, LSU/SSU) and DNA-templated transcription, suggesting roles in ribosome assembly and gene expression. Some GO terms about histone methylation and ubiquitin-dependent ERAD are obsolete or peripheral, but the dominant themes point to RNA processing and transcription.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0051568","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0034729","count":2}]},{"hash":"604223147995508825","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0006891","count":1},{"id":"GO:0015031","count":1},{"id":"GO:0007030","count":1},{"id":"GO:0033227","count":1}]},{"hash":"492620022580357238","title":"Developmental Patterning and Stress Responses","description":"The cluster shows a mix of developmental terms (spinal cord patterning, coronary vasculature development, molting/cuticle-related development) alongside transcription factor regulation, proteolysis, and stress/response terms (response to cold, response to pain) and cholesterol metabolism. With no interactions among proteins (edges/triangles zero) and several obsolete GO terms, there isn\u2019t a single dominant function driving the group. The overall impression is a heterogeneous set centered on developmental signaling interwoven with physiological stress responses, rather than a tightly defined pathway.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042994","count":5},{"id":"GO:0018996","count":5},{"id":"GO:0006508","count":5},{"id":"GO:0030299","count":4},{"id":"GO:0042632","count":4}]},{"hash":"504361583008143558","title":"Growth signaling and development with protein turnover","description":"The proteins show enrichment for growth and development processes (cell division, brain and multicellular development) alongside pathways tied to gene expression and proteome balance (mRNA transport, ribosome biogenesis, TORC1 signaling, SREBP pathway, proteasomal degradation, and GTPase regulation). This suggests a cohesive theme of coordinating growth, development, and protein turnover.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0032933","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0031146","count":3}]},{"hash":"233734721927026377","title":"Plasma Membrane Amino Acid Import","description":"Most of the top GO terms refer to import of specific amino acids (L-arginine, L-ornithine, methionine) across the plasma membrane and general transmembrane transport, pointing to a cluster of amino acid transporters. The other terms (dendritic spine development, nitric oxide production) might reflect broader roles but do not outweigh the amino acid import signal. Therefore, \"Plasma Membrane Amino Acid Import\" captures the cluster's likely function.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097638","count":2},{"id":"GO:0035826","count":2},{"id":"GO:0031283","count":2},{"id":"GO:0098713","count":2},{"id":"GO:0055085","count":2}]},{"hash":"333198506133211565","title":"Ubiquitin-Proteasome Regulation","description":"The most represented GO terms are negative regulation of protein ubiquitination and negative regulation of proteasomal ubiquitin-dependent protein catabolic process, which points to control of protein turnover via the ubiquitin-proteasome system. Other terms (lipidation, stress fiber assembly, EGFR signaling) are secondary and do not redefine the main theme. Therefore, this cluster is best described as proteostasis regulation via the ubiquitin-proteasome pathway.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031397","count":2},{"id":"GO:1903061","count":1},{"id":"GO:0051496","count":1},{"id":"GO:0061084","count":1},{"id":"GO:0032435","count":1}]},{"hash":"1956338392838701239","title":"Gene expression regulation and signaling","description":"Top GO terms include RNA splicing, mRNA transport, translation initiation, transcriptional regulation, ubiquitination, and signaling pathways like TORC1 and GTPase signaling. The cluster appears to gather proteins involved in regulating gene expression at multiple levels (RNA processing, translation, transcription) and in signal transduction, rather than a single cohesive process. This justifies a label focused on gene expression regulation intertwined with signaling networks.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0035556","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0048265","count":2}]},{"hash":"900967757518136881","title":"Unknown","description":"The GO terms are highly diverse (transcription/chromatin-related, muscle contraction, calcium signaling, GABA secretion, bone/mineralization) and include obsolescent entries, with no coherent shared pathway or function; there are no edges connecting proteins, so a single representative label cannot be inferred.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070940","count":1},{"id":"GO:0009301","count":1},{"id":"GO:0034396","count":1},{"id":"GO:0030574","count":1},{"id":"GO:0034724","count":1}]},{"hash":"1651552330978870387","title":"Retroviral DNA Integration and Latency","description":"The GO terms center on steps of the retroviral life cycle: DNA replication, recombination, RNA-templated DNA biosynthesis, DNA integration, and establishment of integrated proviral latency, along with viral entry/penetration into the host nucleus. The presence of host interaction and apoptosis terms (e.g., symbiont-related effects) supports a theme of viral genome integration and latent maintenance within host cells.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0006310","count":6},{"id":"GO:0006278","count":4},{"id":"GO:0039651","count":4},{"id":"GO:0015074","count":4}]},{"hash":"1281446610851116892","title":"Thermoception and Mechanical Pain Sensing","description":"The top GO terms point to temperature and mechanical pain detection (thermoception, response to cold, detection of mechanical stimulus in pain), plus angles on capsazepine response, indicating nociceptive/thermosensory signaling as the central theme. Other terms touch on signaling regulation and stress responses, but the dominant pattern is cold/heat-related pain sensing.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0071901","count":5},{"id":"GO:0009409","count":4},{"id":"GO:0050966","count":4},{"id":"GO:0032212","count":3},{"id":"GO:0048549","count":3}]},{"hash":"1615259514860075449","title":"ER protein processing and COPII trafficking","description":"Top GO terms point to endoplasmic reticulum\u2013related functions (localization to ER, ER unfolded protein response, calcium homeostasis) and vesicle trafficking (COPII-coated vesicle budding), with actin dynamics supporting vesicle transport. Together these suggest a cluster of proteins involved in ER maturation and ER-to-Golgi trafficking, rather than a single signaling pathway. Some virus-related terms appear but seem secondary to the ER/trafficking theme.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070972","count":1},{"id":"GO:0044791","count":1},{"id":"GO:0060304","count":1},{"id":"GO:0044828","count":1},{"id":"GO:0006874","count":1}]},{"hash":"737867678962569585","title":"Ubiquitin-Proteasome Regulation in Development","description":"This cluster is enriched for ubiquitin-related protein catabolic processes (SCF-dependent ubiquitin-protein degradation, ubiquitin-dependent protein catabolic process, protein polyubiquitination) indicating a central role of the ubiquitin-proteasome system, with concurrent development terms (skin development, regulation of epidermal cell division, spinal cord development) that suggest these degradation pathways influence development in skin and neural tissues.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043588","count":3},{"id":"GO:0031146","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0000209","count":2},{"id":"GO:0010482","count":2}]},{"hash":"708269510831592056","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006278","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0039651","count":1},{"id":"GO:0015074","count":1},{"id":"GO:0075713","count":1}]},{"hash":"341216911727537739","title":"TLR4-LPS Innate Immune Signaling","description":"The top GO terms cluster around Toll-like receptor 4 signaling, detection and response to lipopolysaccharide (LPS), and innate immune/inflammatory responses, which together point to a coordinated LPS/TLR4-driven innate immune pathway. A couple of other terms (centriole-related and axonogenesis) appear only once and are likely noise, so the dominant function remains innate immune signaling via TLR4/LPS. Thus the cluster is best described as a TLR4-LPS innate immune signaling module.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034142","count":2},{"id":"GO:0006954","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0032497","count":2},{"id":"GO:0071222","count":2}]},{"hash":"1133967605530125305","title":"Translation initiation and preinitiation complex assembly","description":"Most of the top GO terms cluster around the initiation of protein synthesis, including formation of the translation preinitiation complex, regulation of translational initiation, and assembly of the eIF4F complex. A few terms touch RNA processing and ncRNA-mediated silencing, but the dominant signal ties to initiation control of translation, which justifies a translation-initiation-centric label.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0075525","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0006446","count":3},{"id":"GO:0007118","count":2},{"id":"GO:0031047","count":2}]},{"hash":"1968373341020734636","title":"Unknown","description":"The top terms span developmental processes (spinal cord, retina development), signaling (TGF-beta response, tyrosine phosphorylation), and translation initiation, with no single coherent function tying all proteins together. The cluster appears to be heterogeneous rather than representing one clear biological role.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051260","count":6},{"id":"GO:0021510","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0060041","count":4},{"id":"GO:0071560","count":4}]},{"hash":"1873409813752331329","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016554","count":1},{"id":"GO:0080156","count":1},{"id":"GO:0031425","count":1},{"id":"GO:0090617","count":1},{"id":"GO:1900865","count":1}]},{"hash":"1306594264425493692","title":"Protein quality control and intracellular trafficking","description":"The top GO terms point to degradation and clearance of proteins (ERAD, SCF-proteasome, aggrephagy) and to movement through cellular compartments (Golgi retention, endosomal transport and vesicle fusion, pinocytosis). This pattern suggests a cohesive theme around protein homeostasis and trafficking across the secretory and endocytic pathways, even though a couple terms (like tRNA export) are less tightly connected. Overall, the cluster aligns with intracellular protein quality control and membrane trafficking functions.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0035973","count":3},{"id":"GO:0045053","count":3},{"id":"GO:0031146","count":2}]},{"hash":"1672132177841184746","title":"Plant light sensing and circadian regulation","description":"Multiple GO terms converge on light perception and circadian biology: detection of visible light, protein-chromophore linkage, UV protection, photoreactive repair, stomatal movement, circadian regulation of gene expression, and locomotor rhythm. Together these suggest a cluster of proteins involved in photoreceptors and clock-controlled responses in plants, linking light sensing to downstream processes like stomatal behavior and DNA repair. A defensive systemic acquired resistance term appears but is not central to the main theme.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018298","count":2},{"id":"GO:0009584","count":2},{"id":"GO:1901672","count":1},{"id":"GO:0032922","count":1},{"id":"GO:0009650","count":1}]},{"hash":"1780170805948556730","title":"Mitochondrial import and metabolic regulation","description":"The cluster shows mitochondrial-focused terms (protein import into the mitochondrial matrix; regulation of mitochondrial membrane permeability) alongside diverse metabolic processes (triglyceride biosynthesis, inositol catabolism, redox-related processes, SAM catabolism). This points to a theme of mitochondrial function coupled with metabolism, though the presence of a cell-cycle term and several obsolete terms reduces cohesion. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000134","count":1},{"id":"GO:0070940","count":1},{"id":"GO:0046902","count":1},{"id":"GO:0010867","count":1},{"id":"GO:1903740","count":1}]},{"hash":"280435452294798761","title":"RNA splicing and mRNA processing regulators","description":"The dominant GO terms in this cluster center on RNA splicing, mRNA processing, and regulation of splicing via the spliceosome (including regulation of alternative splicing and negative regulation of splicing). This points to a shared function in spliceosome-mediated RNA maturation and transcript processing, rather than broader transcription or cytoskeletal roles suggested by a few older or incidental terms. Given there are no interaction edges to bolster a single complex, the strongest common theme is RNA splicing and processing regulation.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008380","count":1},{"id":"GO:0000381","count":1},{"id":"GO:0006351","count":1},{"id":"GO:1903507","count":1},{"id":"GO:0006397","count":1}]},{"hash":"1725735198842309897","title":"Autophagy: Cvt pathway and PAS assembly","description":"This cluster shows strong signals for autophagy-related processes: cytoplasm to vacuole targeting via the Cvt pathway, localization to the phagophore assembly site (PAS), and autophagy of peroxisomes. These terms point to a shared function in autophagic vesicle formation and cargo targeting, suggesting the core theme is autophagy machinery and vesicle trafficking. Some other terms (ion transport, antibiotic/nylon metabolism) seem ancillary or incidental, but do not override the dominant autophagy-related signals.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030655","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0033252","count":1},{"id":"GO:0019876","count":1},{"id":"GO:1903830","count":1}]},{"hash":"1963195628562646128","title":"Plant cell wall remodeling and carbohydrate metabolism","description":"The top GO terms are dominated by plant-related processes such as pectin catabolic process, cell wall organization, polysaccharide catabolic process, microsporogenesis, and flower phyllotactic patterning, indicating a theme around cell wall dynamics and carbohydrate metabolism. Some terms (leukotriene biosynthesis, inflammatory response, platelet aggregation) are mammalian and likely reflect annotation noise, but the majority points to extracellular matrix remodeling and polysaccharide processing in plants. Confidence: Medium","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045490","count":5},{"id":"GO:0071555","count":5},{"id":"GO:0060773","count":4},{"id":"GO:0042121","count":3},{"id":"GO:0009556","count":3}]},{"hash":"959258145469949933","title":"Bacterial membrane transport and secretion proteins","description":"This cluster shows a strong emphasis on membrane transport and secretion, with multiple GO terms for branched-chain amino acid transport, carbohydrate and vitamin transport, molybdate transport, and peptide/oligopeptide export, plus protein secretion by Type I secretion system and peptide pheromone export. Although there are outliers related to nucleotide-excision repair and antibiotic response, the dominant signal is transport/secretion across membranes, characteristic of bacterial transport machinery and secretion systems.","confidence":"High","size":21,"edges":15,"triangles":2,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006289","count":4},{"id":"GO:0046677","count":4},{"id":"GO:0090374","count":3},{"id":"GO:0030253","count":3},{"id":"GO:0015803","count":3}]},{"hash":"506664631987675995","title":"Neuronal excitability and sensory perception","description":"The cluster is dominated by terms tied to neuronal signaling: potassium ion transport and homeostasis, stabilization/regulation of membrane potential, and mechanisms for sensing mechanical stimuli and pain (touch detection, sensory perception). While there are accompanying terms for development and transcription, the strongest and most consistent signals point to neuron function and excitability, suggesting a group of proteins involved in neuronal signaling and sensory transduction.","confidence":"High","size":21,"edges":6,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":7},{"id":"GO:0019233","count":7},{"id":"GO:0046827","count":7},{"id":"GO:0006351","count":7},{"id":"GO:0030322","count":7}]},{"hash":"1905467868790410161","title":"Spliceosome-Mediated RNA Splicing Regulation","description":"The top GO terms are dominated by mRNA splicing and spliceosome-related processes (cis/via spliceosome, positive/negative regulation of splicing), plus regulatory ncRNA-mediated gene silencing and translation initiation factor complex assembly, suggesting a cluster centered on post-transcriptional RNA processing and spliceosome regulation. The apoptotic term is secondary and non-dominant but can be linked to stress-related RNA regulation; overall the cluster maps best to spliceosome- and RNA processing\u2013related functions.","confidence":"High","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":3},{"id":"GO:0031047","count":2},{"id":"GO:0048026","count":2},{"id":"GO:1902625","count":2},{"id":"GO:0075525","count":2}]},{"hash":"278423217252008846","title":"Amino acid biosynthesis pathways","description":"The top GO terms point to multiple amino acid biosynthesis processes (homoserine, threonine, tyrosine, lysine via diaminopimelate) and related metabolism (chorismate pathway feeding aromatic amino acids), with one-carbon metabolism also involved. Magnesium ion transport appears as a supportive, potentially cofactor-related term rather than a defining feature. Overall, the cluster is best described as groups of proteins involved in amino acid biosynthesis and related metabolic routes.","confidence":"Medium","size":21,"edges":199,"triangles":1146,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006808","count":2},{"id":"GO:0009090","count":2},{"id":"GO:0046417","count":2},{"id":"GO:0006571","count":2}]},{"hash":"563021832315549798","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0000472","count":3},{"id":"GO:0016441","count":3}]},{"hash":"508240274542264349","title":"Nutrient-Starvation and Stress Response","description":"The cluster centers on cellular responses to starvation (leucine and glucose), oxidative stress (hydrogen peroxide), UV damage, and GCN2-mediated signaling, plus regulation of translation initiation in starvation conditions, suggesting a common theme of nutrient-sensing and stress adaptation; the neuron projection extension term may be an outlier or cross-talk, but does not dominate the set.","confidence":"Medium","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0071494","count":1},{"id":"GO:1990253","count":1},{"id":"GO:1990138","count":1},{"id":"GO:0071264","count":1},{"id":"GO:0031953","count":1}]},{"hash":"1492397447588543569","title":"Glycan and cell wall biosynthesis","description":"The top GO terms are dominated by processes that build cell wall components and extracellular polysaccharides (GDP-mannose biosynthesis, fungal-type cell wall biogenesis, cell wall mannoprotein biosynthetic, slime layer polysaccharide biosynthetic, LPS biosynthesis, glycogen biosynthesis). Translation is present but less representative. This points to a cohesive theme of glycan assembly and cell surface/matrix formation, justifying this label.","confidence":"High","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0009298","count":1},{"id":"GO:0009272","count":1},{"id":"GO:0000032","count":1},{"id":"GO:0019877","count":1}]},{"hash":"2145665027426416528","title":"Fatty acid metabolism and secondary metabolite biosynthesis","description":"The top GO terms cluster around fatty acid alpha-oxidation and methyl-branched fatty acid metabolism, plus biosynthetic processes for ectoine and verruculogen, suggesting a metabolic and secondary metabolite production theme. A few transcription-related or broad plant-specific terms appear incidental, but the dominant signal is metabolic/biosynthetic. ","confidence":"Medium","size":21,"edges":95,"triangles":211,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001561","count":3},{"id":"GO:0097089","count":3},{"id":"GO:1902181","count":3},{"id":"GO:0042400","count":3},{"id":"GO:0019491","count":3}]},{"hash":"967166166123099554","title":"Unknown","description":"The GO terms are highly diverse and cover behavioral fear response, sensory mechanosensation, immune signaling (interferon-beta production), sperm development (axoneme assembly, individualization), RNA biology (ncRNA-mediated silencing, splicing regulation), and even viral translation concepts. There is no single cohesive biological function or pathway connecting these terms, suggesting the cluster represents a heterogeneous set of proteins without a common, interpretable function.","confidence":"","size":21,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001662","count":2},{"id":"GO:0050910","count":1},{"id":"GO:0032608","count":1},{"id":"GO:0007288","count":1},{"id":"GO:0007291","count":1}]},{"hash":"1477647427895924852","title":"Vesicle trafficking and membrane organization","description":"This cluster is enriched for terms related to vesicle formation, trafficking, and membrane remodeling, such as synaptic vesicle budding, lysosomal membrane organization, endosome-to-plasma membrane transport, and positive regulation of membrane tubulation. The involvement of GTPase activity regulation also fits vesicle trafficking. A few terms refer to unrelated developmental or apoptotic processes, but the core signal points to endomembrane dynamics and vesicle transport.","confidence":"High","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030037","count":2},{"id":"GO:0097212","count":2},{"id":"GO:0070142","count":2},{"id":"GO:1903527","count":2},{"id":"GO:1905751","count":2}]},{"hash":"2055407296791066451","title":"RNA processing and transcription regulation","description":"This cluster shows GO terms centered on RNA maturation and transcription control, including pre-miRNA processing, miRNA catabolic process, transcription antitermination, DNA-templated transcription, and CRD-mediated mRNA stabilization. Ubiquitination and DNA damage recognition are also present but less dominant; overall, the strongest theme is RNA metabolism linked to transcription regulation.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0000715","count":2},{"id":"GO:0031054","count":1},{"id":"GO:0006351","count":1},{"id":"GO:1902219","count":1}]},{"hash":"30212956224154973","title":"Myoblast differentiation and vasculogenesis signaling","description":"This cluster is driven by GO terms emphasizing muscle development (positive regulation of myoblast differentiation) and blood vessel formation (positive regulation of vasculogenesis), with associated Notch signaling regulation and transcriptional control, suggesting a cohesive role in developmental signaling for muscle and vascular formation. The presence of GPCR-mediated signaling and protein post-translational modifications further supports a broad signaling/regulatory program rather than a single enzymatic function. Confidence: Medium","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051260","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0007200","count":3},{"id":"GO:0006517","count":3},{"id":"GO:0042265","count":3}]},{"hash":"1290899965127184072","title":"Calcium-Dependent Neuronal Signaling and Morphogenesis","description":"The GO terms point to calcium signaling and neuronal development, with emphasis on calcium detection, postsynaptic calcium regulation, and NFAT signaling, plus regulation of dendrite morphogenesis, indicating a module of calcium-dependent neuronal signaling and morphogenesis. Some terms are unrelated (e.g., DNA recombination, chromatin binding), but the core theme is calcium-driven neural signaling and development.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0090502","count":4},{"id":"GO:0006310","count":4},{"id":"GO:0005513","count":4},{"id":"GO:0060316","count":4},{"id":"GO:0051531","count":4}]},{"hash":"1239769877410189812","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010587","count":2},{"id":"GO:0031564","count":2},{"id":"GO:0010087","count":1},{"id":"GO:0000389","count":1},{"id":"GO:0000395","count":1}]},{"hash":"1815376565164577746","title":"Neuroimmune signaling and synapse development","description":"This cluster mixes innate immune processes (innate immune response, dsRNA response, LPS signaling, interferon-beta production) with neural development and synaptic regulation terms (axonogenesis, corpus callosum development, synapse assembly, dopamine response, pain behavior). The combination suggests proteins that participate in neuroimmune crosstalk affecting brain development and synaptic function, rather than a single, narrow pathway. Confidence: Medium","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0043330","count":2},{"id":"GO:0007409","count":2},{"id":"GO:0061368","count":2},{"id":"GO:1903351","count":2}]},{"hash":"1051973157118508236","title":"Unknown","description":"The GO terms are highly heterogeneous: inflammatory signaling terms (positive regulation of IL-1\u03b2 production; NOD2 signaling; NF-\u03baB regulation) co-occur with diverse developmental terms (oligodendrocyte differentiation; cornea, lacrimal gland, and mammary gland development) and even mitochondrial transcription. This scattered set does not point to a single cohesive biological function or pathway that would define a distinct protein cluster. Because of the lack of a unifying theme, a specific, high-confidence label is not supported.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050718","count":2},{"id":"GO:0048709","count":2},{"id":"GO:0061303","count":2},{"id":"GO:0070431","count":2},{"id":"GO:0032088","count":2}]},{"hash":"1135666654949642940","title":"Gametogenesis and Epigenetic Regulation","description":"This cluster is driven by terms tied to reproduction and epigenetic control, including DNA methylation involved in gamete generation and histone modification (demethylation, deacetylation), as well as sperm capacitation. While there are some unrelated metabolic terms, the dominant theme centers on gamete development and chromatin regulation. ","confidence":"Medium","size":21,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043046","count":6},{"id":"GO:0045654","count":6},{"id":"GO:0045793","count":5},{"id":"GO:0009228","count":5},{"id":"GO:0034720","count":5}]},{"hash":"1838285964076381545","title":"Mitotic and stress-response proteins","description":"Most frequent GO terms point to mitotic cell cycle and cell division, suggesting a core link to cell-cycle control. Additional terms indicate involvement in cellular stress and immune signaling (type I interferon, innate immune response, unfolded protein response) and RNA processing (snoRNP assembly). Together, this implies a group of proteins that function in cell division while also participating in stress/immune signaling and RNA biogenesis; hence the label \u201cMitotic and stress-response proteins.\u201d Some outliers (prostate gland development, male sex differentiation) may reflect broader annotation context.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0071357","count":3},{"id":"GO:0030850","count":3}]},{"hash":"829738237634391760","title":"Unfolded Protein Response and Protein Folding","description":"The GO terms most strongly point to ER stress and protein folding-related processes (response to unfolded protein, translation initiation in response to ER stress, and protein peptidyl-prolyl isomerization), suggesting a coherent theme around the unfolded protein response and chaperone-assisted folding. While a few terms pertain to development or signaling, the ER stress/protein folding signal dominates, making this a reasonable cluster label.","confidence":"Medium","size":21,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048136","count":2},{"id":"GO:0010801","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0007413","count":2},{"id":"GO:0060487","count":2}]},{"hash":"2271280229828161025","title":"Interferon- and cytokine-mediated inflammation","description":"The top GO terms cluster around positive regulation of interferon production (IFN-\u03b1/\u03b2), IL-6 production, and inflammatory responses, including type 2 immunity. This points to a shared function in cytokine signaling and immune activation, despite a few seemingly unrelated terms that may be annotation noise. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042144","count":1},{"id":"GO:0048733","count":1},{"id":"GO:0018230","count":1},{"id":"GO:0051770","count":1},{"id":"GO:0035882","count":1}]},{"hash":"725091579532556503","title":"Neural development and synaptic plasticity","description":"The top GO terms cluster around nervous system development and connectivity: substantia nigra development and myelination point to neuronal maturation, while regulation of long-term synaptic plasticity and long-term potentiation highlight synaptic strength and learning-related processes. Some terms (e.g., cell division, protein transport) are broader, but the dominant signal is neural development and synaptic regulation, possibly with dopaminergic neuron involvement.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043525","count":2},{"id":"GO:0048169","count":2},{"id":"GO:0046909","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0021762","count":2}]},{"hash":"2240728651361463786","title":"Unknown","description":"Top terms span plant secondary metabolism (anthocyanin and phenylpropanoid biosynthesis), primary metabolism (galactose and glutamine), proteolysis, transcription, redox, and a bacterial exopolysaccharide biosynthesis term. The mix across species and the presence of obsolete GO terms show no single clear function binding these proteins, so 'Unknown' is the safest label.","confidence":"","size":21,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006508","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0009718","count":2},{"id":"GO:0006541","count":2}]},{"hash":"118471148201042277","title":"Bacterial Cell Envelope and Metabolite Biosynthesis","description":"These GO terms converge on biosynthetic pathways for lipopolysaccharide, mycolic acid, poly-hydroxybutyrate, melanin, and antibiotics, suggesting a microbial biosynthetic/metabolic module tied to cell envelope components and pigment/secondary metabolite production. The presence of transcription-related terms adds general regulatory context but does not negate the biosynthetic theme.","confidence":"Medium","size":21,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0042619","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0009103","count":2},{"id":"GO:1902987","count":2}]},{"hash":"2298149096694841507","title":"Retroviral integration and proviral latency","description":"Top GO terms cluster around DNA recombination, replication, DNA integration, and explicit retroviral steps such as viral penetration into the host nucleus and establishment of integrated proviral latency, plus RNA-templated DNA biosynthesis. This pattern points to proteins involved in retroviral genome integration and maintenance of proviral latency within the host, with some elements suggesting host defense evasion (e.g., negative regulation of siRNA processing). Overall, the theme is retroviral DNA integration and proviral latency.","confidence":"High","size":21,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":11},{"id":"GO:0006260","count":10},{"id":"GO:0039651","count":10},{"id":"GO:0075732","count":10},{"id":"GO:0046718","count":10}]},{"hash":"1187790826657021053","title":"Thermoception and hypoxia/CO2 sensing","description":"The GO terms show a clear emphasis on sensing environmental cues\u2014especially temperature (thermoception, detection of temperature stimulus) and gas-related signals (detection of CO2, response to hypoxia)\u2014together with rapid physiological responses like vasoconstriction and startle. Some terms appear peripheral (sperm motility, plant hormone regulation), but the dominant theme is sensory detection of environmental stimuli and immediate bodily responses.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043588","count":4},{"id":"GO:0050960","count":4},{"id":"GO:0042310","count":3},{"id":"GO:0001666","count":3},{"id":"GO:0003031","count":3}]},{"hash":"949288962874421833","title":"Thermoception and receptor signaling cluster","description":"This group shows a strong tilt toward sensory and signaling roles, highlighted by thermoception, response to capsazepine, and various receptor/GPCR-related signaling terms, along with related synaptic localization and signaling pathway terms. While some terms (telomere maintenance, NOD1 signaling, obsolete GO entries) are more peripheral or technical artifacts, the prevailing theme is stimulus sensing and signal transduction. Confidence: Medium","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007205","count":12},{"id":"GO:0098907","count":10},{"id":"GO:0032212","count":9},{"id":"GO:0048549","count":9},{"id":"GO:0070427","count":9}]},{"hash":"1536126816689574384","title":"Unknown","description":"The GO terms are spread across phosphorylation, GPCR signaling, cell growth, several metabolic categories, telomere maintenance, pinocytosis, and innate signaling, with no clear unifying function or strong connectivity among the 21 proteins (no edges). This makes it hard to assign a concise, representative label.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0016049","count":3},{"id":"GO:0016042","count":2},{"id":"GO:0006741","count":2}]},{"hash":"321197604556181154","title":"Neuronal synapse signaling and endosomal trafficking","description":"The cluster brings together GO terms related to synaptic transmission (including GABAergic and endocannabinoid signaling), endosomal transport and vesicle fusion, and actin/cytoskeletal remodeling (filopodium assembly, Rho signaling). This pattern suggests proteins that coordinate synaptic function with membrane trafficking and cytoskeletal dynamics, typical of maintaining or modulating neuronal synapses.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046847","count":3},{"id":"GO:0016197","count":2},{"id":"GO:0034058","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0051489","count":2}]},{"hash":"554295266500502237","title":"Ubiquitin-mediated proteolysis and autophagy","description":"Core enrichment for ubiquitin-dependent protein catabolic process, protein ubiquitination, and autophagy indicates a proteostasis/ protein turnover theme. Histone catabolic process supports turnover, while calcium import, vitamin D response, and telomere maintenance appear more peripheral. Overall, the cluster is best described by ubiquitin-mediated degradation and autophagy.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:0098703","count":4},{"id":"GO:0036205","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0000083","count":3}]},{"hash":"1708878432626541810","title":"Unknown","description":"The GO terms are diverse (RNA splicing, spindle organization, actin-related mitosis, VEGF signaling, exocytosis, asymmetric cell division, sperm motility/binding, brain development, vacuole inheritance), showing no single shared function or pathway. With no interactions among members, the cluster lacks a cohesive theme, so a specific label isn\u2019t supported.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008380","count":2},{"id":"GO:0007051","count":1},{"id":"GO:1903480","count":1},{"id":"GO:1900748","count":1},{"id":"GO:0006904","count":1}]},{"hash":"1028239104714873700","title":"Calcium-Dependent Secretory Trafficking","description":"GO terms point to multiple aspects of regulated secretion and intracellular trafficking (neutrophil degranulation, insulin secretion, Golgi ribbon formation, receptor recycling) and calcium signaling in mitochondria, suggesting a cohesive role in calcium-regulated secretory trafficking.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035786","count":1},{"id":"GO:0051561","count":1},{"id":"GO:0036444","count":1},{"id":"GO:0032024","count":1},{"id":"GO:0090161","count":1}]},{"hash":"1270532488982421895","title":"Chloroplast Gene Expression and RNA Modification","description":"The cluster centers on chloroplast/plastid processes (plastid transcription, chloroplast-nucleus signaling) and RNA modification (rRNA base methylation, tRNA aminoacylation), indicating a cohesive role in chloroplast gene expression and RNA processing.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070475","count":1},{"id":"GO:0006432","count":1},{"id":"GO:0009451","count":1},{"id":"GO:0000961","count":1},{"id":"GO:0042793","count":1}]},{"hash":"577326126883337071","title":"Retroviral integration and latency","description":"The dominant GO terms point to retroviral lifecycle processes: DNA integration, establishment of integrated proviral latency, RNA-templated DNA synthesis (reverse transcription), and viral entry into the host nucleus, along with DNA replication and recombination. These together suggest a cluster centered on proviral integration and genome manipulation by retroviruses, with related infection steps.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0015074","count":5},{"id":"GO:0075713","count":5},{"id":"GO:0046718","count":5},{"id":"GO:0006278","count":3},{"id":"GO:0006260","count":3}]},{"hash":"1343678144649094014","title":"Muscle differentiation and stress-responsive signaling","description":"This cluster is dominated by terms tied to muscle development, including myoblast fusion, regulation of skeletal muscle cell differentiation, and the G1 to G0 transition during differentiation, along with calcium signaling linked to muscle function. The presence of a calcium release regulation term reinforces a muscle activation/differentiation theme. Additional terms like response to hypoxia and salt stress fit general cellular stress responses that can occur in muscle tissue. A few terms (digestion, mammary gland involution, blastocyst development) are more peripheral remodeling or developmental processes, making the core theme a best-fit but not perfect match.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001666","count":2},{"id":"GO:0007520","count":2},{"id":"GO:0007586","count":2},{"id":"GO:0060056","count":2},{"id":"GO:0001824","count":2}]},{"hash":"1955634101131404152","title":"Unknown","description":"The top GO terms are highly diverse, spanning immune signaling (CD40), cell death regulation, neural myelin maintenance, fungal lipid metabolism, and general metabolic processes. There is no single, coherent function or pathway tying these proteins together, suggesting the cluster does not reflect a common biological role. Therefore, the appropriate label is Unknown with no confidence in a shared function.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0023035","count":1},{"id":"GO:0060546","count":1},{"id":"GO:0006516","count":1},{"id":"GO:0032286","count":1},{"id":"GO:0006675","count":1}]},{"hash":"906033679069954754","title":"Intracellular vesicle trafficking and melanosome transport","description":"The GO terms show strong enrichment for vesicle transport between ER, Golgi, endosomes, and vacuoles, including anterograde/retrograde and synaptic vesicle recycling, plus pigmentation via melanosome transport. This points to a cohesive function in intracellular trafficking and pigment organelle movement.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0006896","count":1},{"id":"GO:0036465","count":1},{"id":"GO:0043473","count":1}]},{"hash":"1497595841009370472","title":"Cell polarity and developmental signaling","description":"The cluster\u2019s most representative terms center on intracellular signal transduction, Wnt signaling, and regulation of cell polarity and cell shape, with links to neuronal differentiation, suggesting a shared role in signaling networks that control polarity during development. Some plant-related polysaccharide/cell wall terms appear, but the dominant theme remains signaling and polarity in development.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":3},{"id":"GO:0045490","count":3},{"id":"GO:0016567","count":2},{"id":"GO:2000769","count":2},{"id":"GO:0032005","count":2}]},{"hash":"1487685717224941568","title":"Neural synaptic formation and plasticity","description":"Most terms point to neuronal connectivity and synaptic remodeling: dendritic spine morphogenesis, actin filament assembly, positive regulation of synapse structural plasticity, and long-term synaptic depression, along with modulation of excitatory postsynaptic potentials. Behavioral terms like vocalization and social behavior suggest neural circuits underlying behavior. A few terms (apoptotic process, intraciliary retrograde transport, nuclear migration) are less central but can relate to development and cellular transport. Overall, the cluster centers on neuronal development and synaptic plasticity.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":4},{"id":"GO:0030473","count":3},{"id":"GO:2000463","count":3},{"id":"GO:0060997","count":3},{"id":"GO:0071625","count":3}]},{"hash":"2053855011734138312","title":"Transcription Regulation in Development","description":"This cluster centers on GO terms related to transcription by RNA polymerase II (positive and negative regulation, DNA-templated transcription), indicating a shared emphasis on transcriptional control. Auxiliary development-associated terms (heart development, intestinal epithelial differentiation, myotube development) suggest a developmental context for these transcriptional regulators. While some terms are more peripheral (outer dynein arm assembly, kinase activity regulation) and no interactions are observed, the core theme appears to be transcriptional regulation linked to development.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045944","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0060575","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0014904","count":1}]},{"hash":"2110822087742625354","title":"Unknown","description":"The GO terms span very different tissues and processes (muscle development, PNS myelination, kidney morphogenesis, circadian regulation, germinal center formation, etc.), with no clear shared pathway or function linking them. Only a minor hint is protein phosphorylation, but that alone does not define a cohesive cluster theme, and there are no edges or clustering signals to support a single biological role. ","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048741","count":2},{"id":"GO:0022011","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0006468","count":2},{"id":"GO:0042752","count":1}]},{"hash":"1398674693318036683","title":"Cofactor and GPI-anchor biosynthesis","description":"Top GO terms indicate biosynthetic processes for cofactors (pyrroloquinoline quinone, thiamine) and for GPI anchor biosynthesis, suggesting a shared theme of biosynthesis. The presence of one unrelated developmental term is a minor outlier, and the lack of interaction edges implies a loose collection of biosynthetic enzymes rather than a single cohesive complex. Confidence reflects a coherent biosynthesis-centered interpretation, but the outlier term lowers certainty slightly.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018189","count":1},{"id":"GO:0009230","count":1},{"id":"GO:0009229","count":1},{"id":"GO:0009228","count":1},{"id":"GO:0006506","count":1}]},{"hash":"1287068907001546432","title":"Negative Regulation of Signaling and Synaptic Organization","description":"These proteins show strong enrichment for inhibitory control of multiple signaling pathways (T cell receptor signaling, ERK cascade, PI3K-AKT), along with components related to postsynaptic density assembly and synaptic vesicle clustering, suggesting a role as negative regulators coordinating signaling and synaptic architecture.","confidence":"High","size":20,"edges":152,"triangles":738,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0050860","count":15},{"id":"GO:0000200","count":15},{"id":"GO:0070373","count":15},{"id":"GO:0035335","count":13},{"id":"GO:0051898","count":13}]},{"hash":"1573877096288756675","title":"Oxidative stress detoxification and immune regulation","description":"The top GO terms center on cellular oxidant detoxification and responses to toxic substances, along with multiple terms for negative regulation of immune-related processes (e.g., leukocyte proliferation, IL-1\u03b2 production) and nitric oxide storage. This suggests a cohesive theme of redox/homeostatic defense coupled with suppression/modulation of inflammatory signaling, despite some growth factor signaling hints. ","confidence":"High","size":20,"edges":139,"triangles":591,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":15},{"id":"GO:0060316","count":14},{"id":"GO:2000255","count":14},{"id":"GO:0071364","count":13},{"id":"GO:0009636","count":13}]},{"hash":"750559434183036693","title":"Cell Cycle Control and DNA Replication","description":"The top GO terms are dominated by mitotic and replication processes\u2014kinetochore localization, G1/S transition, meiotic cycle, DNA replication, and CDK activity regulation\u2014indicating a coherent theme of cell cycle control. Some terms related to Schwann cell development, T cell signaling, and hormone or drug responses appear as peripheral associations, but the core signal points to cell cycle machinery.","confidence":"High","size":20,"edges":52,"triangles":68,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0034501","count":13},{"id":"GO:0045736","count":11},{"id":"GO:0014044","count":9},{"id":"GO:0060079","count":9},{"id":"GO:0050852","count":8}]},{"hash":"443999190660997898","title":"RNA processing and export with translation regulation","description":"Top GO terms center on mRNA processing (capping, splicing, export) and regulation of translation, with regulatory ncRNA silencing and hypusine-related translation. A few terms reference endosomal transport or obsolete polyadenylation annotations, but the dominant signal is RNA metabolism and translation control.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008612","count":2},{"id":"GO:0006370","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0048026","count":2},{"id":"GO:1900363","count":2}]},{"hash":"798780632878667487","title":"Unknown","description":"The set includes GO terms spanning translation initiation and preinitiation complex formation, chromatin organization and histone modification, chromosome segregation, mRNA splicing, phagolysosome assembly, epithelial cell proliferation, and apoptotic DNA fragmentation, with no single dominant process unifying them. The lack of a cohesive, shared function and zero network connectivity suggest the proteins do not cluster around one clear molecular theme, so an Unknown label with None confidence is appropriate.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002188","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0000747","count":2},{"id":"GO:0050679","count":2},{"id":"GO:1902510","count":2}]},{"hash":"1556256876990236273","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000472","count":5},{"id":"GO:0000480","count":5},{"id":"GO:0051013","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0006888","count":5}]},{"hash":"1579869419650379049","title":"Ribosome biogenesis and translation","description":"This cluster centers on ribosome biogenesis and translation, with strong enrichment for translation, maturation of the SSU rRNA, ribosome assembly (including small subunit biogenesis), and mitochondrial translation, suggesting a cohesive group of proteins involved in ribosome production and protein synthesis across compartments.","confidence":"High","size":20,"edges":166,"triangles":822,"max_degree":19,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0000462","count":6},{"id":"GO:0042254","count":5},{"id":"GO:0042274","count":4},{"id":"GO:0002181","count":3}]},{"hash":"245548744491315738","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":34,"triangles":16,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":4},{"id":"GO:0000480","count":3},{"id":"GO:0000472","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0000398","count":3}]},{"hash":"1668179718276011001","title":"Retroviral genome integration and proviral latency","description":"GO terms in this cluster cluster around retroviral life-cycle steps: RNA-templated DNA biosynthesis, DNA integration, DNA recombination, viral entry and penetration into the host nucleus, and establishment of integrated proviral latency, as well as effects on the host cell cycle. While a couple of terms mention symbiont interactions, the dominant signal is virus\u2013host genome integration and latency.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006278","count":3},{"id":"GO:0039651","count":3},{"id":"GO:0015074","count":3},{"id":"GO:0075713","count":3},{"id":"GO:0090502","count":3}]},{"hash":"380299088588410106","title":"Neuronal dendrite morphogenesis and signaling regulation","description":"The cluster shows strong representation of dendrite and neuron development terms (dendrite morphogenesis, dendritic spine morphogenesis, neuron development) along with MAPK pathway regulation (ERK/JNK) and protein turnover, suggesting a cohesive role in neuronal morphology and signaling.","confidence":"High","size":20,"edges":6,"triangles":1,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031647","count":8},{"id":"GO:0014850","count":7},{"id":"GO:0060997","count":7},{"id":"GO:0048813","count":7},{"id":"GO:0060044","count":7}]},{"hash":"1205893352304676130","title":"Hormone processing and receptor trafficking","description":"The GO terms center on production and maturation of signaling molecules (nerve growth factor, renin, insulin, peptide pheromones) and on regulation of receptor turnover/recycling (LDL receptor catabolic processes, receptor recycling). This points to proteins involved in secretory processing of hormones/peptides and in trafficking or regulating their receptors. Confidence: Medium.","confidence":"","size":20,"edges":31,"triangles":3,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0032902","count":4},{"id":"GO:0002001","count":4},{"id":"GO:0032804","count":4},{"id":"GO:0032802","count":4},{"id":"GO:0032805","count":4}]},{"hash":"947051987607747767","title":"Cell Cycle Checkpoints and Stress Signaling","description":"The cluster\u2019s terms center on cell cycle control (G1/S transition, meiotic spindle organization, spindle checkpoint signaling) and stress-related regulation (p53-mediated signaling, virus response, neuron death, autophagy regulation). This pattern suggests a coherent theme of coordinating cell division with cellular stress responses, even though a few terms (ion transport, cardiac differentiation) may reflect multifunctional proteins. Confidence: Medium","confidence":"","size":20,"edges":5,"triangles":0,"max_degree":2,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006813","count":15},{"id":"GO:0016242","count":14},{"id":"GO:2000727","count":14},{"id":"GO:0010765","count":14},{"id":"GO:0000082","count":14}]},{"hash":"646085639554814898","title":"Protein acetylation pathways","description":"Based on the top GO terms, there is a strong enrichment for acetylation-related processes: histone H4 acetylation, N-terminal acetylation/propionylation, putrescine acetylation, and N-acetylglucosamine metabolic pathway. While some terms (angiogenesis, leaf formation) seem ancillary or noisy, the predominant signal ties to acetyl group transfer and acetylation of proteins and metabolites, suggesting a cohesive cluster around acetylation biology.","confidence":"High","size":20,"edges":2,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001525","count":11},{"id":"GO:0030187","count":9},{"id":"GO:0043967","count":9},{"id":"GO:0017198","count":9},{"id":"GO:0006348","count":9}]},{"hash":"2033914673194674502","title":"Translation initiation and ribosome assembly","description":"Top GO terms cluster around translation processes and initiation complex formation, including translation, translational initiation, formation of preinitiation and cytoplasmic initiation complexes, and ribosome assembly. The presence of negative regulation of translational initiation suggests regulatory control of protein synthesis. A few outlier terms (germ cell proliferation, cyclic nucleotide biosynthesis, ERK cascade regulation) do not undermine the central theme. Overall, the cluster reflects components involved in mRNA translation and initiation complex assembly.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0045947","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0002176","count":1},{"id":"GO:0042256","count":1}]},{"hash":"871867529226978475","title":"Phytochrome-regulated circadian transcription and chromatin remodeling","description":"The cluster centers on plant light signaling (red/far-red phototransduction) and circadian rhythm regulation, with strong links to transcription control and chromatin remodeling, supported by chromatin-related GO terms and transcription regulation terms. A few ribosomal maturation terms appear minor and likely incidental.","confidence":"High","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":2},{"id":"GO:0042753","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0006313","count":2},{"id":"GO:0010018","count":2}]},{"hash":"530999290747676780","title":"Actin Cytoskeleton Remodeling","description":"Top terms center on actin filament dynamics (assembly, severing, depolymerization, reorganization) and terminal web structure, with supporting signals from EGFR and integrin pathways, indicating a cluster focused on actin cytoskeleton remodeling and related signaling.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090527","count":1},{"id":"GO:0070560","count":1},{"id":"GO:0051017","count":1},{"id":"GO:2001046","count":1},{"id":"GO:0090315","count":1}]},{"hash":"353931149588357719","title":"Innate Immune Signaling and Cytokine Regulation","description":"The proteins are linked by GO terms centered on innate immune sensing and cytokine output: TLR4 signaling, detection of muramyl dipeptide, positive regulation of inflammatory responses, and production of interferons and IL-6, suggesting a coherent theme of innate immune activation and cytokine regulation (with a few unrelated terms likely noise). ","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051770","count":1},{"id":"GO:0035882","count":1},{"id":"GO:0050729","count":1},{"id":"GO:0002830","count":1},{"id":"GO:0045359","count":1}]},{"hash":"1013309483132673487","title":"Membrane Transport and Synaptic Signaling","description":"This cluster's GO terms are dominated by transmembrane transport (phosphate, arsenite, K+, Na+) along with broader transport terms, and includes neural signaling-related terms (fasciculation of sensory neuron axon, trans-synaptic signaling) plus a Hedgehog pathway component (Smoothened signaling). These together suggest proteins involved in membrane transport that influence neuronal communication and connectivity, hence the label.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000185","count":1},{"id":"GO:0015700","count":1},{"id":"GO:0055085","count":1},{"id":"GO:0006813","count":1},{"id":"GO:0006814","count":1}]},{"hash":"886009734595071330","title":"Immune regulation and growth-factor signaling","description":"The terms point to immune system modulation (negative regulation of IL-2 production, T cell proliferation, and T cell homeostasis, plus germinal center formation) along with responses to growth factors (EGF and FGF stimuli) and glucocorticoids, with a couple developmental processes (mesendoderm development, chorio-allantoic fusion). This suggests a shared theme of signaling involved in immune regulation and growth factor\u2013related responses, though the set spans multiple related pathways.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071385","count":1},{"id":"GO:0045085","count":1},{"id":"GO:0045647","count":1},{"id":"GO:0060710","count":1},{"id":"GO:0044344","count":1}]},{"hash":"2013483923581776148","title":"Ubiquitin-Dependent Protein Degradation & Chromatin Regulation","description":"The top GO terms point to ubiquitin-mediated proteolysis (ubiquitin-dependent protein catabolic process, autoubiquitination, K6-linked ubiquitination) and chromatin-related processes (histone catabolic process, histone modification), with immune-related terms like V(D)J recombination and TNF signaling, and peroxisomal import. Taken together, the cluster seems centered on ubiquitin-regulated proteolysis and chromatin remodeling, with some immune signaling connections, making a label focused on ubiquitin-dependent degradation and chromatin control representative of the group.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":11},{"id":"GO:0051865","count":9},{"id":"GO:0033151","count":7},{"id":"GO:0009048","count":7},{"id":"GO:0085020","count":7}]},{"hash":"1628647203798568092","title":"Organ and tissue morphogenesis","description":"This cluster\u2019s top GO terms cluster around development and morphogenesis across multiple organs and sensory structures (eye/optic cup, embryonic eye, nose, inner ear) as well as vascular and cardiac tissue development. This suggests a shared theme of embryonic organogenesis and tissue morphogenesis rather than a single biochemical pathway, despite some obsolete terms present.","confidence":"High","size":20,"edges":106,"triangles":342,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0006537","count":7},{"id":"GO:0002072","count":7},{"id":"GO:0006069","count":7},{"id":"GO:0031076","count":7},{"id":"GO:0043584","count":7}]},{"hash":"1281178196260101010","title":"Ubiquitin-mediated protein degradation and ERAD","description":"The cluster is dominated by ubiquitin-related processes (ubiquitin-dependent ERAD, autoubiquitination, and K63-linked ubiquitination) and protein quality control (ER-associated degradation and chaperone-mediated assembly), with some related stress-response terms. This suggests a cohesive role in ubiquitin signaling governing protein fate and proteostasis, rather than a disparate mix of functions.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030579","count":1},{"id":"GO:0008626","count":1},{"id":"GO:0030433","count":1},{"id":"GO:0010200","count":1},{"id":"GO:0051865","count":1}]},{"hash":"752248113717079013","title":"Lipid signaling and vesicle trafficking","description":"This cluster is dominated by GO terms for lipid-mediated signaling (phosphatidylinositol signaling; IP3 biosynthesis; phosphatidylethanolamine biosynthesis) and vesicle trafficking/maintenance (synaptic vesicle maturation; presynapse signaling). The inclusion of GTPase regulation also fits control of trafficking processes. Although a few items touch on immune signaling, the strongest shared theme among the terms is membrane lipid signaling linked to vesicle dynamics. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":2},{"id":"GO:0048015","count":1},{"id":"GO:0016188","count":1},{"id":"GO:0050861","count":1},{"id":"GO:0099526","count":1}]},{"hash":"201708170065004225","title":"Ubiquitin-Dependent Protein Degradation (ERAD)","description":"The dominant terms are ubiquitin-dependent protein catabolic processes and autoubiquitination, including an ERAD-related pathway, pointing to a core function in ubiquitin-mediated proteolysis and protein quality control. Minor terms suggest auxiliary roles in proteostasis regulation, but the primary theme remains protein degradation via the ubiquitin system, especially the ERAD pathway.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0042787","count":3},{"id":"GO:0006511","count":3},{"id":"GO:0090035","count":2}]},{"hash":"984710170580575101","title":"Alcohol metabolism and oxidation","description":"The top GO terms cluster around alcohol-related oxidation and catabolic processes (ethanol oxidation/catabolism, omega-oxidation, xylitol catabolism, Ehrlich pathway for amino-acid to alcohol) and related oxidation-reduction activities, suggesting a theme of oxidative metabolism and alcohol processing. Some terms (lignin biosynthesis, LPS response) are less directly connected, but the dominant signal is alcohol and lipid oxidation. ","confidence":"High","size":20,"edges":189,"triangles":1122,"max_degree":19,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0009809","count":11},{"id":"GO:0006069","count":11},{"id":"GO:0010430","count":11},{"id":"GO:0000947","count":11},{"id":"GO:0042573","count":11}]},{"hash":"208625441546056218","title":"Viral transcription modulation","description":"This cluster shows a pattern around viral process and transcription-related functions (DNA-templated transcription and negative regulation of transcription by RNA polymerase II), suggesting proteins that may influence transcription in a viral context. Despite some obsolete terms and no observed interactions, the combination of viral process with transcription regulation supports naming it as viral transcription modulation.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":2},{"id":"GO:0006351","count":1},{"id":"GO:0000122","count":1},{"id":"GO:1903206","count":1},{"id":"GO:0055114","count":1}]},{"hash":"1141298300641202530","title":"Unknown","description":"The top GO terms span a wide and disparate set of processes (pinocytosis regulation, mRNA splice site recognition, muscle development regulation, telomere maintenance via telomerase, NOD1 signaling, thermoception, response to capsazepine, heat-stress transcription regulation, cell cycle, and synaptic plasticity regulation). With no clear shared function or pathway and no edges connecting the proteins, there isn\u2019t a coherent theme to label this cluster beyond Unknown.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048549","count":2},{"id":"GO:0006376","count":1},{"id":"GO:0045843","count":1},{"id":"GO:0032212","count":1},{"id":"GO:0070427","count":1}]},{"hash":"1101873382373426417","title":"Lipid Biosynthesis and Remodeling","description":"This cluster is dominated by GO terms related to lipid metabolism and remodeling, including cardiolipin, phosphatidylcholine, ether lipids, triglyceride biosynthesis, and CDP-diacylglycerol biosynthesis, suggesting a cohesive role in lipid production and membrane lipid remodeling. A couple of immune-related terms appear but are secondary to the lipid-focused pattern.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035965","count":1},{"id":"GO:0070236","count":1},{"id":"GO:0019432","count":1},{"id":"GO:0008611","count":1},{"id":"GO:0070970","count":1}]},{"hash":"1565262312646715816","title":"Diverse metabolite biosynthesis","description":"These proteins show a strong enrichment for various biosynthetic GO terms, spanning mycolic acid, antibiotic, melanin, PHB, tetrahydrobiopterin, and hormone (androgen/estrogen) biosynthesis. Although there are some oxidation-reduction and catabolic terms present, the unifying theme is synthesis of diverse metabolites, implying a broad biosynthetic role rather than a single, narrow pathway.","confidence":"High","size":20,"edges":101,"triangles":213,"max_degree":17,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0071768","count":20},{"id":"GO:0055114","count":20},{"id":"GO:0017000","count":20},{"id":"GO:0042438","count":20},{"id":"GO:0042619","count":20}]},{"hash":"109491896299443018","title":"Transcription Regulation and Cell Cycle Control","description":"The top GO terms cluster around DNA-templated transcription and negative regulation of transcription by RNA polymerase II, paired with G1/S transition of the mitotic cell cycle and positive regulation of CDK activity, suggesting a shared theme of transcriptional control coordinating cell cycle progression. While several biosynthetic and xenobiotic response terms appear (biotin/cobalamin biosynthesis, cellular response to xenobiotic stimulus), the strongest signal centers on transcriptional regulation and cell cycle control, with auxiliary metabolic annotations likely reflecting broader regulatory roles or annotation noise.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0000122","count":3},{"id":"GO:0000082","count":3},{"id":"GO:0007595","count":3},{"id":"GO:0045737","count":3}]},{"hash":"1664980464045191997","title":"Polysaccharide synthesis and cell wall remodeling","description":"The top GO terms cluster around polysaccharide biosynthesis and catabolism (alginic acid, pectin, polysaccharide) and cell wall organization/modification, linking synthesis and remodeling of extracellular matrix in plants/algae; with some development terms (flower phyllotaxis, microsporogenesis) suggesting broader plant developmental context. This points to a shared function in building/modifying cell walls and polysaccharide metabolism across these organisms, despite no strong connectivity between specific proteins. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042121","count":4},{"id":"GO:0045490","count":4},{"id":"GO:0060773","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0009405","count":2}]},{"hash":"1026367388643427932","title":"Unknown","description":"The GO terms are very diverse, including xenobiotic response, several biosynthetic processes, lipid catabolism, and responses to specific compounds like cocaine and amine. There isn\u2019t a clear, shared function or pathway linking these proteins, so a cohesive label isn\u2019t identifiable.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":3},{"id":"GO:0016049","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0017000","count":2}]},{"hash":"834409129722516019","title":"Ubiquitin-Proteasome System Components","description":"This cluster is dominated by GO terms for ubiquitin-dependent protein catabolic processes, including protein polyubiquitination, SCF-dependent proteasomal ubiquitin-dependent degradation, and K48-linked ubiquitination, with autoubiquitination also represented. While a few terms touch on peroxisome import and immune-related functions, the central theme is ubiquitin tagging and proteasomal degradation, indicating these proteins largely function within the UPS. ","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":6},{"id":"GO:0000209","count":4},{"id":"GO:0031146","count":4},{"id":"GO:1900095","count":3},{"id":"GO:0070936","count":3}]},{"hash":"747362842082034317","title":"Epithelial and retinal differentiation and signaling","description":"The top GO terms center on tissue-specific differentiation (lung epithelium, retina) and associated signaling, with supporting involvement in cell cycle, transcription regulation, GTPase activity, PI-mediated signaling, calcium sensing, and GPI anchor biosynthesis. This points to a theme of developmental differentiation intertwined with general cellular signaling and processes, though the cluster appears diverse rather than focused on a single pathway.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060487","count":3},{"id":"GO:0032465","count":3},{"id":"GO:0010842","count":3},{"id":"GO:0045944","count":2},{"id":"GO:0043547","count":2}]},{"hash":"1786870913683218132","title":"Unknown","description":"The top GO terms span several unrelated biological themes (actin cytoskeleton assembly, protein ADP-ribosylation, telomere maintenance, endocytosis, NOD1 signaling, thermosensation/heat response, transcriptional response to heat, cell cycle, and neuronal synaptic regulation) with no clear single function tying the cluster together, and there are no edges to suggest a cohesive interaction. ","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051017","count":5},{"id":"GO:0070212","count":5},{"id":"GO:0032212","count":4},{"id":"GO:0048549","count":4},{"id":"GO:0070427","count":4}]},{"hash":"622169787313028017","title":"Unknown","description":"The Top Terms span telomere maintenance, pinocytosis, NOD1 signaling, thermoception, response to capsazepine, heat-stress transcription, synaptic receptor localization, calcium release, and epithelial polarity, with no clear shared function.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":2},{"id":"GO:0048549","count":2},{"id":"GO:0070427","count":2},{"id":"GO:0050955","count":2},{"id":"GO:1901594","count":2}]},{"hash":"1676583301535613822","title":"Retroviral life cycle and genome integration","description":"The top GO terms collectively describe reverse transcription (RNA-templated DNA synthesis), DNA integration, and establishment of proviral latency, alongside viral entry and nuclear penetration. This combination strongly points to a retroviral life cycle with genome integration and latency, rather than general DNA metabolism. Thus the cluster likely groups proteins involved in retroviral infection, replication, and integration.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006278","count":2},{"id":"GO:0039651","count":2},{"id":"GO:0015074","count":2},{"id":"GO:0075713","count":2}]},{"hash":"1197081758218110504","title":"Temperature-Sensory Signaling and Calcium Regulation","description":"This cluster centers on temperature-related sensory signaling, evidenced by thermoception and response to capsazepine, and includes a clear calcium signaling component (release of sequestered calcium into cytosol) along with neural/synaptic regulation. While some terms pertain to ubiquitination, telomere maintenance, or immune-like signaling, the dominant theme is temperature sensing linked to calcium-dependent signaling and synaptic regulation.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":4},{"id":"GO:0032212","count":3},{"id":"GO:0048549","count":3},{"id":"GO:0070427","count":3},{"id":"GO:0050955","count":3}]},{"hash":"601235618577988650","title":"Unknown","description":"Top terms are very diverse: translation (2) alongside neural development/innervation, epithelial migration, smooth muscle contraction, lipoteichoic acid biosynthesis, and FGFR signaling regulation. There is no dominant biological process linking the 20 proteins, and the cluster has no edges, suggesting a lack of functional cohesion. Hence Unknown with None confidence.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0035860","count":1},{"id":"GO:0061580","count":1},{"id":"GO:0014846","count":1},{"id":"GO:0070395","count":1}]},{"hash":"1161354904522856469","title":"Transcription Regulation","description":"Top GO terms are dominated by transcription-related activities (DNA-templated transcription, transcription regulation by RNA polymerase II, and regulation of transcription by galactose), with additional but less coherent terms related to cell-cycle progression and differentiation. The shared theme appears to be gene expression control rather than a single pathway, so the label Transcription Regulation captures the cluster. Confidence: Medium.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":1},{"id":"GO:0000411","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0033598","count":1},{"id":"GO:1990069","count":1}]},{"hash":"788504791170795494","title":"Cardiac Membrane Potential and Ion Transport","description":"The terms cluster around membrane potential maintenance (stabilization, resting potential, atrial repolarization) and ion handling (potassium and sodium transport/homeostasis), with links to cardiac stress signaling (hypertrophy) and cyclic nucleotide signaling (cAMP/cGMP). Together these point to electrophysiological regulation in cardiac muscle rather than a disparate set of processes.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0098914","count":12},{"id":"GO:0050976","count":12},{"id":"GO:0030007","count":12},{"id":"GO:0071805","count":12},{"id":"GO:0030322","count":11}]},{"hash":"1953132788057311665","title":"Unknown","description":"The GO terms point to a variety of unrelated processes (fat cell differentiation, epithelial proliferation, chromatin organization, chromosome segregation, splicing, phagolysosome assembly, growth hormone response, apoptosis regulation), with no single cohesive function tying the proteins together. The lack of edges reinforces the absence of a shared molecular role, so there is no clear cluster-level theme beyond general cellular processes.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045444","count":3},{"id":"GO:0000747","count":2},{"id":"GO:0050679","count":2},{"id":"GO:1902510","count":2},{"id":"GO:0001845","count":2}]},{"hash":"885890374028055291","title":"Temperature-sensing and neuronal signaling cluster","description":"The Top Terms are dominated by temperature-related and neural signaling processes: thermoception, response to capsazepine, calcium release, and receptor localization at synapses. A couple terms relate to broader stress responses (telomere maintenance, NOD1 signaling), but the central pattern points to temperature-triggered signaling in neural contexts, justifying the label. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":2},{"id":"GO:0048549","count":2},{"id":"GO:0070427","count":2},{"id":"GO:0050955","count":2},{"id":"GO:1901594","count":2}]},{"hash":"2085122222149046821","title":"Unknown","description":"Top terms are highly heterogeneous, including signaling (Wnt pathway) and a range of metabolism-related processes (alkaloid, stilbene, menaquinone, antibiotic biosynthesis), plus plant-specific signals (strigolactone) and environmental degradation terms. Several terms are obsolete, and there are no network connections (edges) among proteins, making it hard to identify a single cohesive function for the cluster. Consequently, there isn't a clear, representative label beyond Unknown.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016055","count":3},{"id":"GO:0019260","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0097755","count":2}]},{"hash":"288272109095630477","title":"Proteostasis and Autophagy Regulation","description":"The proteins are enriched for ubiquitin-related processes (deubiquitination, autoubiquitination) and autophagy/mitophagy regulation, plus ER stress and apoptotic signaling control, with additional terms on ribosome biogenesis. This points to a cohesive module focused on protein quality control and degradation pathways, linked to autophagy and stress responses, with some ties to ribosome maturation and cell remodeling.","confidence":"Medium","size":19,"edges":165,"triangles":871,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0034140","count":7},{"id":"GO:0016579","count":7},{"id":"GO:1903071","count":6},{"id":"GO:0000423","count":6},{"id":"GO:0000028","count":6}]},{"hash":"1493970291656350462","title":"Mitotic Cell Cycle Regulation","description":"The top GO terms cluster around mitosis and cell-cycle control (G1/S transition, mitotic cell cycle, meiotic spindle organization), indicating proteins that coordinate division and progression through the cell cycle. Additional terms related to p53 signaling, autophagy, and stress responses often intersect with cell-cycle regulation, reinforcing a cohesive theme of division control. Some unrelated terms (e.g., visual perception, cardiac differentiation) are present but do not override the dominant mitotic signals.","confidence":"High","size":19,"edges":155,"triangles":732,"max_degree":18,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":19},{"id":"GO:0000278","count":19},{"id":"GO:0016242","count":18},{"id":"GO:2000727","count":18},{"id":"GO:0010765","count":18}]},{"hash":"2140467412430967565","title":"Hippo signaling and differentiation network","description":"The cluster is dominated by Hippo signaling (GO:0035329) and apoptosis (GO:0006915), with strong representation of differentiation processes (keratinocyte differentiation, myotube differentiation) and related signaling cascades (MAPK). Additional terms touch on cardiac proliferation regulation, osmosensory signaling, brain development, and telomere maintenance, suggesting a broad but cohesive theme of growth control, cell fate decisions, and tissue development guided by signaling networks. This points to a network of signaling pathways coordinating proliferation, survival, and differentiation across multiple tissues, with Hippo signaling as a central axis. Medium","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0035329","count":10},{"id":"GO:0006915","count":10},{"id":"GO:0030216","count":10},{"id":"GO:0006813","count":10},{"id":"GO:0060044","count":10}]},{"hash":"2237392195560923251","title":"Unknown","description":"The top GO terms span immune responses (defense against Gram-positive bacteria, innate immunity, response to dsRNA) and diverse developmental/neural processes (axonogenesis, neural patterning, dopamine response, mesoderm formation, multicellular development). There is no single dominant function tying these terms together, and the absence of edges suggests a mixed collection rather than a cohesive cluster. As such, there isn't a clear, interpretable label beyond Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0050830","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0045087","count":3},{"id":"GO:0043330","count":3},{"id":"GO:0007409","count":3}]},{"hash":"1791160282951680710","title":"Vacuolar amino acid transport","description":"The top GO terms converge on transmembrane import of multiple amino acids into the vacuole (L-lysine, L-arginine, L-serine, L-glutamine, L-glutamate, L-tyrosine, L-histidine) and an export (L-arginine) from the vacuole, pointing to a cluster of proteins involved in vacuolar amino acid trafficking under nitrogen starvation. Some obsolete terms about pH regulation appear but do not define the core function. The lack of observed edges just reflects the dataset rather than a lack of shared function. Confidence reflects a coherent functional theme centered on vacuolar amino acid transport. ","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901482","count":2},{"id":"GO:0090518","count":2},{"id":"GO:0090516","count":2},{"id":"GO:2000487","count":2},{"id":"GO:0090514","count":2}]},{"hash":"1741757367901072320","title":"Calcium Handling in Heart and Kidney Development","description":"The cluster centers on calcium signaling and cardiac function, as shown by terms for calcium import and RyR regulation, and for heart contraction and hypertrophy, with additional notes on caffeine response. Kidney-related terms (metanephric development) indicate a secondary but clear link to renal development, while ion transport (sodium, manganese) supports a broader theme of ionic homeostasis. Together, these suggest proteins involved in calcium-dependent signaling in heart tissue along with participating roles in kidney development.","confidence":"Medium","size":19,"edges":59,"triangles":35,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0035725","count":3},{"id":"GO:0060315","count":3},{"id":"GO:0098703","count":2},{"id":"GO:0072205","count":2},{"id":"GO:0035502","count":2}]},{"hash":"2294767260489013506","title":"Glucose and carbohydrate transporters","description":"These proteins are enriched for membrane transport of sugars and related metabolites (D-glucose, trehalose, dehydroascorbic acid, selenite, organic anions), plus responses to glucose availability (glucose starvation, insulin-stimulated glucose import). Together they point to a cohesive role in nutrient uptake across the plasma membrane.","confidence":"Medium","size":19,"edges":8,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0052106","count":2},{"id":"GO:1904659","count":2},{"id":"GO:1904728","count":2},{"id":"GO:0097080","count":2},{"id":"GO:0043252","count":2}]},{"hash":"762855315588867088","title":"Membrane Transporters and Secretion","description":"The cluster is mainly tied to membrane transport (vitamin and xenobiotic transmembrane transport; branched-chain amino acid transport) and secretion (protein secretion by the Type I secretion system), suggesting a cohesive theme around transport and secretion functions. Some other terms (DNA replication, ATP metabolism) are present but less representative, indicating heterogeneity beyond the core transport/secretion signal.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":2},{"id":"GO:0001824","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0060291","count":2},{"id":"GO:0015803","count":1}]},{"hash":"152212452690104715","title":"Immune Regulation and Growth Factor Signaling","description":"The cluster\u2019s top GO terms cluster around T cell regulation (IL-2 production, T cell proliferation, germinal center formation, T cell homeostasis) and cellular responses to growth factors and hormones (glucocorticoid, EGF, FGF). This points to a shared theme of immune signaling modulated by hormonal and growth-factor cues, with some developmental context suggested by mesendoderm development and chorio-allantoic fusion. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071385","count":2},{"id":"GO:0045085","count":2},{"id":"GO:0045647","count":2},{"id":"GO:0060710","count":2},{"id":"GO:0044344","count":2}]},{"hash":"264979769247513841","title":"RNA processing and stress-response regulation","description":"The cluster is dominated by GO terms related to RNA processing and regulation of RNA fate, including regulatory ncRNA-mediated gene silencing, spliceosome-driven mRNA splicing, mRNA export, and stress-related mRNA stability. Additional terms for DNA replication and SOS response suggest a broader cellular stress-response context that intersects transcriptional and post-transcriptional control, with potential ties to viral genome replication. Together, these suggest a group of proteins involved in RNA processing and stress-responsive gene regulation.","confidence":"Medium","size":19,"edges":11,"triangles":4,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":6},{"id":"GO:0048026","count":6},{"id":"GO:0006260","count":5},{"id":"GO:0009432","count":5},{"id":"GO:0070934","count":4}]},{"hash":"1160616675450174446","title":"Chromatin organization and transcription","description":"The set of terms centers on chromatin organization, heterochromatin formation, chromatin assembly, DNA replication, and transcription elongation, pointing to a nucleus-based chromatin and transcription-focused cluster. A few terms (bitter taste, membrane insertion) appear unrelated noise. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001580","count":1},{"id":"GO:0051205","count":1},{"id":"GO:0006612","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0070869","count":1}]},{"hash":"660600910737698132","title":"Broad Regulators of Cellular Processes","description":"These proteins do not map to a single pathway; rather, their GO terms emphasize regulation across many processes (telomere maintenance, Wnt signaling, autophagy, differentiation, ion transport, cell cycle transitions, spindle organization, and stress responses). The common theme is regulatory influence across diverse cellular activities, so a label like Broad Regulators of Cellular Processes best captures the cluster.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":2},{"id":"GO:1904355","count":2},{"id":"GO:0090263","count":2},{"id":"GO:0016242","count":1},{"id":"GO:2000727","count":1}]},{"hash":"306207252671307693","title":"Amino acid and cofactor biosynthesis","description":"This cluster shows strong enrichment for amino acid biosynthetic processes (lysine, histidine, phenylalanine) and cofactor biosynthesis (biotin, protoporphyrinogen IX), suggesting a core role in producing essential metabolites. The presence of DNA-templated transcription indicates coordinated regulation, while the Notch signaling term appears as an outlier. Overall, the dominant theme is biosynthesis of amino acids and cofactors with accompanying transcriptional regulation.","confidence":"Medium","size":19,"edges":157,"triangles":758,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006782","count":11},{"id":"GO:0009102","count":10},{"id":"GO:0019878","count":10},{"id":"GO:0006351","count":8},{"id":"GO:0042853","count":8}]},{"hash":"1508039729006917884","title":"Thyroid Hormone-Regulated Cardiac Development","description":"This cluster centers on heart development and thyroid hormone metabolism, with a clear emphasis on calcium signaling and calcineurin-NFAT\u2013driven transcription. The presence of TH metabolic process, heart development, and NFAT/calcium-related terms suggests TH-regulated cardiac development via calcium signaling pathways, with other terms fitting into signaling and transcriptional regulation contexts. Some terms appear peripheral or noisy, but the core pattern points to TH-dependent cardiac development.","confidence":"High","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":3},{"id":"GO:0042403","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0048015","count":2},{"id":"GO:0045944","count":2}]},{"hash":"2070117598692858792","title":"Neuromuscular signaling and myelination","description":"The terms cluster around neural communication (neurotransmitter secretion, synaptic potentiation, GPCR signaling, calcium dynamics) and peripheral myelination, with supporting cues from skeletal muscle differentiation and satellite cell\u2013mediated regeneration, suggesting coordinated neuromuscular signaling and myelination processes.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0070315","count":2},{"id":"GO:2001015","count":2},{"id":"GO:0007269","count":2},{"id":"GO:0022011","count":2}]},{"hash":"1214465200300103912","title":"Methanogenesis and Acetyl-CoA Metabolism","description":"The terms point to microbial energy metabolism, with methanogenesis from acetate, carbon fixation, and acetyl-CoA metabolism forming a coherent metabolic theme; proton transmembrane transport and proton motive force-driven ATP synthesis indicate membrane energy coupling, while sodium transport and vacuolar/organellar terms suggest related cellular homeostasis. Together, they describe a cluster of proteins involved in methane-based carbon processing and associated energy generation, with some annotations reflecting organelle-related housekeeping.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015977","count":1},{"id":"GO:0019385","count":1},{"id":"GO:0006084","count":1},{"id":"GO:0015991","count":1},{"id":"GO:0006878","count":1}]},{"hash":"1542475606184573129","title":"Unknown","description":"The terms span diverse biosynthetic and metabolic processes, methylation, and xenobiotic responses with no single dominant function, indicating a heterogeneous cluster without a clear shared theme.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042136","count":6},{"id":"GO:0046340","count":6},{"id":"GO:0030245","count":6},{"id":"GO:0017000","count":5},{"id":"GO:0009102","count":5}]},{"hash":"1164005275766020494","title":"Retroviral DNA Integration and Latency","description":"The cluster is dominated by GO terms for reverse transcription (RNA-templated DNA biosynthesis), DNA replication, recombination, DNA integration, and proviral latency, plus viral entry into the host nucleus. Together these point to proteins involved in the retroviral life cycle, especially genome replication and proviral integration/latency, with hints of viral counter-defense against RNA silencing.","confidence":"High","size":19,"edges":60,"triangles":65,"max_degree":15,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":10},{"id":"GO:0006278","count":8},{"id":"GO:0006260","count":8},{"id":"GO:0039651","count":8},{"id":"GO:0015074","count":8}]},{"hash":"703642045470880588","title":"Unknown","description":"The GO terms span diverse processes\u2014from cell cycle and telomere maintenance/localization to endocytosis, innate immune signaling (NOD1), thermoception and heat-stress responses, transcriptional regulation under stress, calcium signaling, and synaptic receptor localization\u2014without a clear shared theme. With no edges tying these functions together, there is no coherent functional focus to name this cluster beyond Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0032212","count":2},{"id":"GO:0048549","count":2},{"id":"GO:0070427","count":2},{"id":"GO:0050955","count":2}]},{"hash":"658671385559556767","title":"Unknown","description":"The top GO terms span telomere maintenance, chromosome/telomere localization, endocytic regulation, innate immune signaling (NOD1), temperature/heat-stress responses, thermoception, synaptic plasticity, calcium release, and cell cycle, with no clear single process linking them all. Therefore a cohesive, specific label cannot be assigned. ","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":2},{"id":"GO:0048549","count":2},{"id":"GO:0070427","count":2},{"id":"GO:0050955","count":2},{"id":"GO:1901594","count":2}]},{"hash":"473996466654904718","title":"Neuronal signaling and calcium dynamics","description":"Based on the presence of terms like thermoception, response to capsazepine, regulation of synaptic plasticity by receptor localization to the synapse, and calcium release into the cytosol, the cluster appears enriched for neural signaling and calcium-mediated synaptic activity. While cell cycle, telomere maintenance, and some housekeeping terms are also present, the strongest shared theme is sensory-neural signaling and calcium dynamics, suggesting a cohesive neuronal signaling module for this group of proteins.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":4},{"id":"GO:0032212","count":3},{"id":"GO:0048549","count":3},{"id":"GO:0070427","count":3},{"id":"GO:0050955","count":3}]},{"hash":"1324592275138865396","title":"Mitochondrial Translation and Metabolic Pathways","description":"Dominated by mitochondrial biology: mitochondrial translation, TCA cycle, fatty acid catabolism, glutathione metabolism, and mitochondria-specific tRNA biosynthesis; these point to mitochondrial protein synthesis and energy metabolism. A few terms touch unrelated processes (ciliary motility, ER organization), but the core signal is mitochondrial translation paired with metabolic pathways.","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032543","count":3},{"id":"GO:0060296","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006099","count":2},{"id":"GO:0006749","count":2}]},{"hash":"156680699432159887","title":"Ubiquitin-Dependent Protein Degradation","description":"The Top Terms are strongly dominated by ubiquitination and proteolysis processes (ubiquitin-dependent protein catabolic process, autoubiquitination, ERAD, polyubiquitination, and K48/K63-linked ubiquitination), indicating the cluster centers on the ubiquitin-proteasome system and protein turnover. A couple of terms (V(D)J recombination, dosage compensation) appear as less related or incidental annotations.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":10},{"id":"GO:0051865","count":9},{"id":"GO:0030433","count":9},{"id":"GO:0000209","count":6},{"id":"GO:1900095","count":5}]},{"hash":"500811700184171530","title":"Mitochondrial Transporters and Energy Metabolism","description":"Proteins in this cluster predominantly involve transport across mitochondrial membranes (alpha-ketoglutarate, ornithine, ATP, nucleotide import) and energy-related processes (malate-aspartate shuttle, membrane fission, adaptive thermogenesis, magnesium export), indicating a cohesive theme of mitochondrial transport and metabolic energy regulation.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015742","count":3},{"id":"GO:0000066","count":3},{"id":"GO:1990544","count":3},{"id":"GO:1990519","count":3},{"id":"GO:1990845","count":3}]},{"hash":"1843347811108806566","title":"Viral entry, integration, and proviral latency","description":"This cluster centers on viral life-cycle processes: entry into the host cell, penetration of the host nucleus, DNA integration and recombination, and establishment of integrated proviral latency. While a couple of terms relate to general translation or replication, the key signals are viral infection steps and proviral latency, justifying the label. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006278","count":1},{"id":"GO:0039651","count":1},{"id":"GO:0015074","count":1},{"id":"GO:0043137","count":1}]},{"hash":"788155900508648423","title":"Ribosome biogenesis and export","description":"The top GO terms cluster around ribosome production and processing, including ribosome biogenesis, small and large subunit biogenesis, and export of ribosomal subunits from the nucleus, which together define a ribosome assembly/export function for this cluster. A few terms (cell cycle, iron transport, conjugation) are less central but do not outweigh the ribosome-focused terms.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0015970","count":1},{"id":"GO:0042274","count":1},{"id":"GO:0000747","count":1}]},{"hash":"352807623544961858","title":"Unknown","description":"The terms are scattered among regulatory processes (transcription, DNA binding) and membrane-related processes (plasma membrane repair, regulation of synaptic vesicle exocytosis), with obsolete GO terms and no edges connecting proteins. There isn\u2019t a clear, cohesive functional theme tying the cluster together, so a concise, representative label cannot be assigned.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903206","count":2},{"id":"GO:0010796","count":2},{"id":"GO:0031384","count":2},{"id":"GO:2000300","count":2},{"id":"GO:0001778","count":2}]},{"hash":"573301747193250115","title":"Vacuolar amino acid transport","description":"The top terms cluster around transmembrane import (and export) of diverse amino acids into the vacuole, plus a nod to nitrogen starvation responses. This suggests a cohesive function in vacuolar amino acid uptake and related nutrient stress signaling, despite some obsolete terms and isolated transcription notes. ","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901482","count":2},{"id":"GO:0090518","count":2},{"id":"GO:0090516","count":2},{"id":"GO:2000487","count":2},{"id":"GO:0090514","count":2}]},{"hash":"996099057689972598","title":"Deubiquitinase-regulated mucosal innate immunity","description":"The cluster centers on mucosal immune responses and regulation of inflammatory signaling, with terms for MDP/ NOD-like pathways, negative regulation of IL-1\u03b2 and IL-8 production, and multiple types of protein deubiquitination (K48, K63, K27, K33). This points to a coherent theme where deubiquitinases modulate innate immune signaling in mucosal tissues, dampening inflammatory responses to maintain homeostasis.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032495","count":1},{"id":"GO:0032691","count":1},{"id":"GO:0071108","count":1},{"id":"GO:0002385","count":1},{"id":"GO:0032717","count":1}]},{"hash":"916476290547904683","title":"Cellular trafficking and organelle dynamics","description":"The cluster's top GO terms cluster around intracellular transport and organelle maintenance (Golgi organization and Golgi-to-lysosome transport, negative regulation of mitochondrial fusion) with related cytoskeletal and autophagy aspects (Rho signaling, dendrite extension, aggrephagy). This points to a common theme of organelle dynamics and trafficking coupled with cytoskeletal regulation, rather than a single linear pathway. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010637","count":2},{"id":"GO:1903861","count":2},{"id":"GO:1903358","count":2},{"id":"GO:0090160","count":2},{"id":"GO:0035023","count":2}]},{"hash":"1041402904248528875","title":"Calcium signaling in Schwann cell development and myelination","description":"This cluster centers on calcium-related processes, including calcium ion detection, regulation of calcium release and calmodulin/calcineurin-NFAT signaling, and it also includes clear peripheral nervous system syncho-glial functions such as Schwann cell development and myelination. Together these terms point to a theme of calcium-regulated Schwann cell maturation and PNS myelination, with broader roles in neuronal connectivity and glial regulation.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0005513","count":2},{"id":"GO:0060316","count":2},{"id":"GO:0051531","count":2},{"id":"GO:0001569","count":2},{"id":"GO:0051343","count":2}]},{"hash":"265365701551885050","title":"Unknown","description":"TheGO terms span a wide range of unrelated processes (cardiac action potential regulation, telomere maintenance, pinocytosis, NOD1 signaling, thermoception, heat-stress transcription, cell cycle, synaptic localization/ plasticity, and telomeric chromosome localization), and there are no interactions among proteins (Edges: 0). There isn\u2019t a coherent, single theme linking these terms, so the cluster is best labeled Unknown with no confidence.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098907","count":4},{"id":"GO:0032212","count":3},{"id":"GO:0048549","count":3},{"id":"GO:0070427","count":3},{"id":"GO:0050955","count":3}]},{"hash":"1762176545387682900","title":"Chromatin Remodeling and Mitotic Chromosome Segregation","description":"The cluster's top GO terms point to nuclear processes: chromatin organization, histone acetylation, and homologous chromosome segregation, plus mitotic spindle orientation, all reflecting chromosome dynamics during cell division. A few terms (phagolysosome assembly, growth hormone response) are less related and may be annotation noise or multifunctionality. Overall, the recurring theme is chromatin state and mitotic chromosome handling, supporting this label with moderate confidence.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000132","count":2},{"id":"GO:0000747","count":1},{"id":"GO:0050679","count":1},{"id":"GO:1902510","count":1},{"id":"GO:0001845","count":1}]},{"hash":"644218653871508030","title":"Membrane Lipid Remodeling and Endocytosis","description":"The top GO terms cluster around lipid metabolism (sphingomyelin and phosphatidylcholine catabolic processes, triglyceride storage) and membrane trafficking (receptor-mediated endocytosis), with related effects on cell migration and lamellipodium formation. This suggests a shared theme of membrane dynamics involving lipid remodeling and endocytic/trafficking regulation, with some signaling context (estradiol response). It\u2019s a concise, representative label for a cluster tied to membrane and trafficking processes, though the terms are diverse.  ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090305","count":3},{"id":"GO:0030334","count":2},{"id":"GO:0006898","count":2},{"id":"GO:0071392","count":2},{"id":"GO:0030505","count":2}]},{"hash":"1166156955147995058","title":"Epigenetic regulation and transcription control","description":"Proteins in this cluster are enriched for chromatin and transcription-related functions, including DNA-templated transcription, RNA guanine-N7 methylation, and histone H3-K9 methylation, pointing to epigenetic regulation of gene expression. The presence of telomere maintenance regulation and broader multicellular/developmental terms suggests these factors also participate in growth and development programs, but the core theme remains transcriptional control via chromatin state and RNA processing.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":3},{"id":"GO:0036265","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0051567","count":2},{"id":"GO:0032212","count":2}]},{"hash":"1220201404593209779","title":"Carbohydrate and lipid metabolism","description":"This cluster shows multiple GO terms tied to carbohydrate and lipid processing, including glycolytic process and several lipid catabolic/remodeling steps (triglyceride, monoacylglycerol, acyl-chain remodeling, phosphatidylserine catabolic). There are also vitamin biosynthesis terms (menaquinone, cobalamin) and dephosphorylation, suggesting broader metabolic capabilities rather than a single dedicated pathway. The label \"Carbohydrate and lipid metabolism\" best captures the dominant functional theme, with a moderate level of confidence due to some outlier terms. ","confidence":"Medium","size":18,"edges":15,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0009234","count":2},{"id":"GO:0016311","count":2},{"id":"GO:0006096","count":2},{"id":"GO:0009236","count":2},{"id":"GO:0019433","count":2}]},{"hash":"1622216714329761876","title":"RNA Modification and Reverse Transcription","description":"The cluster centers on RNA modification activities (tRNA and rRNA methylation, peptidyl-lysine methylation) and protein isomerization, with links to RNA-templated DNA biosynthesis and proviral latency, suggesting a shared theme of RNA processing/modification and reverse-transcription\u2013related processes. Some terms (like cobalamin biosynthesis) appear as outliers, but the core signal points to RNA modification and reverse transcription\u2013related functions.","confidence":"Medium","size":18,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1901407","count":3},{"id":"GO:0006278","count":2},{"id":"GO:0075713","count":2},{"id":"GO:0000413","count":2},{"id":"GO:0030488","count":2}]},{"hash":"891776789892476253","title":"DNA damage response and cell cycle control","description":"The GO terms center on DNA replication, DNA repair (NHEJ), and G1/S transition, with apoptosis and genome stability themes, suggesting a focus on genomic integrity and cell cycle regulation. Calcium/NFAT signaling and immune-regulatory terms appear as supporting, secondary associations within stress-response networks.","confidence":"Medium","size":18,"edges":9,"triangles":7,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006915","count":3},{"id":"GO:2000324","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0005513","count":3},{"id":"GO:0001915","count":3}]},{"hash":"148544458419355106","title":"DNA replication and telomere/chromatin regulation","description":"This cluster centers on genome maintenance activities: DNA replication and unwinding, recombination, DNA-templated transcription, and chromatin dynamics including subtelomeric heterochromatin formation and nucleosome mobilization, with a theme of telomere maintenance regulation. The mix of replication and chromatin-related GO terms suggests a cohesive role in maintaining genome integrity during replication and chromosome end regulation.","confidence":"High","size":18,"edges":109,"triangles":400,"max_degree":16,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0032508","count":7},{"id":"GO:0006260","count":5},{"id":"GO:0006268","count":5},{"id":"GO:0006348","count":4},{"id":"GO:0044806","count":4}]},{"hash":"1105302750122950738","title":"Translation initiation and preinitiation complex formation","description":"Most prominent GO terms are related to translation initiation, including translation reinitiation (GO:0002188) and formation of translation preinitiation complex (GO:0001731), each appearing multiple times in the cluster. While other terms touch on chromatin organization, histone acetylation, cell fusion, phagolysosome assembly, and chromosome segregation, these appear less represented. The core signal points to components involved in initiating translation, so the label Translation initiation and preinitiation complex formation best fits the cluster.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002188","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0000747","count":2},{"id":"GO:0050679","count":2},{"id":"GO:1902510","count":2}]},{"hash":"1816907365203550384","title":"Muscle and fat cell differentiation","description":"This cluster's top GO terms point to differentiation programs for mesenchymal lineages, including muscle (myotube differentiation, response to muscle stretch, cell migration) and adipose tissue (fat cell differentiation). The presence of cell cycle regulation signals suggests proliferative phases during differentiation, with telomere maintenance terms reflecting genomic stability during this process. Overall, the theme is differentiation toward muscle and fat cell lineages.","confidence":"Medium","size":18,"edges":9,"triangles":2,"max_degree":4,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0016477","count":11},{"id":"GO:0035994","count":11},{"id":"GO:0045736","count":11},{"id":"GO:0006397","count":11},{"id":"GO:0032212","count":11}]},{"hash":"355231737918720316","title":"DNA Repair and UV Damage Response","description":"The cluster is dominated by terms tied to DNA replication, nucleotide-excision repair, and DNA damage signaling, including mitotic intra-S checkpoint, meiotic/mitotic recombination repair, and UV-B\u2013related repair pathways, suggesting a cohesive module for sensing and repairing DNA damage and coordinating replication/mitosis under UV stress.","confidence":"High","size":18,"edges":13,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0031573","count":1},{"id":"GO:0006289","count":1},{"id":"GO:0045951","count":1},{"id":"GO:0010777","count":1},{"id":"GO:0010224","count":1}]},{"hash":"2096861750141766860","title":"Diphthamide and wobble tRNA modifications","description":"These proteins are annotated with GO terms tied to RNA modification in translation: diphthamide formation on histidine and wobble uridine modification of tRNA, both key to translation fidelity. The third term, budding, is less clearly connected but may reflect a growth context in yeast. Overall, the cluster appears centered on translation-associated RNA modifications. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002098","count":1},{"id":"GO:0007117","count":1},{"id":"GO:0017183","count":1}]},{"hash":"25170501931980020","title":"Type I interferon-mediated antiviral innate immunity","description":"The cluster repeatedly shows GO terms for cellular response to type I interferon, innate immune response, dsRNA sensing, and TLR3 signaling, plus endosomal transport/fusion and pinocytosis, pointing to a group of proteins involved in antiviral sensing and interferon-driven innate immunity with endosomal trafficking.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071357","count":1},{"id":"GO:0008277","count":1},{"id":"GO:0045087","count":1},{"id":"GO:0050689","count":1},{"id":"GO:0071360","count":1}]},{"hash":"1033251529762688994","title":"Post-transcriptional mRNA processing regulators","description":"These proteins repeatedly map to regulation of mRNA splicing, polyadenylation, and stability, plus terms related to spliceosome activity and translation initiation factor assembly, indicating a coherent focus on RNA processing and maturation prior to translation.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":2},{"id":"GO:0043488","count":2},{"id":"GO:0031047","count":1},{"id":"GO:0048026","count":1},{"id":"GO:1902625","count":1}]},{"hash":"1155211271207602274","title":"Nuclear RNA processing and genome maintenance","description":"The top terms cluster around nuclear activities: RNA processing and surveillance (nuclear mRNA surveillance, snoRNA catabolic processes, polyadenylation-dependent pathways), tethering of RNA polymerase II genes to the nuclear periphery, and genome maintenance processes (telomeric D-loop disassembly, dosage compensation, regulation of recombination). A plastid DNA replication term is present but does not override the dominant nuclear RNA metabolism theme, suggesting the proteins mainly participate in nuclear RNA processing and genome maintenance.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032066","count":1},{"id":"GO:0071039","count":1},{"id":"GO:0000973","count":1},{"id":"GO:0009048","count":1},{"id":"GO:0090503","count":1}]},{"hash":"2025038410912406352","title":"Unknown","description":"GO terms in this cluster span translation, telomere maintenance, endocytosis, immune signaling, sensory perception, and cell cycle with no clear unifying function, and there are no connecting edges to tie the proteins to a single pathway. Therefore, there is no coherent theme to assign a specific label, making Unknown the appropriate designation. ","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":2},{"id":"GO:0070475","count":1},{"id":"GO:0006432","count":1},{"id":"GO:0032212","count":1},{"id":"GO:0048549","count":1}]},{"hash":"1997160545906263813","title":"Unknown","description":"These 18 proteins have a highly diverse set of GO terms, ranging from chromatin regulation and DNA repair to transcription control, translation initiation, protein degradation, and stem cell differentiation, with no apparent shared pathway or interaction pattern (no edges/triangles). The lack of a cohesive theme makes a confident, specific label inappropriate.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090054","count":1},{"id":"GO:0000715","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0000973","count":1},{"id":"GO:1902416","count":1}]},{"hash":"1348267606993170343","title":"Integrin-mediated cell adhesion and epithelial migration","description":"The Top Terms include integrin-mediated cell-cell adhesion (GO:0033631), cell-matrix adhesion involved in ameboidal cell migration (GO:0003366), positive regulation of epithelial cell migration (GO:0010634), and maintenance of epithelial integrity (GO:0035160). Together these point to a cohesive theme of adhesion to the extracellular matrix and promotion of epithelial cell movement, with other terms being less central. Overall, this cluster appears to be about adhesion/migration processes in epithelial contexts.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061084","count":2},{"id":"GO:0010694","count":1},{"id":"GO:0033631","count":1},{"id":"GO:0045715","count":1},{"id":"GO:0006507","count":1}]},{"hash":"965366633229212774","title":"Unknown","description":"Top GO terms are diverse, spanning bone resorption, thyroid hormone metabolism, renin-angiotensin signaling, iron import, redox and hydrogen peroxide biosynthesis, integrin biosynthesis regulation, and response to glutamine. This broad mix lacks a single cohesive function or theme, making a representative, specific label impractical. ","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045453","count":2},{"id":"GO:0050790","count":2},{"id":"GO:0003081","count":1},{"id":"GO:0098706","count":1},{"id":"GO:0006590","count":1}]},{"hash":"950667303709623718","title":"Retroviral entry, reverse transcription, and genome integration","description":"The most represented GO terms converge on retroviral processes: DNA integration, proviral latency establishment, RNA-templated DNA biosynthesis (reverse transcription), DNA replication and recombination, and host entry/nucleus penetration, along with suppression of host RNAi. Together these indicate a cluster of proteins involved in the retroviral life cycle and genome integration within host cells.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0015074","count":3},{"id":"GO:0075713","count":3},{"id":"GO:0046718","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0006278","count":2}]},{"hash":"313348945097550816","title":"Mitochondrial dynamics and apoptosis","description":"The top terms cluster around mitochondria-related processes (fission, membrane organization, intracellular distribution) and apoptosis, with supporting signals from cell cycle/division terms and mitochondrial protein complexes. This suggests a theme of mitochondrial dynamics influencing apoptosis and, to some extent, cell-cycle-related regulation.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0007049","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0048312","count":2},{"id":"GO:0051260","count":2}]},{"hash":"878121842216333546","title":"Unknown","description":"The GO terms are highly diverse, with only a couple clearly tied to ubiquitin-mediated proteolysis (ubiquitin-dependent protein catabolic process and K48-linked ubiquitination) while others relate to development, lipid metabolism, mitochondrial dynamics, and immune regulation. With no edges linking proteins and no a priori cohesive function, there isn't a confident, single theme that unites the cluster. ","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016348","count":1},{"id":"GO:0042787","count":1},{"id":"GO:0034389","count":1},{"id":"GO:0070936","count":1},{"id":"GO:0006471","count":1}]},{"hash":"47694408019992179","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0035690","count":3},{"id":"GO:0034628","count":3},{"id":"GO:1990966","count":3},{"id":"GO:0097171","count":3}]},{"hash":"2164126989069286660","title":"Proviral genome integration and host transcription/splicing","description":"Reasoning: The top GO terms converge on viral proviral processes\u2014DNA integration, establishment of integrated proviral latency, DNA recombination, viral entry into the host nucleus, RNA-templated DNA biosynthesis, DNA-templated transcription, and spliceosomal complex assembly. This combination suggests proteins involved in proviral genome integration and subsequent manipulation of host transcription/splicing machinery.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0015074","count":4},{"id":"GO:0075713","count":4},{"id":"GO:0006310","count":4},{"id":"GO:0046718","count":4},{"id":"GO:0006278","count":3}]},{"hash":"1630679612871827216","title":"Unknown","description":"The set of terms spans telomere biology, cell cycle, calcium signaling, sensory/thermoception, and various signaling pathways, with no clear, shared function that ties the proteins together, so a cohesive label is not supported.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0032212","count":3},{"id":"GO:0048549","count":3},{"id":"GO:0070427","count":3},{"id":"GO:0050955","count":3},{"id":"GO:1901594","count":3}]},{"hash":"1111296670028916935","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006541","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0009409","count":3},{"id":"GO:0035556","count":3},{"id":"GO:0006355","count":3}]},{"hash":"1734865220217772639","title":"Ubiquitin-dependent proteolysis in development","description":"This cluster centers on ubiquitin-mediated protein degradation (ubiquitin-dependent catabolic process and K29-linked ubiquitination) and several developmental terms across tissues (lung, kidney, skeletal muscle). The co-occurrence of organ development GO terms with ubiquitin signaling suggests a theme of regulated protein turnover guiding differentiation and organogenesis. Despite zero edges, the GO signal points to a coherent functional axis rather than random associations.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0060487","count":3},{"id":"GO:0032465","count":3},{"id":"GO:0048741","count":3},{"id":"GO:0001822","count":2}]},{"hash":"1544591924980823169","title":"Retroviral integration and latency","description":"This cluster is dominated by GO terms tied to retroviral biology: RNA-templated DNA synthesis, DNA replication, DNA recombination, and DNA integration, along with the establishment of integrated proviral latency and viral penetration into the host nucleus. A few terms hint at virus-host interactions (host apoptosis and interleukin-4 response). Together, they point to proteins participating in retroviral genome integration and latency within the host genome.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006278","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0039651","count":1},{"id":"GO:0015074","count":1},{"id":"GO:0075713","count":1}]},{"hash":"135254609865496352","title":"Sphingolipid metabolism","description":"The core signals are sphingosine biosynthetic process and ceramide catabolic process, indicating a sphingolipid metabolism module. The remaining, mostly diverse terms suggest additional, less coherent functions or cross-species annotations.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046512","count":2},{"id":"GO:0046718","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0048235","count":1},{"id":"GO:0040015","count":1}]},{"hash":"789789867762083212","title":"Developmental Morphogenesis and Cell Migration","description":"This cluster shows a convergence on developmental and morphogenesis-related processes, with multiple terms for forebrain, skeletal system, and multicellular organism development, plus cell migration and tissue remodeling. A few terms point to stress or immune responses (cadmium exposure, defense against Gram-positive bacteria), which adds noise, but the developmental/morphogenetic theme is dominant. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0016477","count":3},{"id":"GO:0035994","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0045736","count":3},{"id":"GO:0030900","count":3}]},{"hash":"1935170745776990829","title":"Retroviral replication and proviral latency","description":"GO terms cluster around reverse transcription and proviral integration, i.e., retroviral life cycle (RNA-templated DNA synthesis, DNA integration, proviral latency, viral entry into nucleus). Some terms reflect broader virus\u2013host interactions and common cellular processes, but the predominant signal is retroviral replication and latent provirus establishment.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006278","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0039651","count":2},{"id":"GO:0015074","count":2},{"id":"GO:0075713","count":2}]},{"hash":"1302789688393827500","title":"Unknown","description":"The terms span RNA and histone methylation and modification (tRNA wobble uridine modification, rRNA modification, tRNA methylation, histone H4-R3 methylation) but also include antibiotic biosynthesis, nodulation, ubiquinone biosynthesis, metal ion response, and cellular senescence. This mix does not reveal a single cohesive function for the cluster, so a clear, specific label cannot be assigned with confidence.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002098","count":1},{"id":"GO:0032259","count":1},{"id":"GO:0000154","count":1},{"id":"GO:0017000","count":1},{"id":"GO:0009877","count":1}]},{"hash":"798048723849176090","title":"Diverse Regulation of Signaling and Metabolism","description":"The enriched terms span telomere maintenance, chromosomal localization, innate immune signaling (NOD1/2), calcium signaling, thermoception, and tissue-specific differentiation (foam cell, SA node, brown fat). There isn\u2019t a single cohesive pathway uniting all terms, implying a broad set of regulatory roles rather than a specific function. The name captures this general theme of diverse regulatory processes across systems.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":6},{"id":"GO:0048549","count":6},{"id":"GO:0070427","count":6},{"id":"GO:0050955","count":6},{"id":"GO:0070198","count":6}]},{"hash":"10749486827655667","title":"Oxidative signaling and cuticle development","description":"The terms point to redox processes (hydrogen peroxide and superoxide production) coupled with signaling (cAMP response, guanylate cyclase regulation) and a developmental/structural term related to adult chitin-based cuticle development, suggesting a theme where oxidative signaling modulates insect cuticle formation and associated cellular processes.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0000272","count":3},{"id":"GO:0008360","count":3},{"id":"GO:0060316","count":3},{"id":"GO:0051591","count":3}]},{"hash":"1518424237235670011","title":"Unknown","description":"The GO terms are scattered across multiple, unrelated processes (diverse metabolic pathways like galactose, sorbitol, inositol, and heme catabolism) and regulatory activities (negative regulation of kinase activity and transcription by RNA polymerase II), with several obsolete terms as well. There is no clear, cohesive functional theme linking the proteins, and the cluster shows no edges, supporting an Unknown label.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019877","count":1},{"id":"GO:0009089","count":1},{"id":"GO:0033673","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0006012","count":1}]},{"hash":"1068201820078284959","title":"Cell wall and capsule polysaccharide biosynthesis","description":"Owing to explicit enrichment for cell wall polysaccharide biosynthetic and capsule polysaccharide biosynthetic processes, the cluster appears tied to construction of surface polysaccharides. Additional terms on cell cycle, cell division, and regulation of cell shape suggest involvement in growth and structural remodeling, coordinating surface polysaccharide production with cell division.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070592","count":1},{"id":"GO:0019853","count":1},{"id":"GO:1903457","count":1},{"id":"GO:0009823","count":1},{"id":"GO:0045227","count":1}]},{"hash":"1227508766731180746","title":"Antiviral Innate Immune Response","description":"The cluster\u2019s top GO terms are dominated by innate immunity and antiviral defense, including innate immune response, defense response to virus, regulation of interferon-alpha production, and inflammatory signaling. This points to a core function in antiviral innate defense and inflammatory regulation, with a few outlier terms related to development that may reflect multifunctional proteins or annotation noise.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0033674","count":1},{"id":"GO:0007286","count":1},{"id":"GO:0070100","count":1}]},{"hash":"2076416564719095105","title":"Bacterial energy metabolism and cofactor biosynthesis","description":"The top GO terms cluster around metabolic pathways: antibiotic biosynthesis, fatty acid beta-oxidation, valine and phenylacetate catabolism, and the biosynthesis of menaquinone and phylloquinone. This points to a group of proteins involved in core energy metabolism and the production of important cofactors, with some secondary metabolite potential (antibiotics). A few additional terms (estrogen response, hydrogen peroxide response) appear at low frequency, likely reflecting broader stress-responsive roles, but do not disrupt the central metabolic theme. Confidence in this label is High.","confidence":"","size":17,"edges":133,"triangles":637,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":13},{"id":"GO:0006635","count":13},{"id":"GO:0006574","count":12},{"id":"GO:0010124","count":12},{"id":"GO:0009234","count":12}]},{"hash":"1438554346099703465","title":"Angiogenesis and Cardiovascular Development","description":"This cluster is dominated by GO terms related to blood vessel formation, including positive regulation of endothelial cell migration and angiogenesis, along with positive regulation of cardiac muscle cell differentiation, pointing to vascular development and heart-related differentiation as the core theme. The presence of DNA replication and transcription terms likely reflects the proliferative state of developing cardiovascular tissues, rather than a separate, distinct function. Thus, labeling it as angiogenesis and cardiovascular development captures the main shared function of the proteins.","confidence":"High","size":17,"edges":30,"triangles":30,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0043536","count":12},{"id":"GO:0006260","count":12},{"id":"GO:0001525","count":12},{"id":"GO:0006351","count":12},{"id":"GO:0016242","count":11}]},{"hash":"273672456585640685","title":"Mitochondrial Transport and Energy Metabolism","description":"The top GO terms cluster around mitochondrial transport processes (alpha-ketoglutarate, ornithine, nucleotide import, ATP transport) and energy-related functions (adaptive thermogenesis, energy homeostasis), with supporting links to metabolic regulation (glucocorticoid response, insulin secretion) and heart development. This suggests a cohesive theme of mitochondria-driven transport coupled to energy metabolism, justifying this label.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097274","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0051384","count":2},{"id":"GO:0015742","count":1},{"id":"GO:0000066","count":1}]},{"hash":"1763574433989814145","title":"Mitophagy and Autophagy Regulation","description":"This cluster is dominated by autophagy-related terms, especially mitophagy (GO:0000423) and regulation of autophagosome maturation, along with mitochondrial fusion regulation, suggesting a theme of autophagy control and mitochondrial dynamics. Ubiquitin-dependent protein catabolic processes and ER-associated degradation align with protein turnover linked to autophagy machinery. A couple of ribosome biogenesis terms may be incidental noise. Overall, the core cluster theme centers on mitophagy and autophagy regulation.","confidence":"High","size":17,"edges":10,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0014070","count":5},{"id":"GO:1903071","count":4},{"id":"GO:0000423","count":4},{"id":"GO:0000028","count":4},{"id":"GO:1902236","count":4}]},{"hash":"1567234460206013544","title":"Chloroplast Gene Expression & Signaling","description":"The cluster centers on plastid/chloroplast transcription and chloroplast\u2013nucleus signaling, with several RNA metabolism and transcription-related terms (RNA modification, DNA-templated transcription, transcription termination), plus related RNA processing activities. This points to coordinated plastid gene expression and inter-organelle communication as the common theme.","confidence":"Medium","size":17,"edges":63,"triangles":65,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0042793","count":2},{"id":"GO:0009451","count":2},{"id":"GO:0000961","count":2},{"id":"GO:0010019","count":2},{"id":"GO:0046677","count":1}]},{"hash":"1054551714223002666","title":"cGMP Signaling and Olfactory Perception","description":"These proteins cluster around cyclic GMP signaling, including negative regulation of guanylyl cyclase pathways and cellular responses to cGMP, with an olfactory sensory term (smell) also appearing and suggesting sensory transduction. Additional terms hint at broader neuromodulatory signaling (epinephrine, serotonin) and cardiac-related processes, but the core theme appears to be cGMP-mediated signaling linked to sensory perception. ","confidence":"Medium","size":17,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010754","count":3},{"id":"GO:0007608","count":3},{"id":"GO:0071321","count":3},{"id":"GO:0019933","count":2},{"id":"GO:0030593","count":2}]},{"hash":"1287563813912461153","title":"Proviral integration and latency","description":"The cluster shows strong signals for viral/proviral processes: DNA recombination, RNA-templated DNA synthesis (reverse transcription), DNA replication, and establishment of integrated proviral latency, along with entries into host cells and viral/nuclear penetration. There is also evidence of host RNA interference modulation, suggesting viral genome manipulation and host defense evasion. These together indicate a cohesive theme of proviral integration, replication, and latency with host interaction.","confidence":"High","size":17,"edges":131,"triangles":615,"max_degree":16,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":12},{"id":"GO:0006278","count":10},{"id":"GO:0006260","count":10},{"id":"GO:0039651","count":10},{"id":"GO:0015074","count":10}]},{"hash":"312820420142917886","title":"Pain and environmental sensory responses","description":"The cluster's top GO terms cluster around nociception, thermoception, startle response, CO2 detection, hypoxia response, and vasoconstriction, suggesting an overarching theme of acute sensory signaling and physiological responses to environmental stress. Some terms (multicellular development, protein tetramerization, jasmonic acid regulation) appear as outliers and may reflect broader or cross-kingdom annotations, but the dominant pattern is sensory/defense signaling.","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":12},{"id":"GO:0019233","count":12},{"id":"GO:0051262","count":9},{"id":"GO:0042310","count":8},{"id":"GO:0001666","count":8}]},{"hash":"1571229380216586952","title":"COPII Secretion and ECM Deposition","description":"This cluster is dominated by GO terms related to the COPII secretory pathway (coat regulation and cargo loading) and secretion of extracellular matrix components, pointing to a shared role in exporting ECM proteins via COPII vesicles. Additional terms on morphogenesis and lipid/homeostasis align with developmental and membrane trafficking contexts, but the strongest common thread is COPII-dependent secretion and ECM deposition.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003400","count":1},{"id":"GO:1901301","count":1},{"id":"GO:0048702","count":1},{"id":"GO:0016236","count":1},{"id":"GO:0061156","count":1}]},{"hash":"2109264899308669267","title":"Unknown","description":"Top terms span plant development (root meristem growth, regulation of auxin polar transport, cytokinin signaling) and diverse processes (lung development, glucocorticoid signaling, pericentriolar material localization, telomerase assembly), with several obsolete terms. There is no unifying function across the proteins, so a single cohesive label cannot be assigned.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043947","count":2},{"id":"GO:0010449","count":2},{"id":"GO:1905323","count":2},{"id":"GO:2000299","count":2},{"id":"GO:2000012","count":2}]},{"hash":"129212303296308595","title":"RNA and Protein Methylation Enzymes","description":"The cluster's top GO terms are dominated by RNA and protein methylation/modification processes (tRNA wobble uridine modification, tRNA methylation, rRNA modification, and various peptide methylations), pointing to a group of methyltransferase enzymes. Other terms appear peripheral and do not define the core function.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035902","count":1},{"id":"GO:0002098","count":1},{"id":"GO:1901052","count":1},{"id":"GO:0000154","count":1},{"id":"GO:0017000","count":1}]},{"hash":"1054241565562134304","title":"Neuronal vesicle trafficking and signaling","description":"The prominent GO terms point to vesicle transport between ER and Golgi, synaptic vesicle maturation, PI-mediated signaling, and presynaptic to nuclear signaling, all indicative of neuronal intracellular trafficking and synaptic communication; brain development reinforces the neural context. Some ribosome turnover and nuclear export terms appear, but can relate to neuronal remodeling processes. Therefore the cluster is best described as neuronal vesicle trafficking and signaling.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034517","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0048015","count":1}]},{"hash":"1673915556671961404","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":22,"triangles":5,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0031425","count":4},{"id":"GO:0016554","count":3},{"id":"GO:0080156","count":3},{"id":"GO:0042793","count":3},{"id":"GO:1900865","count":3}]},{"hash":"737661946075139147","title":"Thiamine Biosynthesis","description":"The top GO terms include thiamine diphosphate biosynthetic process and thiazole biosynthetic process, suggesting a metabolic module for vitamin B1 production. A few additional terms related to stress responses (lipopolysaccharide and xenobiotic stimulus) and regulatory processes are present but sparse, so the strongest signal is thiamine biosynthesis. This supports a moderate level of confidence that the cluster centers on thiamine biosynthesis.","confidence":"Medium","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0042135","count":1},{"id":"GO:0009229","count":1},{"id":"GO:0032496","count":1},{"id":"GO:0042493","count":1}]},{"hash":"1154951922434488149","title":"Glucocorticoid-Responsive T Cell Regulation","description":"This cluster centers on immune modulation, with GO terms for glucocorticoid response, IL-2 suppression, T cell proliferation control, and T cell homeostasis, suggesting a theme of T cell regulation under glucocorticoid signaling; a few development-related terms may be incidental.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":2},{"id":"GO:0071385","count":1},{"id":"GO:0045085","count":1},{"id":"GO:0045647","count":1},{"id":"GO:0060710","count":1}]},{"hash":"184755771902551440","title":"RNA granule assembly and translational control","description":"The cluster shows a consistent emphasis on RNA metabolism: P-body and stress granule assembly, cytoplasmic mRNA processing body assembly, mRNA deadenylation/decay, and negative regulation of translation initiation. While there is a neuronal signaling term (long-term synaptic potentiation), the strongest shared signal is RNA granule dynamics governing mRNA fate and protein synthesis, especially under stress. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900271","count":1},{"id":"GO:0071347","count":1},{"id":"GO:0045947","count":1},{"id":"GO:0000288","count":1},{"id":"GO:0002091","count":1}]},{"hash":"743686159369776318","title":"Nucleic Acid Metabolism and Stress Response","description":"The terms cluster around nucleic acid processing and regulation (DNA recombination, RNA hydrolysis, DNA demethylation, mRNA stability) together with cellular stress responses (xenobiotic exposure, oxidative stress, peptide hormone signaling), suggesting a group of proteins involved in genome maintenance and rapid stress adaptation.","confidence":"Medium","size":17,"edges":4,"triangles":0,"max_degree":3,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":9},{"id":"GO:0090502","count":8},{"id":"GO:0080111","count":6},{"id":"GO:0014912","count":6},{"id":"GO:0042493","count":6}]},{"hash":"1457061239735044657","title":"Membrane transport and secretion","description":"The top GO terms are dominated by transport activities for amino acids, taurine, vitamins, carbohydrates, and molybdate, plus secretion-related terms (peptide pheromone export, oligopeptide export, type I secretion). While translation initiation terms appear, the central, recurring theme across the cluster is membrane transport and secretion processes, so a concise label is \"Membrane transport and secretion.\" ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0001731","count":5},{"id":"GO:0002188","count":5},{"id":"GO:0090374","count":4},{"id":"GO:0030253","count":4},{"id":"GO:0015803","count":4}]},{"hash":"564024155799790785","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048568","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0000472","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0000462","count":3}]},{"hash":"1039482989564870146","title":"Membrane Organization and Stress-Induced Cell Cycle Regulation","description":"The GO profile shows strong signals for plasma membrane organization together with cellular responses to heat and osmotic stress, plus negative regulation of G2/M transition. This combination suggests proteins that coordinate membrane dynamics with stress-responsive control of mitosis, justifying a label that links membrane organization to stress-driven cell cycle regulation.","confidence":"High","size":17,"edges":14,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0007009","count":16},{"id":"GO:0010972","count":16},{"id":"GO:0034605","count":16},{"id":"GO:0071470","count":16}]},{"hash":"44714392637347014","title":"Thermoception and nociception signaling","description":"The top GO terms cluster around temperature sensing (thermoception, response to cold) and pain response, with a clue from response to capsazepine indicating TRP-channel\u2013mediated sensing. Calcium ion import supports calcium signaling in sensory neurons, which fits thermoception and nociception. Some terms address vascular or metabolic processes, but the dominant theme appears to be temperature/pain perception with related signal transduction.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050955","count":2},{"id":"GO:1901594","count":2},{"id":"GO:0098907","count":2},{"id":"GO:1903444","count":2},{"id":"GO:0098703","count":2}]},{"hash":"2000425887180640918","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning intracellular signaling, GPCR-related pathways, cell shape regulation, renal system process, telomere maintenance, pinocytosis, NOD1 signaling, thermoception, and responses to capsazepine; there is no single coherent function tying all members together, so a confident, specific label cannot be defined.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0008360","count":2},{"id":"GO:0003014","count":1},{"id":"GO:0032212","count":1}]},{"hash":"1618036337267019076","title":"Nuclear RNA Surveillance and Decay","description":"The cluster is driven by GO terms related to nuclear RNA processing, surveillance, and decay, including nuclear mRNA surveillance (and its export), nonfunctional rRNA decay, RNA phosphodiester bond hydrolysis, CUT catabolic processes, and miRNA decay. While a couple terms touch cell cycle or telomere regulation, the dominant theme is nuclear RNA quality control and degradation pathways, justifying a concise label focused on RNA surveillance and decay.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":2},{"id":"GO:0070651","count":2},{"id":"GO:0051306","count":1},{"id":"GO:0071032","count":1},{"id":"GO:1904354","count":1}]},{"hash":"1290269082002755642","title":"Phosphate Homeostasis and Starvation Response","description":"This cluster centers on GO terms related to phosphate ion transport, cellular response to phosphate starvation, and intracellular phosphate homeostasis, with additional links to regulation of phosphate transport and vacuolar/autophagic processes. The dominant signal is phosphate metabolism and the cellular response to phosphate availability, suggesting a cohesive module around phosphate uptake, regulation, and homeostasis, with secondary connections to vacuolar functions. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046475","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0042144","count":1},{"id":"GO:0035435","count":1},{"id":"GO:0080040","count":1}]},{"hash":"800365066296029059","title":"MAPK Signaling in Growth Factor Response and Cell Cycle","description":"The top GO terms point to MAPK signaling cascades (p38 and ERK1/ERK2) triggered by growth factor stimuli (GM-CSF, PMA) and linked processes like cell cycle and cell migration, suggesting a cluster of proteins operating in MAPK-driven responses to growth signals and proliferation. Some telomere maintenance terms appear as secondary associations but do not define the primary theme.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097011","count":3},{"id":"GO:0038066","count":3},{"id":"GO:0070371","count":3},{"id":"GO:1904628","count":3},{"id":"GO:0032212","count":2}]},{"hash":"439823977468653966","title":"Endomembrane trafficking and endosomal transport","description":"This cluster centers on vesicle movement and organization within the endomembrane system, with terms for endosomal transport, endosomal vesicle fusion, Golgi-to-lysosome transport, and endomembrane system organization. Supporting signals include pinocytosis, filopodium assembly (membrane remodeling), and PI5P metabolic processes that regulate trafficking. A few terms reference TGF-beta/SMAD signaling, which can influence receptor trafficking, but the dominant pattern is vesicular transport and endomembrane organization.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016197","count":1},{"id":"GO:0034058","count":1},{"id":"GO:0034141","count":1},{"id":"GO:0048549","count":1},{"id":"GO:0007179","count":1}]},{"hash":"236645049514996592","title":"Immune signaling and inflammation","description":"The top GO terms are dominated by immune-related processes: TLR8 signaling, B cell proliferation in immune response, interferon-beta production, and positive/negative regulation of inflammatory responses, indicating proteins in this cluster mainly participate in immune signaling and inflammatory pathways. There are a few non-immune terms present (acrosomal exocytosis, zygotic axis), but the strongest signal is immune-focused.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008285","count":1},{"id":"GO:0002322","count":1},{"id":"GO:1900155","count":1},{"id":"GO:0035902","count":1},{"id":"GO:0034158","count":1}]},{"hash":"668483403915986478","title":"RNA Silencing and Translation Control","description":"The cluster is dominated by GO terms for RNA-mediated gene silencing (miRNA and regulatory ncRNA\u2013mediated) and for translation initiation complex assembly, pointing to a cohesive theme of post-transcriptional gene regulation. The presence of translation-related and RNA-processing terms, along with growth-related signaling (Hippo) and cell morphogenesis, suggests these proteins participate in tuning gene expression at the RNA level and influencing cell fate, growth, or stress responses. ","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035278","count":2},{"id":"GO:0035329","count":2},{"id":"GO:0000902","count":2},{"id":"GO:0070059","count":2},{"id":"GO:0031047","count":1}]},{"hash":"2041247925807702334","title":"Insect NF-kappaB\u2013mediated immune and molting signaling","description":"This cluster centers on NF-kappaB activation and inflammatory cytokine responses (NF-kappaB-inducing kinase activity; IL-1, IL-6, IL-8 related terms) alongside developmental processes tied to chitin-based cuticle and ecdysis, suggesting a coherent theme of immune signaling integrated with insect molt/cuticle development. The presence of apoptotic processes further supports dynamic tissue remodeling during development and immune responses.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007250","count":2},{"id":"GO:0071347","count":1},{"id":"GO:0009612","count":1},{"id":"GO:0000272","count":1},{"id":"GO:0040003","count":1}]},{"hash":"1397604929555789128","title":"Unknown","description":"The top GO terms span telomere maintenance, endocytosis, innate immune signaling, heat/stress responses, transcriptional regulation, cell cycle, synaptic localization, chromosomal telomere localization, and calcium signaling. There isn\u2019t a clear, cohesive functional theme that ties these together into a single interpretable cluster label.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":3},{"id":"GO:0048549","count":3},{"id":"GO:0070427","count":3},{"id":"GO:0050955","count":3},{"id":"GO:1901594","count":3}]},{"hash":"1331238076453004031","title":"Cell stress and apoptosis signaling","description":"This cluster's top GO terms are dominated by apoptotic processes in hepatocytes and myeloid cells, plus cell cycle and telomere maintenance signals. Additional terms touch on epithelial polarity, endocytosis, immune signaling (NOD1), and sensory/chemical response (thermoception and capsazepine), suggesting a broad cellular stress and death signaling program rather than a single pathway. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097284","count":5},{"id":"GO:0090162","count":5},{"id":"GO:0033028","count":5},{"id":"GO:2000171","count":5},{"id":"GO:0007049","count":4}]},{"hash":"2118920013484536640","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":2},{"id":"GO:0033260","count":1},{"id":"GO:0006398","count":1},{"id":"GO:0036089","count":1},{"id":"GO:0048015","count":1}]},{"hash":"2196083574956349191","title":"Neuronal Signaling and Dendrite Growth","description":"The terms point to neuronal communication and morphology: phosphatidylinositol signaling and inositol trisphosphate biosynthesis suggest lipid-mediated signaling; synaptic vesicle maturation and presynapse-to-nucleus signaling indicate synaptic function; and positive regulation of dendrite extension plus regulation of GTPase activity hint at neurite outgrowth and cytoskeletal dynamics. While a few terms touch on other contexts (e.g., B cell signaling), the dominant theme is signaling in neurons and dendritic development, justifying this label.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048015","count":1},{"id":"GO:0016188","count":1},{"id":"GO:0050861","count":1},{"id":"GO:0099526","count":1},{"id":"GO:2000203","count":1}]},{"hash":"337867329928910725","title":"Unknown","description":"The Top Terms are a highly heterogeneous mix, including obsolete ubiquitin-dependent ERAD, chromatin organization and histone modification, chromosome segregation, mRNA splicing, phagolysosome assembly, and growth hormone\u2013related signaling. With no clear common function linking most proteins (and no interactions observed), it is not possible to assign a coherent, representative label beyond Unknown.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0000747","count":1},{"id":"GO:0050679","count":1},{"id":"GO:1902510","count":1},{"id":"GO:0001845","count":1}]},{"hash":"1113230837992136970","title":"Unknown","description":"The GO terms are highly diverse, spanning immune signaling (T cell receptor signaling), growth and cycle control (Hippo signaling, CDK regulation), metabolism (fatty acid oxidation), apoptosis, differentiation (keratinocytes), stress responses, and kinetochore localization. There isn\u2019t a single coherent function tying these 16 proteins together, so no clear cluster theme emerges.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050852","count":4},{"id":"GO:0071375","count":4},{"id":"GO:0035329","count":4},{"id":"GO:0045736","count":4},{"id":"GO:0019395","count":4}]},{"hash":"1961560360526574202","title":"Nuclear RNA Processing and Transcription Regulation","description":"This cluster is dominated by GO terms tied to RNA maturation and processing in the nucleus (tRNA processing, spliceosome assembly, mRNA splicing, deadenylation-dependent decapping, histone mRNA metabolism) as well as nuclear import and transcriptional control (negative regulation of RNA polymerase II transcription). The convergence on RNA processing and transcription-related processes, plus a few stress-response terms (ABA and water deprivation), suggests a cohesive module centered on nuclear RNA metabolism and gene expression regulation in a plant context.","confidence":"High","size":16,"edges":119,"triangles":546,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":4},{"id":"GO:0070317","count":4},{"id":"GO:0000122","count":3},{"id":"GO:0051170","count":3},{"id":"GO:0009737","count":3}]},{"hash":"2235609120900613847","title":"Ribosome Biogenesis and Translation Machinery","description":"The top GO terms congregate around translation, ribosome biogenesis, tRNA aminoacylation, rRNA modification, and translational fidelity, which together point to proteins involved in assembling ribosomes and driving protein synthesis. The presence of transcription-related terms likely reflects co-regulated or adjacent pathways, but the dominant signals are ribosome assembly and the translation apparatus, including stress-related regulation of translation. This supports a cohesive label centered on the ribosome/translation machinery.","confidence":"High","size":16,"edges":16,"triangles":1,"max_degree":15,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0000455","count":2},{"id":"GO:0006437","count":2}]},{"hash":"1955521922267408361","title":"Ribosome Biogenesis and Preribosome Assembly","description":"The top GO terms cluster around ribosome production and maturation, including ribosome biogenesis, maturation of LSU-rRNA, assembly of large subunit preribosome, and cytosolic ribosome assembly, indicating a coherent theme of ribosome assembly and rRNA processing. A few terms such as chromatin organization and collagen catabolic process appear as secondary associations, likely due to multifunctional proteins or annotation noise, but the dominant signal points to ribosome-related functions.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0000463","count":2},{"id":"GO:1902626","count":2},{"id":"GO:0034396","count":2},{"id":"GO:0034724","count":2}]},{"hash":"1985820510024266634","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":30,"triangles":20,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0098789","count":1},{"id":"GO:0006378","count":1},{"id":"GO:0006398","count":1},{"id":"GO:0007021","count":1},{"id":"GO:0071629","count":1}]},{"hash":"1133573912816945963","title":"Cell cycle control and centrosome dynamics","description":"The top terms are dominated by DNA replication, centrosome cycle and centrosome separation, and transcription/nuclear transport processes, pointing to cell cycle regulation and centrosome dynamics as the core function. Immune signaling and development terms appear as secondary associations rather than defining the cluster. ","confidence":"High","size":16,"edges":36,"triangles":20,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010571","count":13},{"id":"GO:0048701","count":13},{"id":"GO:0006260","count":13},{"id":"GO:0007098","count":13},{"id":"GO:0050852","count":12}]},{"hash":"2298731222603743919","title":"Mitotic spindle and microtubule dynamics","description":"The cluster is dominated by mitotic spindle and microtubule-related processes (spindle assembly, centrosome separation, spindle elongation, spindle orientation, and cytokinesis). A few terms relate to stress granules, chloroplast movement, and neuronal structure, but these appear peripheral to the core mitotic/cytoskeletal theme. Overall, it represents mitosis and microtubule dynamics.","confidence":"High","size":16,"edges":74,"triangles":178,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":10},{"id":"GO:0035617","count":10},{"id":"GO:0007100","count":10},{"id":"GO:1990942","count":9},{"id":"GO:0021693","count":9}]},{"hash":"2068137394400457542","title":"RNA and Protein Methylation and Signaling","description":"Top GO terms are dominated by methylation-related processes: RNA guanine-N7 methylation, rRNA modification, and protein methylation, indicating a module centered on RNA and protein modification. Additional terms touch on transcription regulation and signaling pathways (phosphatidylinositol signaling, calcium detection), with some development-associated terms that are less central. Overall, the cluster appears to reflect a methylation- and signaling-centered regulatory program rather than a single tissue- or organ-specific function.","confidence":"Medium","size":16,"edges":119,"triangles":546,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":2},{"id":"GO:0006479","count":2},{"id":"GO:0035774","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0000154","count":2}]},{"hash":"1787233696489963252","title":"Development and immune signaling pathways","description":"The cluster features GO terms centered on signaling pathways (MAPK/ERK, JNK, ephrin receptor signaling, Hippo signaling) together with development-related terms (hippocampus development, axonogenesis) and immune signaling (T cell receptor signaling, mast cell degranulation). This suggests a cohesive theme around signal transduction coordinating development and immune responses across tissues, despite including mitotic cell cycle as a less central term.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":11},{"id":"GO:0070374","count":10},{"id":"GO:0050852","count":10},{"id":"GO:0046330","count":10},{"id":"GO:0021766","count":10}]},{"hash":"2246371068262917160","title":"Mitotic Regulation and Immune Signaling","description":"This cluster centers on regulators of the cell cycle (G2/M transition, mitotic cell cycle) and signaling control (negative regulation of protein kinase activity, NF-kappaB signaling, Fc-epsilon receptor signaling), with support from ubiquitin-proteasome turnover pathways and calcium signaling. While there are some muscle differentiation terms, the strongest and most cohesive theme is coordinated control of mitosis and signaling pathways plus protein turnover. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006469","count":3},{"id":"GO:0043123","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0038095","count":3},{"id":"GO:0000086","count":3}]},{"hash":"349135743818717698","title":"ECM Formation and Tissue Development","description":"This cluster is dominated by GO terms tied to extracellular matrix production and tissue morphogenesis, including collagen biosynthetic process, cartilage development, cuticle development, and cell adhesion. These core terms point to ECM assembly and structural tissue development as the unifying theme for the proteins. Some additional terms related to immune regulation (complement activation, lymphangiogenesis, foam cell differentiation) may be secondary or context-dependent, but do not override the ECM/tissue-development signal. Confidence: Medium","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901492","count":1},{"id":"GO:0045715","count":1},{"id":"GO:1903225","count":1},{"id":"GO:0010743","count":1},{"id":"GO:2000534","count":1}]},{"hash":"811664119317156639","title":"DNA Damage Response and Mitotic Spindle Assembly","description":"This cluster combines terms tied to genome integrity maintenance (DNA repair, DNA damage checkpoint signaling, response to ionizing radiation, apoptotic signaling in response to DNA damage) with terms tied to microtubule organization and spindle formation (mitotic spindle assembly, gamma-tubulin complex localization, spindle pole body/centrosome nucleation). The co-occurrence suggests a coordinated link between DNA damage signaling and mitotic spindle dynamics during cell division.","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042386","count":1},{"id":"GO:0090307","count":1},{"id":"GO:0051417","count":1},{"id":"GO:0051415","count":1},{"id":"GO:0033566","count":1}]},{"hash":"1092682840866442710","title":"Endosomal trafficking and receptor signaling","description":"This cluster centers on endomembrane transport activities (endosomal transport, vesicle fusion, Golgi to lysosome traffic) and endomembrane system organization, with supporting themes in pinocytosis and PI5P metabolism, plus TGF-\u03b2 receptor signaling and SMAD-related assembly. The combination suggests a cohesive module of vesicle trafficking linked to receptor-mediated signaling rather than unrelated processes.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016197","count":1},{"id":"GO:0034058","count":1},{"id":"GO:0034141","count":1},{"id":"GO:0048549","count":1},{"id":"GO:0007179","count":1}]},{"hash":"587191415421558021","title":"One-Carbon Metabolism and Methylation","description":"GO terms show a focus on methylation (protein methylation; methylation) and vitamin biosynthetic processes\u2014cobalamin (B12), thiamine (B1), and tetrahydrofolate (THF)\u2014which are linked by one-carbon metabolism. The inclusion of rDNA heterochromatin formation aligns with methylation-dependent chromatin regulation, while the response to xenobiotic stimulus suggests broader stress-related regulation. The lignin biosynthetic process stands out as plant-specific and may reflect annotation noise or multifunctionality. Overall, the cluster seems to represent enzymes and regulators tied to methylation-linked metabolism rather than a single well-defined pathway.","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":3},{"id":"GO:0042135","count":2},{"id":"GO:0032259","count":2},{"id":"GO:0000183","count":2},{"id":"GO:0009228","count":2}]},{"hash":"1248950671827456606","title":"Unknown","description":"The top GO terms span diverse processes\u2014from immune signaling (T cell regulation, IL-2) to growth factor responses (EGF, FGF) and even development (mesendoderm, chorio-allantoic fusion). There isn\u2019t a clear, single function tying all 16 proteins together, and the low frequencies with no edges suggest the cluster does not have a cohesive theme. Therefore, Unknown with None.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071385","count":1},{"id":"GO:0045085","count":1},{"id":"GO:0045647","count":1},{"id":"GO:0060710","count":1},{"id":"GO:0044344","count":1}]},{"hash":"796182653177824326","title":"Unknown","description":"These proteins associate with a highly heterogeneous set of GO terms, spanning kidney development, tooth dentin formation, bone resorption, steroid hormone response, and multiple transport and intracellular processes (ER-to-Golgi trafficking, chloride transport, CO2 transport) as well as chromatin remodeling. There is no single, common biological process tying them together, so a meaningful, specific label cannot be assigned beyond Unknown.","confidence":"","size":16,"edges":9,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0001822","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0006348","count":2},{"id":"GO:0048545","count":1},{"id":"GO:0042475","count":1}]},{"hash":"2112040112604787826","title":"RNA processing and post-transcriptional regulation","description":"The top GO terms cluster around mRNA processing events (polyadenylation, splicing via the spliceosome) and post-transcriptional regulation (ncRNA-mediated gene silencing), with hints of translation-related assembly (eIF4F complex). This suggests a cohesive theme of RNA maturation and translation control, despite several obsolete annotations. The set appears to reflect proteins involved in RNA processing and its regulatory pathways rather than a single canonical pathway.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":4},{"id":"GO:1901407","count":4},{"id":"GO:0031047","count":3},{"id":"GO:0048026","count":3},{"id":"GO:1902625","count":3}]},{"hash":"1336502135618584523","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000464","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0045944","count":1},{"id":"GO:0006260","count":1}]},{"hash":"949698347682984905","title":"Unknown","description":"The top GO terms are highly diverse, including telomere maintenance, pinocytosis, NOD1 signaling, thermoception, responses to a chemical modulator, heat stress transcription, synaptic plasticity regulation, telomeric chromosome localization, calcium release, and epithelial polarity. With no edges or connectivity (edges 0, triangles 0, max degree 0), there isn\u2019t a unifying biological theme tying these proteins together. This appears to be a noisy or heterogeneous set rather than a coherent functional cluster. ","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":1},{"id":"GO:0048549","count":1},{"id":"GO:0070427","count":1},{"id":"GO:0050955","count":1},{"id":"GO:1901594","count":1}]},{"hash":"1224115914287109468","title":"Calcium signaling and neural development","description":"The top GO terms cluster around calcium-related signaling (detection of calcium ion; regulation of calcineurin-NFAT signaling; calcium-release channel activity) and neural/sensory development (retina layer formation; short-term memory), suggesting these proteins participate in calcium-dependent signaling influencing neural and sensory functions. Although there are some tissue-specific development terms (kidney development) and structural assembly terms (terminal web), the dominant theme is calcium signaling coupled to neural development and memory-related pathways. Confidence: Medium","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0005513","count":5},{"id":"GO:0072221","count":5},{"id":"GO:0060316","count":5},{"id":"GO:0008218","count":5},{"id":"GO:0051531","count":5}]},{"hash":"1268485325820161231","title":"Rho GTPase-mediated cytoskeletal dynamics","description":"It is driven by actin cytoskeleton remodeling\u2014filopodium assembly, Rho/small GTPase signaling, and regulation of cell spreading\u2014along with related membrane trafficking terms, making this a cohesive label for the cluster.","confidence":"Medium","size":16,"edges":28,"triangles":13,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000266","count":6},{"id":"GO:0051489","count":6},{"id":"GO:0045792","count":6},{"id":"GO:0051932","count":6},{"id":"GO:1900026","count":6}]},{"hash":"1190597985048939430","title":"Diverse carbon-source catabolism","description":"This cluster aggregates proteins involved in a range of catabolic processes across several carbon substrates, including glucose, galactose, xylitol, and fatty acids, as well as amino acid-to-alcohol pathways and related oxidation steps, with additional signals related to lipopolysaccharide response and respiration. The common thread is broad, energy-generating metabolism from diverse carbon sources rather than a single, cohesive pathway, so the label reflects a general metabolic theme rather than a specific pathway. ","confidence":"Medium","size":16,"edges":83,"triangles":218,"max_degree":14,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0032496","count":9},{"id":"GO:0009809","count":8},{"id":"GO:0006069","count":8},{"id":"GO:0019595","count":8},{"id":"GO:0010430","count":8}]},{"hash":"2125809285299463608","title":"Central metabolism and cofactor biosynthesis","description":"Proteins in this cluster are enriched for glycolysis, the TCA cycle, glyoxylate cycling, L-alanine catabolism, and biosynthetic pathways for quinolinate (NAD) and thiamine, along with Fe-S cluster assembly and iron incorporation. This points to a cohesive module of energy production and cofactor biosynthesis, with Notch signaling appearing as a minor annotation. ","confidence":"High","size":16,"edges":50,"triangles":65,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":5},{"id":"GO:0042853","count":4},{"id":"GO:0019805","count":4},{"id":"GO:0006096","count":4},{"id":"GO:0018283","count":3}]},{"hash":"1662608746933568509","title":"Synapse Localization and Dendritic Spine Morphogenesis","description":"The GO terms are dominated by neuronal synapse-related processes: protein localization to the synapse, dendritic spine morphogenesis, and receptor clustering, with Rho signaling reinforcing actin remodeling in spine formation; together these point to neuronal synapse organization and spine development as the core function of this cluster, despite a couple of more general or peripheral terms.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008285","count":2},{"id":"GO:0035418","count":2},{"id":"GO:0007266","count":2},{"id":"GO:0060997","count":2},{"id":"GO:0043113","count":2}]},{"hash":"2131627476226511545","title":"Ribosome Biogenesis and Cell Division","description":"The cluster is driven by ribosome-related terms (small and large subunit biogenesis/export, tRNA modification) and core cell-cycle/division terms (cell cycle, cell division, cell septum assembly), suggesting proteins linked to assembling the translation machinery and coordinating cytokinesis. A Hedgehog-related term appears less connected, but the dominant theme supports translation apparatus construction coupled with division processes.","confidence":"High","size":16,"edges":2,"triangles":0,"max_degree":1,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0007049","count":6},{"id":"GO:0000055","count":6},{"id":"GO:0051301","count":6},{"id":"GO:0000747","count":5},{"id":"GO:0006400","count":5}]},{"hash":"1412008526723602296","title":"Stress-Induced Apoptosis Regulation","description":"The top terms feature negative regulation of mitochondrial membrane potential and intrinsic apoptotic signaling in response to oxidative stress, pointing to apoptosis control under cellular stress. While other terms reference ER-Golgi transport, ubiquitination, and transcription, the strongest common theme is stress-related regulation of apoptosis, so a label focusing on this function is appropriate.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010917","count":1},{"id":"GO:0002037","count":1},{"id":"GO:0008631","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0019089","count":1}]},{"hash":"1567417428416803848","title":"Retrovirus replication and proviral integration","description":"The set of GO terms centers on reverse transcription (RNA-templated DNA synthesis), DNA replication and recombination, DNA integration, and establishment of integrated proviral latency, plus viral entry into the host nucleus. These are hallmark steps of the retroviral life cycle and provirus formation. Some terms about host-symbiont interactions and siRNA processing may reflect broader host\u2013pathogen interactions present in the data, but the dominant signal clearly points to retroviral replication and genome integration.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006278","count":14},{"id":"GO:0006260","count":14},{"id":"GO:0039651","count":14},{"id":"GO:0015074","count":14},{"id":"GO:0075713","count":14}]},{"hash":"2250878285270518226","title":"Spliceosome-Mediated mRNA Splicing Regulation","description":"The top GO terms are dominated by mRNA splicing and spliceosome-related processes (positive and negative regulation, cis splicing, splice site recognition), indicating a cohesive role in RNA processing through the spliceosome. A translation initiation term is present but ancillary. Overall, the cluster centers on splicing regulation via the spliceosome and related RNA processing pathways.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":3},{"id":"GO:0048026","count":2},{"id":"GO:1902625","count":2},{"id":"GO:0075525","count":2},{"id":"GO:1905663","count":2}]},{"hash":"175158381490355552","title":"Autophagy and selective organelle turnover","description":"The top GO terms point to autophagy and its cargo-specific variants, including autophagosome assembly, mitophagy, glycophagy, CVT pathway\u2013mediated cytoplasm-to-vacuole targeting, and microautophagy of the nucleus. This pattern suggests the proteins collectively participate in autophagic degradation and selective organelle turnover, justifying a concise label centered on autophagy.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044805","count":1},{"id":"GO:0006612","count":1},{"id":"GO:0050765","count":1},{"id":"GO:0000045","count":1},{"id":"GO:0032258","count":1}]},{"hash":"674687941950248603","title":"Unknown","description":"The terms span neural behavior, transcription control, immune function, and metabolic processes with no clear shared pathway, so there isn't a single coherent theme to label the cluster.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048149","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0042420","count":1},{"id":"GO:0003081","count":1}]},{"hash":"2188169164926164731","title":"Metabolic Biosynthesis and Detoxification","description":"The proteins span a range of metabolic processes, including biosynthesis (antibiotic, menaquinone, biotin) and pigment/compound turnover (chlorophyll catabolic), along with detoxification and processing of toxic compounds (response to toxic substance, cellular oxidant detoxification, catabolic degradation of xenobiotics like 1,2-dichloroethane). This mix points to a broad theme of metabolite production and breakdown/detoxification rather than a single specific pathway, so a label capturing both biosynthesis and detoxification is appropriate.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":6},{"id":"GO:0055114","count":5},{"id":"GO:0009636","count":5},{"id":"GO:0009234","count":5},{"id":"GO:0098869","count":5}]},{"hash":"38744482884199321","title":"Unknown","description":"No GO terms or functional themes are reported for this cluster (Edges: 0, Max Degree: 0, Triangles: 0). With no shared terms to tie the proteins together, and only 16 protein IDs with some re-added by ReCIPE, a consistent function cannot be inferred.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"573806806092954686","title":"Proviral DNA Integration and Host Entry Pathways","description":"The top GO terms center on genome integration and related DNA processes (DNA replication, recombination, RNA-templated DNA biosynthesis, proviral latency) alongside host-symbiont interaction processes (symbiont entry and apoptosis activation) and cytoskeletal/trafficking activities (lamellipodium assembly, ER-to-Golgi transport). This combination suggests a cluster focused on proviral genome integration and the cellular pathways enabling host entry and subsequent interactions, rather than a single isolated function.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0030032","count":2},{"id":"GO:0006278","count":1},{"id":"GO:0006260","count":1}]},{"hash":"613961198292825410","title":"Chromatin Organization and Cell Cycle Regulation","description":"The top GO terms point to nuclear processes: chromatin organization, histone modification, and chromosome segregation, with supporting signals from mRNA branch site recognition. These suggest a coherent theme of chromatin remodeling and cell division regulation. A few terms (e.g., phagolysosome assembly, growth hormone response) appear less directly related and may reflect pleiotropy or annotation noise, but the dominant pattern supports a chromatin- and mitosis-centered cluster.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051260","count":4},{"id":"GO:0000747","count":3},{"id":"GO:0050679","count":3},{"id":"GO:1902510","count":3},{"id":"GO:0001845","count":3}]},{"hash":"188421889284934309","title":"Unknown","description":"The top GO terms span a wide range of processes from heart rhythm-electrophysiology (regulation of SA node action potential) and GPCR signaling to endocytosis, GTPase regulation, telomere maintenance, innate immune signaling (NOD1), temperature sensation (thermoception) and cell cycle. This diversity suggests no singular, cohesive functional theme for the cluster, so a unique, representative label cannot be confidently assigned.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098907","count":5},{"id":"GO:0007205","count":5},{"id":"GO:0048549","count":4},{"id":"GO:0043547","count":3},{"id":"GO:0032212","count":3}]},{"hash":"2009715163951340865","title":"Unknown","description":"The terms cover several unrelated processes (cell cycle and ubiquitination; a GPCR signaling pathway; telomere maintenance; endocytosis; immune signaling via NOD1; thermoception and heat-stress transcription; synaptic plasticity). There's no single, dominant function tying the proteins together, so I label this cluster Unknown.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":4},{"id":"GO:0016567","count":4},{"id":"GO:0007205","count":4},{"id":"GO:0032212","count":3},{"id":"GO:0048549","count":3}]},{"hash":"1542671333108549803","title":"Ubiquitin\u2013Proteasome Degradation","description":"The top GO terms are dominated by ubiquitin-dependent protein catabolic processes, including SCF-dependent proteasomal degradation and protein polyubiquitination, indicating a cluster enriched for components of the ubiquitin-proteasome system and related ERAD turnover. Some other terms relate to stress responses and cell cycle regulation, but the central theme remains proteostasis via ubiquitin tagging and proteasomal degradation.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":9},{"id":"GO:0031146","count":8},{"id":"GO:0000209","count":6},{"id":"GO:0000083","count":6},{"id":"GO:0030433","count":6}]},{"hash":"2086398427552470663","title":"Unknown","description":"The top GO terms cover prostate development, male differentiation, interferon response, steroid receptor complex assembly, and several disparate metabolic processes (lignin biosynthesis, fatty acid omega-oxidation, glucose catabolism, retinoic acid metabolism, Ehrlich pathway). This mix spans plants and animals and lacks a unifying theme or shared function for the cluster, so a coherent label cannot be assigned beyond Unknown.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030850","count":1},{"id":"GO:0046661","count":1},{"id":"GO:0071357","count":1},{"id":"GO:0006463","count":1},{"id":"GO:0009809","count":1}]},{"hash":"53379433552730943","title":"Kidney metanephric development and tubule morphogenesis","description":"Primarily driven by metanephric and tubule development terms (distal tubule, collecting duct, duct development, kidney development), indicating a cohesive cluster of proteins involved in kidney morphogenesis. A few terms for other organ morphogenesis appear but kidney-related terms dominate.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072287","count":2},{"id":"GO:0060428","count":2},{"id":"GO:0031659","count":2},{"id":"GO:0072177","count":2},{"id":"GO:0036303","count":2}]},{"hash":"2141044360403959638","title":"Developmental transcriptional regulation","description":"These proteins show GO terms spanning multiple tissue developmental processes (myotube development, cerebellar cortex development, uterine gland development, hepatocyte homeostasis) and broad transcriptional control (DNA-templated transcription, RNA polymerase II transcription). The combination suggests a cluster involved in coordinating gene expression programs during development and differentiation, with some epigenetic regulation context via histone acetylation terms (even though some are obsolete). ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014904","count":1},{"id":"GO:2000134","count":1},{"id":"GO:0045944","count":1},{"id":"GO:2000616","count":1},{"id":"GO:0021695","count":1}]},{"hash":"878555970987925871","title":"Unknown","description":"The top GO terms span both nuclear processes (mRNA processing, spindle assembly, telomere maintenance) and cytoskeletal/cell behavior processes (actin bundle assembly, cell migration, response to muscle stretch) plus signaling and proteasome-related terms. With no edges or cohesive unifying function, there isn\u2019t a single clear theme tying these proteins together, so a precise label isn\u2019t justifiable.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":3},{"id":"GO:0032212","count":3},{"id":"GO:0051017","count":2},{"id":"GO:0090501","count":2},{"id":"GO:0051225","count":2}]},{"hash":"792682741457996202","title":"Proteoglycan Biosynthesis and Glycosaminoglycan Metabolism","description":"The top GO terms are dominated by dermatan sulfate and heparan sulfate proteoglycan biosynthetic/metabolic processes (and related sulfated glycosaminoglycans like chondroitin sulfate), plus polysaccharide localization. This points to a cohesive theme of extracellular matrix proteoglycan assembly and glycosaminoglycan metabolism, with developmental terms like chondrocyte development and ureteric bud formation supporting the ECM/developmental context. Overall, the cluster seems to group proteins involved in proteoglycan biosynthesis and ECM glycosaminoglycan pathways.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030208","count":2},{"id":"GO:0060676","count":2},{"id":"GO:0015014","count":2},{"id":"GO:0050655","count":2},{"id":"GO:0030206","count":2}]},{"hash":"937899946105564343","title":"Renin-Angiotensin and Ciliary Kidney Signaling","description":"The GO terms point to kidney-focused regulation of fluid balance and blood pressure (renin secretion, regulation of renal output by angiotensin) and to ciliary-related signaling (cilium assembly and smoothened signaling), which is linked to Hedgehog pathways mediated by primary cilia. This suggests a coherent module where renin-angiotensin system activity intersects with ciliary signaling in kidney function.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002001","count":1},{"id":"GO:0007224","count":1},{"id":"GO:0002035","count":1},{"id":"GO:0060271","count":1},{"id":"GO:0051220","count":1}]},{"hash":"550657620561656966","title":"Meiosis-linked RNA modification and translation","description":"The cluster's GO terms center on RNA modifications (rRNA/tRNA methylation) and translation, along with meiotic processes such as chromosome condensation and spermatid differentiation, suggesting a theme of RNA-based regulation of protein synthesis during meiosis; antibiotic-related terms appear incidental.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0036265","count":1},{"id":"GO:0000154","count":1},{"id":"GO:0017000","count":1},{"id":"GO:0006400","count":1}]},{"hash":"530182550825518056","title":"Wnt Signaling and Developmental Patterning","description":"The proteins in this cluster are enriched for GO terms centered on the Wnt signaling pathway and its regulation, including neural tube patterning and negative regulation of canonical Wnt signaling, which suggests a shared role in Wnt-mediated developmental processes. Some other terms appear ancillary (e.g., transcription, cell wall organization), but the dominant theme points to Wnt signaling and related development.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016055","count":3},{"id":"GO:0006470","count":2},{"id":"GO:0007205","count":2},{"id":"GO:1990697","count":2},{"id":"GO:0006507","count":2}]},{"hash":"260320184723086751","title":"Unknown","description":"This cluster has no shared GO terms or network connections (edges/triangles are zero) to suggest a common function. The only hint is that 4 proteins were re-added by RECIPE with degree 0.75, but without functional terms or interactions to tie the proteins together, there is no basis to assign a meaningful label. Therefore, Unknown with no confidence.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"109199018678170218","title":"DNA Replication and Cell Cycle Regulation","description":"This cluster centers on core genome maintenance and mitotic control, with strong terms for DNA replication, double-strand break repair via NHEJ, G1/S transition, and kinetochore localization. Calcium/NFAT signaling and glucocorticoid signaling appear as supporting regulatory layers, suggesting coordinated cellular signaling with genome maintenance.","confidence":"High","size":15,"edges":86,"triangles":298,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:2000324","count":13},{"id":"GO:0006260","count":13},{"id":"GO:0005513","count":13},{"id":"GO:0001915","count":13},{"id":"GO:0060316","count":13}]},{"hash":"1836802546056851277","title":"Cell cycle control and signaling","description":"Its top terms center on mitosis and cell cycle regulation (kinetochore localization, CDK activity inhibition, DNA-templated transcription, cell cycle). Other terms point to diverse signaling pathways (T cell receptor signaling, insulin signaling, GM-CSF response, vascular permeability) and transcriptional control. Taken together, the cluster likely represents proteins involved in cell cycle control with broader signaling roles.","confidence":"Medium","size":15,"edges":30,"triangles":21,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0034501","count":8},{"id":"GO:0045736","count":8},{"id":"GO:0006351","count":7},{"id":"GO:0050852","count":6},{"id":"GO:0043117","count":6}]},{"hash":"68941578627581369","title":"Unknown","description":"The GO terms are very diverse (carbon utilization, CO2 response, stomatal development, calcium signaling, transcription regulation, bioluminescence, and even kidney development), with no clear, single biological function uniting the cluster. Because there isn\u2019t a cohesive theme across the terms, a specific, representative label isn\u2019t apparent. Therefore, Unknown with None confidence is most appropriate.","confidence":"","size":15,"edges":99,"triangles":381,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0015976","count":1},{"id":"GO:2000122","count":1},{"id":"GO:0071244","count":1},{"id":"GO:0048015","count":1},{"id":"GO:0045944","count":1}]},{"hash":"176591559515036472","title":"Meiosis and mitotic spindle regulation","description":"The top GO terms cluster around meiotic spindle organization, meiotic spindle assembly checkpoint signaling, and the G1/S transition of the mitotic cell cycle, plus cell surface receptor serine/threonine kinase signaling. Together these point to a core function in cell cycle control and spindle dynamics across meiosis and mitosis. Some other terms (virus response, autophagy-related regulation) appear as peripheral signals but do not define the main module. ","confidence":"High","size":15,"edges":9,"triangles":1,"max_degree":5,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0016242","count":6},{"id":"GO:2000727","count":6},{"id":"GO:0010765","count":6},{"id":"GO:0000082","count":6},{"id":"GO:0000212","count":6}]},{"hash":"1216548278778368826","title":"Multitissue Development","description":"The top GO terms point to development across diverse tissues (heart, neural/glial, and sensory systems), suggesting proteins involved in broad differentiation and organogenesis rather than a single pathway. Some outliers (abscisic acid signaling, karyogamy) may reflect cross-species annotations or broad regulatory roles, but the overarching theme is cross-tissue development.","confidence":"Medium","size":15,"edges":34,"triangles":30,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0055003","count":7},{"id":"GO:0007507","count":7},{"id":"GO:0009738","count":7},{"id":"GO:0014044","count":7},{"id":"GO:0000278","count":7}]},{"hash":"870960833877660229","title":"mRNA processing and translational control","description":"Most terms center on mRNA maturation (splicing, polyadenylation) and on controlling when and how mRNA is translated (preinitiation complex formation, translational initiation/reinitiation, IRES). The presence of stress response and viral initiation hints extends this to regulation of translation during stress or infection. This supports a label focused on RNA processing with translational regulation.","confidence":"Medium","size":15,"edges":35,"triangles":17,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0075525","count":2},{"id":"GO:0001731","count":2}]},{"hash":"1927106899739381574","title":"Rac GTPase-Mediated Spine Morphogenesis","description":"This cluster is dominated by terms related to Rac and small GTPase signaling, regulation and morphogenesis of dendritic spines, and associated cytoskeletal dynamics (lamellipodium assembly, synaptic vesicle exocytosis). The convergence on Rac/GTPase pathways and spine morphogenesis strongly ties the proteins to cytoskeletal remodeling driving spine growth and synaptic function, supporting a cohesive, high-level function label.","confidence":"High","size":15,"edges":31,"triangles":18,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060999","count":9},{"id":"GO:0045792","count":8},{"id":"GO:0010796","count":8},{"id":"GO:0007264","count":8},{"id":"GO:0031384","count":8}]},{"hash":"93074670821949940","title":"Mitochondrial respiration and translation regulation","description":"The strongest GO signals are mitochondrial respiration and electron transport (aerobic respiration; GO:0009060, GO:1902979), plus mitochondrial electron transport components (GO:1902979), pointing to mitochondrial energy metabolism as the core theme. There are also translation initiation regulation terms (GO:0001731, GO:0006446), suggesting a secondary link to protein synthesis control or potential annotation overlap. The remaining terms are sparse and less cohesive, so the dominant pattern is mitochondrial energy production with a secondary translational regulation signal.","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0050999","count":1},{"id":"GO:0040022","count":1},{"id":"GO:0071171","count":1}]},{"hash":"1346475396286751619","title":"Spliceosome-Mediated mRNA Splicing Regulation","description":"The GO terms are dominated by mRNA splicing via the spliceosome and its regulation (both positive and negative) and splice site recognition, pointing to a cohesive cluster focused on post-transcriptional mRNA processing and splicing control. Additional terms about regulatory ncRNA-mediated gene silencing and translation initiation complex assembly align with broader RNA metabolism, but the core signal is spliceosome-driven splicing regulation.","confidence":"High","size":15,"edges":94,"triangles":336,"max_degree":14,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":8},{"id":"GO:0031047","count":7},{"id":"GO:0048026","count":7},{"id":"GO:1902625","count":7},{"id":"GO:0075525","count":7}]},{"hash":"486185833113185882","title":"Ribosome biogenesis and translation machinery","description":"The dominant GO terms cluster around ribosome biogenesis, large subunit assembly, and cytoplasmic translation, with related processes like SRP-dependent targeting to the membrane, indicating a core theme of ribosome function and protein synthesis. Additional terms reference DNA replication and cell division, suggesting a broader growth/proliferation context, while a couple terms (antibiotic response, proviral latency) may reflect secondary or context-specific signals. Overall, the cluster appears to be driven by ribosome assembly and translation machinery.","confidence":"Medium","size":15,"edges":14,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0075713","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0006260","count":2}]},{"hash":"1559109234801175882","title":"Actin Cytoskeleton Remodeling in Morphogenesis and Division","description":"The top GO terms cluster around actin cytoskeleton dynamics and cell morphology\u2014actin reorganization, regulation of cell shape, contractile ring assembly, centrosome and spindle localization\u2014along with development-related processes (muscle assembly, meiotic events, organ invasion). This points to a cohesive theme of actin-driven remodeling coordinating morphology, movement, and division across development and cell cycles.","confidence":"High","size":15,"edges":55,"triangles":75,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0060292","count":3},{"id":"GO:0006929","count":3},{"id":"GO:2000251","count":3},{"id":"GO:0008360","count":3},{"id":"GO:0055003","count":3}]},{"hash":"92635006886872801","title":"Spliceosome-Mediated mRNA Splicing Regulation","description":"The terms cluster around regulation of mRNA splicing via the spliceosome, cis-splicing through the spliceosome, and splice-site recognition, indicating the proteins function together in RNA processing and splicing regulation (with one term touching translation initiation as a related RNA process). ","confidence":"High","size":15,"edges":75,"triangles":204,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":1},{"id":"GO:0048026","count":1},{"id":"GO:1902625","count":1},{"id":"GO:0075525","count":1},{"id":"GO:1905663","count":1}]},{"hash":"2016351273380826065","title":"Translation Initiation Machinery","description":"This cluster is dominated by GO terms for translation and initiation of translation (translation, formation of cytoplasmic translation initiation complex, translational initiation). The other terms appear infrequently and are likely incidental, so the main theme is initiation of protein synthesis.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0001732","count":1},{"id":"GO:0006413","count":1},{"id":"GO:0048515","count":1},{"id":"GO:0003351","count":1}]},{"hash":"1934055255222502746","title":"Cellular stress response and redox metabolism","description":"The top GO terms point to redox homeostasis, xenobiotic/stress responses, and various metabolic processes (serine biosynthesis, phosphorylation/dephosphorylation, and pollutant catabolism), suggesting the cluster reflects metabolic adjustments under cellular stress rather than a single, tight pathway. Thus the label emphasizes a broad stress-induced metabolic and redox-related function. Some terms are obsolete or broad, so confidence is moderate.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:0046835","count":2},{"id":"GO:0016311","count":2},{"id":"GO:0006564","count":2},{"id":"GO:0006915","count":2}]},{"hash":"1774119779827838112","title":"Kinase signaling regulators of cell proliferation","description":"GO terms here emphasize regulation of kinase activity (positive/negative, autophosphorylation, serine/threonine), GTPase signaling, and processes tied to growth, development, and the cell cycle. This suggests the proteins act as regulators of signaling pathways that govern proliferation and differentiation, with ancillary links to hypoxia response and organismal development. Therefore, labeling the cluster as kinase signaling regulators of cell proliferation captures the shared functional theme.","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008284","count":6},{"id":"GO:0006469","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0098907","count":5},{"id":"GO:0007275","count":5}]},{"hash":"1576969170330952331","title":"Neural development and innate immune signaling","description":"This cluster includes terms tied to central nervous system development (cerebellar cortex formation, forebrain development, Bergmann glial differentiation, multicellular organism development) alongside immune-related signaling (innate immune response, T cell receptor signaling, NF-kappaB activity). The combination suggests proteins that may participate in both neural development processes and immune signaling pathways, or a set of broadly involved signaling components. The label aims to reflect the dominant themes without assuming a single cohesive function across all members, so confidence is Medium.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045087","count":4},{"id":"GO:0051092","count":4},{"id":"GO:0035372","count":4},{"id":"GO:0050852","count":3},{"id":"GO:0060020","count":3}]},{"hash":"2023980208751883594","title":"Ubiquitin-regulated signaling and antigen presentation","description":"This cluster centers on ubiquitin-related processes (deubiquitination, ERAD, regulation of ubiquitin ligase activity) and immune signaling pathways (stimulatory C-type lectin receptor signaling, MHC class I antigen presentation, TNF-mediated signaling), with additional links to Wnt signaling and mRNA stability. The combination suggests a theme of ubiquitin-mediated regulation coordinating immune signaling and antigen processing, though a few terms are obsolete or peripheral (e.g., some Wnt and transcription regulation terms). Overall, the cluster appears to reflect ubiquitin-dependent signaling intertwined with immune functions.","confidence":"Medium","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":9},{"id":"GO:0030433","count":5},{"id":"GO:0051436","count":5},{"id":"GO:0002223","count":5},{"id":"GO:0061418","count":5}]},{"hash":"1590632671054794404","title":"Ion Transport and cAMP/cGMP Signaling","description":"This cluster\u2019s terms are centered on membrane ion transport (potassium transmembrane transport; sodium import) and intracellular signaling linked to cyclic nucleotides (cellular responses to cAMP and cGMP; regulation of guanylyl cyclase signaling). A few terms touch transcription or aerotaxis, but the dominant theme is ion transport coupled to signaling pathways, suggesting proteins involved in maintaining ion homeostasis and modulating cyclic-nucleotide signaling.","confidence":"Medium","size":15,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":2},{"id":"GO:0010754","count":2},{"id":"GO:0009454","count":2},{"id":"GO:0098719","count":2},{"id":"GO:0071320","count":2}]},{"hash":"623665627165955152","title":"Light-regulated circadian transcription","description":"The top terms center on circadian rhythm regulation and light signaling pathways (especially far-red/red light signaling and phototransduction) together with transcriptional regulation, suggesting proteins involved in light-driven transcriptional control and circadian outputs. Some DNA maintenance terms appear but are less clearly connected to the core theme. Therefore, the cluster is best labeled as light-regulated circadian transcription.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042753","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0006313","count":1},{"id":"GO:0010018","count":1},{"id":"GO:0009585","count":1}]},{"hash":"1857710332586940197","title":"Nucleolar RNA Processing and Telomere Maintenance","description":"The GO terms indicate strong signals for nucleolar RNA processing (rRNA and snRNA pseudouridylation, rRNA processing) and for telomere maintenance via telomerase (including telomerase RNA localization to Cajal bodies). A few terms touch DNA replication, but the dominant pattern points to nucleolar RNA biogenesis and telomere regulation, justifying this combined label.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":1},{"id":"GO:0031118","count":1},{"id":"GO:0031120","count":1},{"id":"GO:0000469","count":1},{"id":"GO:0007004","count":1}]},{"hash":"1579617122288735142","title":"RNA processing and post-transcriptional regulation","description":"The strongest signals in the cluster come from RNA processing and splicing-related terms (RNA splicing; regulation of alternative splicing via spliceosome; RNA splicing; mRNA cap1 methylation), supported by a helicase activity term often tied to RNA metabolism. There are also a couple of protein homeostasis-related terms (protein folding in ER and redox homeostasis) that suggest broader involvement in cellular quality control. Overall, the common theme is RNA processing and post-transcriptional regulation, with some ancillary functions.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0097309","count":1}]},{"hash":"267683006084009564","title":"Proteostasis and ubiquitin-mediated quality control","description":"The enriched GO terms cluster around nuclear quality control by the ubiquitin-proteasome system, ER-associated degradation and misfolded protein transport, and regulation of protein activity, pointing to a shared theme of protein homeostasis and turnover. Some terms (DNA replication, mesoderm formation) are likely secondary annotations or multifunctional roles, but the dominant signal is proteostasis.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0097428","count":2},{"id":"GO:0032781","count":2},{"id":"GO:0001707","count":2},{"id":"GO:0006469","count":2}]},{"hash":"2236700704131249573","title":"Stress-responsive signaling and metabolism regulation","description":"The terms cluster around oxidative and xenobiotic stress responses (hydrogen peroxide, xenobiotic stimulus), hormone signaling, and regulation of gene expression and metabolism (mRNA stability, glycogen synthase activity, PI dephosphorylation). This suggests a cohesive theme of how cells sense stress and coordinate signaling with metabolic control, though some items (like obsolete terms and hemolysis) may reflect noise or peripheral roles.","confidence":"Medium","size":15,"edges":46,"triangles":58,"max_degree":11,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0080111","count":5},{"id":"GO:0090502","count":5},{"id":"GO:0014912","count":5},{"id":"GO:0042493","count":5},{"id":"GO:0070301","count":5}]},{"hash":"1017664715856283174","title":"Triglyceride catabolism and lipid remodeling","description":"The cluster shows strong enrichment for triglyceride catabolic processes, triglyceride mobilization, acyl-chain remodeling, and phospholipid catabolic (phosphatidylcholine and phosphatidylethanolamine) catabolism, indicating a cohesive set of proteins involved in triglyceride breakdown and lipid component turnover. A few other terms (e.g., xenobiotic response, cell budding) are present but do not outweigh the lipid-centric pattern. ","confidence":"High","size":15,"edges":39,"triangles":11,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0010898","count":4},{"id":"GO:0007114","count":4},{"id":"GO:0019433","count":4},{"id":"GO:0036153","count":4},{"id":"GO:0006642","count":4}]},{"hash":"1825477751737407076","title":"Exocyst-Mediated Membrane Trafficking","description":"This cluster\u2019s top GO terms cluster around vesicle trafficking and plasma membrane delivery, including exocyst assembly/localization, exocytosis, endosome organization, and Golgi to plasma membrane transport, indicating a shared role in secretory traffic and cell surface polarity. A few terms (spliceosomal assembly, meiosis cytokinesis, ECM disassembly) appear less related, likely representing noise.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045199","count":1},{"id":"GO:0000245","count":1},{"id":"GO:0001927","count":1},{"id":"GO:0051601","count":1},{"id":"GO:0007111","count":1}]},{"hash":"888034652716628460","title":"Immune Signaling and Autophagy Regulation","description":"This cluster centers on immune-related GO terms (T cell homeostasis, Th2 cytokine production) and protein quality control/autophagy processes (macroautophagy, ubiquitin-dependent ERAD). The inclusion of negative regulation of protein kinase activity also points to modulation of signaling pathways, tying immune signaling to protein turnover and autophagy. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0043029","count":2},{"id":"GO:0030433","count":2},{"id":"GO:2000769","count":1},{"id":"GO:2000553","count":1}]},{"hash":"819936055232717879","title":"Transcription Regulation and Cell Cycle Control","description":"Dominant signals are transcriptional regulation and cell-cycle control (DNA-templated transcription; regulation of transcription by RNA polymerase II; positive regulation of transcription by galactose; regulation of G2/M and G1/S transitions). A few terms touch on autophagy, glycogen metabolism, and differentiation, but the core pattern points to coordinated control of gene expression and cell division.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0016242","count":1},{"id":"GO:0000411","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0005981","count":1}]},{"hash":"681648723410211457","title":"Chondrogenesis and Hedgehog signaling","description":"This cluster centers on cartilage development and Hedgehog pathway regulation, reflected by terms for chondrocyte differentiation and positive regulation of the Smoothened signaling pathway. Additional signals related to nitric oxide signaling and vascular regulation appear, suggesting broader developmental signaling context, but the strongest common thread is chondrogenesis linked to Hedgehog signaling.","confidence":"Medium","size":15,"edges":58,"triangles":79,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0007263","count":2},{"id":"GO:0006695","count":2},{"id":"GO:0045880","count":1},{"id":"GO:0006809","count":1},{"id":"GO:0014740","count":1}]},{"hash":"52776737518348382","title":"Unknown","description":"The GO terms span plant light-response and development (photomorphogenesis, red/blue light, ethylene signaling) alongside immune and inflammatory processes (interferon production, inflammatory and type 2 immune responses), plus miRNA processing and a development term. This mix suggests no single cohesive function or pathway dominating the cluster, making a specific, representative label inappropriate.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010099","count":1},{"id":"GO:0009873","count":1},{"id":"GO:0010114","count":1},{"id":"GO:0035196","count":1},{"id":"GO:0009637","count":1}]},{"hash":"1358289795128140762","title":"Unknown","description":"The top GO terms are very diverse (cold response, lipopolysaccharide response, dopamine and other neurotransmitter metabolism, thiamine biosynthesis, histone demethylation, and growth regulation), with several obsolete terms. There isn\u2019t a clear, single biological theme tying these proteins together, so a specific functional label isn\u2019t supported. ","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009409","count":4},{"id":"GO:2000648","count":4},{"id":"GO:0042420","count":3},{"id":"GO:0042135","count":3},{"id":"GO:0055114","count":3}]},{"hash":"662909654269671085","title":"Neural development and synaptic signaling","description":"The top GO terms are dominated by nervous system\u2013related processes: axonogenesis, long-term potentiation, excitatory postsynaptic potential, visual perception, and Schwann cell development, all pointing to neuronal development and synaptic function. There are also broader cellular process terms (mitotic cell cycle, transcription), but they do not override the neural theme. Overall, the cluster centers on neural development and synaptic activity.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046826","count":12},{"id":"GO:0000278","count":12},{"id":"GO:0006351","count":12},{"id":"GO:0007409","count":11},{"id":"GO:0060291","count":11}]},{"hash":"1882397511008080961","title":"Mitophagy and mitochondrial maintenance","description":"The GO terms strongly point to mitochondrial autophagy (mitophagy) and related mitochondrial quality-control processes, with explicit mentions of autophagy of mitochondrion and its regulation. While other terms touch on broader RNA maintenance and protein turnover, the dominant theme is mitochondria-centered autophagy/turnover, giving a cohesive functional label despite lack of network edges.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000134","count":1},{"id":"GO:1903204","count":1},{"id":"GO:1903599","count":1},{"id":"GO:0045736","count":1},{"id":"GO:0006626","count":1}]},{"hash":"896148919115118746","title":"Thermal and Pain Response with Vascular Endocrine Regulation","description":"Top terms indicate thermoception and cold/pain responses, along with calcium ion import and endocrine/vasculature processes (vasopressin secretion, endothelial remodeling) and inflammatory signaling. This suggests a cluster where sensory temperature/pain signals are integrated with vascular and hormonal responses, rather than a single narrow pathway, hence a name capturing both sensory and vascular/endocrine aspects.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050955","count":2},{"id":"GO:1901594","count":2},{"id":"GO:0098907","count":2},{"id":"GO:1903444","count":2},{"id":"GO:0098703","count":2}]},{"hash":"1185127881487539267","title":"Lipid and aromatic compound catabolism","description":"The top GO terms cluster around various catabolic processes, including triglyceride and monoacylglycerol breakdown, phosphatidylserine degradation, and beta-ketoadipate/aromatic compound catabolism, with a notable link to lipid signaling via regulation of endocannabinoid pathways. This supports a core theme of metabolic breakdown and lipid-associated processes, though some terms also touch on cellular maintenance mechanisms (autophagy, microtubule dynamics), which may reflect broader cellular turnover. Therefore, the label focusing on lipid and aromatic compound catabolism appears representative of the cluster.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":2},{"id":"GO:0019433","count":2},{"id":"GO:0042952","count":2},{"id":"GO:0052651","count":2},{"id":"GO:2000124","count":2}]},{"hash":"853922415738142956","title":"Retroviral reverse transcription and genome integration","description":"GO terms point to steps of a retroviral life cycle: RNA-templated DNA biosynthesis (reverse transcription), DNA replication and recombination, DNA integration, and establishment of integrated proviral latency. Additional terms describe viral entry into the host nucleus and host defense modulation (e.g., negative regulation of siRNA processing), consistent with proviral infection and latency in a host cell. Overall, the cluster appears to represent retroviral genome replication and integration.","confidence":"High","size":15,"edges":9,"triangles":0,"max_degree":7,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":13},{"id":"GO:0006278","count":12},{"id":"GO:0006260","count":12},{"id":"GO:0039651","count":12},{"id":"GO:0015074","count":12}]},{"hash":"1396494777401524129","title":"Unknown","description":"The GO terms describe a highly heterogeneous set of functions including intracellular signal transduction, immune signaling (NOD1), temperature sensing, synaptic receptor localization, telomere maintenance, and cell cycle processes. Because there is no single cohesive biological theme tying these terms together, a concise, specific functional label cannot be confidently assigned.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":6},{"id":"GO:0032212","count":5},{"id":"GO:0048549","count":5},{"id":"GO:0070427","count":5},{"id":"GO:0050955","count":5}]},{"hash":"436628318712849900","title":"Unknown","description":"The top GO terms include telomere maintenance, telomeric chromosome localization, and cell cycle, but also seemingly unrelated processes such as thermoception, response to capsazepine, NOD1 signaling, calcium release, and synaptic plasticity localization. This mix lacks a single dominant biological theme, so a coherent, specific cluster label cannot be assigned.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":15},{"id":"GO:0048549","count":15},{"id":"GO:0070427","count":15},{"id":"GO:0050955","count":15},{"id":"GO:1901594","count":15}]},{"hash":"1784344876606273567","title":"Mitochondrial Transport and Energy Metabolism","description":"This cluster centers on mitochondrial functions: transport of metabolites (alpha-ketoglutarate, ornithine, nucleotides), mitochondrial ATP transport, the malate-aspartate shuttle, and mitochondrial membrane fission, plus links to adaptive thermogenesis and insulin-secretion regulation. Together these terms point to mitochondrial bioenergetics and metabolite trafficking as the shared theme. The phylloquinone biosynthesis term is less directly connected and may be an outlier, but does not negate the overall mitochondrial energy metabolism signal.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042372","count":3},{"id":"GO:0015742","count":1},{"id":"GO:0000066","count":1},{"id":"GO:1990544","count":1},{"id":"GO:1990519","count":1}]},{"hash":"1523390575948956428","title":"Unknown","description":"The GO terms are scattered across distinct processes (cell migration, innate immune response, response to muscle stretch, CDK activity regulation, mRNA processing, cadmium response, telomere maintenance/capping, and mitotic cell cycle). With zero edges and no clear shared pathway, there isn\u2019t a coherent functional theme to define a specific label for this cluster.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0035994","count":2},{"id":"GO:0045736","count":2},{"id":"GO:0006397","count":2}]},{"hash":"1690107742250794690","title":"Nucleotide and methionine metabolism","description":"This cluster\u2019s top GO terms center on adenine biosynthesis, homocysteine metabolism, and methylation, with methionine biosynthesis (obsolete) also appearing, suggesting a metabolic module linking nucleotide and sulfur amino acid pathways. Some terms are peripheral or obsolete (interferon response, cilium assembly, prostate development), likely noise. Therefore, the label captures the core function without overfitting to outliers.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046084","count":2},{"id":"GO:0050667","count":2},{"id":"GO:0032259","count":2},{"id":"GO:0019280","count":2},{"id":"GO:0044416","count":2}]},{"hash":"755548590909619366","title":"Mitochondrial import and signaling","description":"This cluster centers on mitochondrial-associated processes: protein import into the mitochondrial matrix, regulation of mitochondrial membrane permeability, and calcium- and phosphatidylinositol-mediated signaling at membranes. These together point to a mitochondria-focused signaling/metabolic theme. Some terms (e.g., cell cycle regulation and development) appear less connected and may reflect broader or incidental annotations, but the mitochondrial-related functions predominate.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000134","count":2},{"id":"GO:0070940","count":2},{"id":"GO:0046902","count":2},{"id":"GO:0010867","count":2},{"id":"GO:1903740","count":2}]},{"hash":"464744640505139195","title":"ERAD and ER Retrograde Transport","description":"This cluster centers on ubiquitin-dependent ER-associated degradation and ER-to-cytosol retrograde transport, with related ER localization terms; the endosome localization annotation is supportive but secondary.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010936","count":1},{"id":"GO:0036010","count":1},{"id":"GO:0097051","count":1},{"id":"GO:0030970","count":1},{"id":"GO:0030433","count":1}]},{"hash":"540932873489542583","title":"Inflammation Modulation and Glucocorticoid Response","description":"The top GO terms point to modulation of inflammatory signaling and stress hormone responses (cellular response to glucocorticoid stimulus, negative regulation of TNF and IL-1\u03b2 signaling), along with prostaglandin and nitric oxide pathways and redox-related glutathione biosynthesis. While there are a few broader terms like CNS development and fibroblast proliferation, the dominant theme is regulation of inflammation and immune signaling in response to glucocorticoids.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071385","count":1},{"id":"GO:0010804","count":1},{"id":"GO:0032691","count":1},{"id":"GO:0007417","count":1},{"id":"GO:0060316","count":1}]},{"hash":"487588465824494246","title":"Innate Immune Signaling and Cytoskeletal Remodeling","description":"These proteins show enrichment for innate immune response and regulation of NFAT signaling, pointing to immune signaling activity. Concurrently, terms for cytoskeletal and membrane remodeling (focal adhesion, ruffle assembly, endomembrane organization) and lipid biosynthesis suggest coordinated signaling with cytoskeletal dynamics and membrane trafficking, implying a module involved in immune-related signal transduction linked to cytoskeletal/membrane remodeling rather than a single enzyme activity.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0051533","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0007409","count":2},{"id":"GO:1902635","count":1}]},{"hash":"616210815592089735","title":"Cell Division and Chromatin Regulation","description":"The Top Terms are dominated by cell division and chromatin-related processes (cell division, homologous chromosome segregation, chromatin organization, histone acetylation) and relate to proliferative signaling (positive regulation of epithelial cell proliferation, response to growth hormone). While some terms (phagolysosome assembly, apoptotic DNA fragmentation regulation, mRNA branch site recognition) are less directly tied to division, they can be linked to broader gene expression and stress responses during proliferation. Overall, the cluster centers on cell-cycle progression with chromatin remodeling.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0000747","count":1},{"id":"GO:0050679","count":1},{"id":"GO:1902510","count":1},{"id":"GO:0001845","count":1}]},{"hash":"2085424800845886510","title":"Neural development and signaling regulators","description":"The top GO terms cluster around brain and retina development, neural signaling pathways (GPCR/PKC-related), and regulation of kinase and GTPase activity, suggesting a set of proteins involved in neural development and modulation of signaling. Some terms like hypoxia response and defense may reflect broader or overlapping functions or annotation noise.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007420","count":4},{"id":"GO:0007205","count":3},{"id":"GO:0060041","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0071456","count":3}]},{"hash":"2130526804425792899","title":"Intracellular membrane trafficking","description":"The GO terms cluster around movements of materials within the cell, especially among the Golgi, endosomes, lysosomes, and related secretory compartments (Golgi to vacuole transport, retrograde transport to Golgi, endocytic recycling, lysosomal transport, and dense core granule transport). A few terms touch on sphingolipid homeostasis and ectodermal development, but the dominant pattern is internal trafficking within the endomembrane system, suggesting these proteins participate in intracellular transport processes.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006896","count":1},{"id":"GO:0090326","count":1},{"id":"GO:0032456","count":1},{"id":"GO:0042147","count":1},{"id":"GO:0007041","count":1}]},{"hash":"238127185507858856","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042793","count":3},{"id":"GO:0000961","count":3},{"id":"GO:0016554","count":2},{"id":"GO:0080156","count":2},{"id":"GO:0031425","count":2}]},{"hash":"1435062548671946606","title":"Cell Cycle Regulation and Signaling","description":"The top GO terms cluster around regulation of cell cycle progression (G1/S transition), spindle organization and checkpoint signaling, and various signaling pathways (receptor kinase signaling, p53-mediated regulation). While a few terms touch autophagy and stress responses (virus response), the core pattern points to coordination of cell division with cellular signaling and stress management.","confidence":"Medium","size":14,"edges":43,"triangles":64,"max_degree":10,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0016242","count":13},{"id":"GO:2000727","count":13},{"id":"GO:0010765","count":13},{"id":"GO:0000082","count":13},{"id":"GO:0000212","count":13}]},{"hash":"483347258245299248","title":"Nuclear genome maintenance and RNA processing","description":"The top GO terms cluster around nuclear roles in genome maintenance and RNA handling: DNA replication and unwinding, transcription, spliceosome dynamics, nonsense-mediated decay, translational regulation, and chromatin/chromatin-related RNA regulation. Although a few terms touch development, the dominant signal points to nuclear genome maintenance and RNA processing functions.","confidence":"Medium","size":14,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0000184","count":4},{"id":"GO:0000388","count":3},{"id":"GO:1990416","count":3},{"id":"GO:0006268","count":3}]},{"hash":"1547978614992399300","title":"Stress-responsive translation and ribosome biogenesis","description":"This cluster is driven by translation and cytosolic ribosome biogenesis signals (translation, rRNA maturation, ribosome assembly) with additional links to transcription regulation and stress responses (DNA damage and UV/gamma radiation signaling), suggesting a cohesive group of proteins coordinating protein synthesis and ribosome production under stress.","confidence":"High","size":14,"edges":88,"triangles":331,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":12},{"id":"GO:0000462","count":3},{"id":"GO:0045727","count":3},{"id":"GO:0006354","count":3},{"id":"GO:0006353","count":3}]},{"hash":"1160739130823017510","title":"Retroviral integration and latency","description":"The top GO terms cluster around reverse transcription (RNA-templated DNA biosynthesis), DNA integration, DNA recombination, and establishment of proviral latency, plus viral entry into and penetration of the host nucleus. This combination maps to key retroviral life cycle steps\u2014integration of viral DNA into the host genome and latency\u2014so the label Retroviral integration and latency is appropriate, with high confidence.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0090502","count":4},{"id":"GO:0006278","count":3},{"id":"GO:0039651","count":3},{"id":"GO:0015074","count":3},{"id":"GO:0043137","count":3}]},{"hash":"475024556467899215","title":"Chromatin remodeling and DNA packaging dynamics","description":"The top GO terms center on nucleosome assembly/disassembly and histone modification (acetylation), including sperm DNA decondensation, which together point to chromatin structure and remodeling as the shared function. A few terms touch on cell cycle processes (microtubule polymerization, budding growth), which are contexts where chromatin changes occur, supporting a chromatin-dynamics theme overall.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006337","count":1},{"id":"GO:0043085","count":1},{"id":"GO:0007117","count":1},{"id":"GO:0006334","count":1},{"id":"GO:0015031","count":1}]},{"hash":"1670588560765428340","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070940","count":2},{"id":"GO:0090084","count":1},{"id":"GO:0006260","count":1},{"id":"GO:1905259","count":1},{"id":"GO:0042787","count":1}]},{"hash":"1701347378713702431","title":"Spliceosome-Mediated mRNA Splicing Regulation","description":"This cluster is dominated by GO terms about regulating mRNA splicing via the spliceosome (positive and negative regulation, and cis-splicing via the spliceosome), with another term pointing to ncRNA-mediated gene silencing\u2014both pointing to RNA processing and regulation. A secondary hint is the involvement of translation initiation factor complex assembly, which can relate to coordinated control of gene expression at the RNA level. Overall, the shared theme is regulation of mRNA splicing and RNA processing via the spliceosome.","confidence":"High","size":14,"edges":51,"triangles":131,"max_degree":10,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":9},{"id":"GO:0031047","count":9},{"id":"GO:1901407","count":9},{"id":"GO:1902625","count":8},{"id":"GO:0075525","count":8}]},{"hash":"1747885004988353744","title":"ER Protein Folding and ERAD Quality Control","description":"This cluster centers on endoplasmic reticulum\u2013related protein processing, including protein folding in the ER and ubiquitin-dependent ER-associated degradation (ERAD), with supporting redox homeostasis. Additional terms for DNA-templated transcription, ribosome biogenesis, and translation suggest a broader surrounding of protein synthesis and gene expression that feeds into ER quality control. Overall, the cohesive theme appears to be ER\u2013associated handling of proteins and quality control mechanisms, with transcription/translation machinery providing the production context.","confidence":"Medium","size":14,"edges":11,"triangles":4,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0042254","count":4},{"id":"GO:0030433","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0000747","count":3}]},{"hash":"2302766624300207876","title":"Spliceosome Regulation and Splicing","description":"The cluster is enriched for GO terms related to mRNA splicing via the spliceosome and its regulation (positive/negative regulation, cis splicing, splice site recognition), indicating a cohesive role in RNA processing by the spliceosome. A few terms about translation initiation are present but appear secondary to the core splicing theme.","confidence":"High","size":14,"edges":21,"triangles":11,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":1},{"id":"GO:0048026","count":1},{"id":"GO:1902625","count":1},{"id":"GO:0075525","count":1},{"id":"GO:1905663","count":1}]},{"hash":"741148004972854933","title":"ER Stress and Redox-Regulated Transcription","description":"The top terms cluster around protein folding in the endoplasmic reticulum and redox homeostasis, pointing to ER/oxidative stress handling. The presence of transcription-related terms (DNA-templated transcription and negative regulation of RNA Pol II) suggests these proteins also participate in linking ER redox status and stress signals to transcriptional regulation. This combination supports a theme of ER-associated stress responses modulating transcription.","confidence":"Medium","size":14,"edges":12,"triangles":3,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0034975","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0006351","count":1},{"id":"GO:0000122","count":1},{"id":"GO:1903206","count":1}]},{"hash":"534576056344173846","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":30,"triangles":8,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0006607","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0006406","count":2},{"id":"GO:1900182","count":1}]},{"hash":"728900893823517822","title":"Proteostasis and mitotic chromatin assembly","description":"The top terms cluster around protein quality control and trafficking (ubiquitin-dependent ERAD, proteasome assembly, chaperone-related refolding, ER-Golgi transport) together with chromatin assembly and cell division (CENP-A\u2013containing chromatin assembly, DNA replication, microtubule severing, cell division). This suggests a cohesive theme where proteostasis mechanisms interface with chromosomal dynamics during the cell cycle.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0070682","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0009408","count":3},{"id":"GO:0006260","count":2}]},{"hash":"789274732696234738","title":"Mitotic cell cycle control and spindle organization","description":"The strongest represented GO terms point to regulation of CDK activity, G1/S transition, and spindle/kinetochore functions (mitotic spindle organization, kinetochore localization). These collectively indicate roles in cell-cycle control and chromosome segregation during mitosis/meiosis, with other terms like stress responses being secondary. ","confidence":"High","size":14,"edges":19,"triangles":10,"max_degree":7,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0045736","count":14},{"id":"GO:0034501","count":14},{"id":"GO:0016242","count":12},{"id":"GO:2000727","count":12},{"id":"GO:0010765","count":12}]},{"hash":"242997142497672647","title":"Cell cycle regulation and signaling","description":"The terms centre on cell cycle control (G1/S, spindle assembly, checkpoint signaling) and signaling pathways (serine/threonine kinase signaling; p53-mediated regulation). Additional terms reflect stress responses (virus response, neuron death regulation) and differentiation cues (cardiac muscle differentiation). Together, they point to proteins that coordinate cell division with signaling and cellular stress responses, making 'Cell cycle regulation and signaling' a fitting label.","confidence":"Medium","size":14,"edges":29,"triangles":24,"max_degree":9,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0016242","count":14},{"id":"GO:2000727","count":14},{"id":"GO:0010765","count":14},{"id":"GO:0000082","count":14},{"id":"GO:0000212","count":14}]},{"hash":"392619980051653739","title":"Cell cycle and polysaccharide biosynthesis","description":"The top GO terms cluster around cell division and cell cycle, with strong representation of polysaccharide biosynthetic processes for cell wall and capsule, indicating a theme of growth-related cell surface assembly in this cluster. While other metabolic terms are present, the dominant signal ties to cell proliferation and surface polysaccharide production.","confidence":"Medium","size":14,"edges":9,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":9},{"id":"GO:0007049","count":8},{"id":"GO:0070592","count":7},{"id":"GO:0019853","count":7},{"id":"GO:1903457","count":7}]},{"hash":"223483405850597009","title":"GTPase-driven cell migration and cytoskeleton dynamics","description":"Dominant terms point to positive regulation of GTPase activity, cell migration, and intracellular signal transduction, with actin cortical organization also represented. This suggests a cluster of proteins coordinating cytoskeletal remodeling and movement via GTPase signaling; additional terms such as neural tube closure and vacuole inheritance may reflect broader developmental or trafficking roles, but the core signal remains cytoskeleton dynamics and motility.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0035556","count":2},{"id":"GO:0000011","count":2},{"id":"GO:0007050","count":2}]},{"hash":"1629005731781095312","title":"Unknown","description":"The top terms span very different biological areas\u2014telomere maintenance, NOD1 signaling, pinocytosis, thermoception, synaptic receptor localization, calcium release, and epithelial polarity\u2014without a clear, shared function tying all proteins together. This makes it hard to assign a coherent, specific label. ","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":5},{"id":"GO:0032212","count":4},{"id":"GO:0048549","count":4},{"id":"GO:0070427","count":4},{"id":"GO:0050955","count":4}]},{"hash":"2122417205288531020","title":"Oxidative Stress Response and Redox Homeostasis","description":"This cluster is dominated by GO terms tied to responding to oxidative stress and maintaining redox balance (cellular response to oxidative stress, cellular oxidant detoxification, cell redox homeostasis, oxidation-reduction processes). Additional terms about nucleotide biosynthesis and ion transport may reflect metabolic adjustments under stress; one neural crest migration term likely represents noise or unrelated context. Overall, the core theme is redox regulation and oxidative stress response.","confidence":"High","size":14,"edges":6,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0003147","count":3},{"id":"GO:1903026","count":3},{"id":"GO:0034599","count":3},{"id":"GO:0098869","count":3}]},{"hash":"2186653787041964199","title":"Unknown","description":"The terms are highly diverse, spanning mitosis, vesicle trafficking, reproduction, neural development, and vascular signaling, with no single, dominant shared function evident in the cluster. Therefore no cohesive label; Unknown.","confidence":"","size":14,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007051","count":1},{"id":"GO:1903480","count":1},{"id":"GO:1900748","count":1},{"id":"GO:0006904","count":1},{"id":"GO:0045769","count":1}]},{"hash":"1610784800658020810","title":"Actin Remodeling and Migration Signaling","description":"This cluster's key GO terms cluster around actin-driven motility and chemotaxis (actin polymerization-dependent cell motility; dendritic cell chemotaxis), supported by signaling activities like regulation of GTPase and JNK cascades and IP3/calcium signaling. These together suggest a module focused on cytoskeletal remodeling to enable cell movement, despite a few peripheral terms that touch on lipid metabolism or chromatin organization. ","confidence":"Medium","size":14,"edges":13,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0070358","count":1},{"id":"GO:0051282","count":1},{"id":"GO:0060988","count":1},{"id":"GO:0002408","count":1},{"id":"GO:0032959","count":1}]},{"hash":"549793136280655115","title":"Immunoregulation and developmental cues","description":"The terms center on immune signaling and regulation (negative regulation of IL-2 production, regulation of T cell proliferation, T cell homeostasis, germinal center formation) and include a glucocorticoid response, with a couple of development-related processes (mesendoderm development, chorio-allantoic fusion) suggesting broader signaling roles. Taken together, the cluster seems to reflect signaling that coordinates immune function with development, likely involving glucocorticoid pathways. Medium","confidence":"","size":14,"edges":18,"triangles":7,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":1},{"id":"GO:0071385","count":1},{"id":"GO:0045085","count":1},{"id":"GO:0045647","count":1},{"id":"GO:0060710","count":1}]},{"hash":"1107072722034459523","title":"RNA Methylation and Translation","description":"The top GO terms include RNA guanine-N7-methylation, rRNA modification, and translation, suggesting a core cluster around RNA metabolism and protein synthesis. Other terms reference signaling and stress responses, which may be incidental annotations, but the RNA-related terms provide the strongest cohesive theme.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0007234","count":1},{"id":"GO:0009736","count":1},{"id":"GO:0080038","count":1},{"id":"GO:0016310","count":1}]},{"hash":"945554935019013198","title":"DNA replication and cell cycle regulation","description":"The top GO terms cluster around DNA replication, DNA recombination, and regulation of cyclin-dependent kinase activity, all of which point to cell cycle control and DNA metabolism. Other terms like T cell homeostasis and oxidative stress appear as less representative signals, but the dominant pattern supports a module of DNA processing and cell-cycle\u2013related proteins. ","confidence":"High","size":14,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0000083","count":2},{"id":"GO:0045736","count":2},{"id":"GO:0006310","count":2},{"id":"GO:0090502","count":2}]},{"hash":"1521506759235763497","title":"Golgi- and SNARE-mediated synaptic vesicle trafficking","description":"The top GO terms cluster around Golgi apparatus processes (ribbon formation, intra-Golgi and ER-to-Golgi transport) and vesicle fusion, with SNARE complex assembly, plus exocytic delivery of neurotransmitter receptors to the postsynaptic membrane and links to long-term potentiation. This points to a cohesive role in coordinating Golgi-based vesicle trafficking and SNARE-driven exocytosis at synapses, i.e., trafficking of receptors and other cargo that underpins synaptic plasticity.","confidence":"High","size":14,"edges":53,"triangles":107,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0090161","count":9},{"id":"GO:0060291","count":9},{"id":"GO:0048280","count":9},{"id":"GO:0098967","count":9},{"id":"GO:0006891","count":9}]},{"hash":"178278780904415098","title":"Unknown","description":"The terms are highly heterogeneous: stem cell proliferation regulation, camphor and dopamine catabolism, obsolete neurotransmitter catabolic and redox processes, plus various stress and biosynthetic/size regulation terms. There is no single cohesive function tying these together, suggesting annotation noise or a mixed cluster. ","confidence":"","size":14,"edges":8,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2000648","count":4},{"id":"GO:0019383","count":3},{"id":"GO:0042420","count":3},{"id":"GO:0042135","count":3},{"id":"GO:0055114","count":3}]},{"hash":"688169382256193303","title":"Intracellular vesicle trafficking and signaling","description":"This cluster is dominated by terms tied to vesicle movement and signaling within the cell: phosphatidylinositol-mediated signaling, intracellular transport, endosomal vesicle fusion, Golgi retention, and GTPase activity regulation, with additional hints from synaptic vesicle maturation and presynapse-to-nucleus signaling that point to a neuron-related transport-signaling axis. These together support a cohesive theme of vesicle trafficking coupled to intracellular signaling.","confidence":"High","size":14,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0048015","count":2},{"id":"GO:0045053","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0045945","count":2},{"id":"GO:0043547","count":2}]},{"hash":"1870658174332290932","title":"Ubiquitin-Dependent ERAD and Innate Immunity","description":"This cluster centers on ubiquitin-mediated protein degradation (ERAD/ubiquitination) and innate immune signaling. The GO terms for ubiquitin-dependent protein catabolic process and protein ubiquitination point to proteostasis via the ubiquitin-proteasome system, while innate immune response and IL-17\u2013related signaling connect to immune function. Vitamin D response and spleen development terms further support immune-related roles. Overall, a cohesive theme of proteostasis linked to immunity.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0042787","count":4},{"id":"GO:0045087","count":3},{"id":"GO:0033280","count":3},{"id":"GO:0016567","count":3}]},{"hash":"1556064435745670688","title":"Ribosome biogenesis and export","description":"Most of the top GO terms revolve around ribosome assembly and maturation, including ribosome biogenesis, large subunit biogenesis, and ribosomal large subunit export from the nucleus, with endonucleolytic processing of rRNA being part of ribosome maturation. A single outlier term exists (hematopoietic progenitor differentiation), but the dominant signal is clearly ribosome-related, supporting a cohesive biogenesis/export function for this cluster.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":1},{"id":"GO:0007080","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0000055","count":1},{"id":"GO:0042273","count":1}]},{"hash":"974448519328024375","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010936","count":1},{"id":"GO:0036010","count":1},{"id":"GO:0097051","count":1},{"id":"GO:0030970","count":1},{"id":"GO:0030433","count":1}]},{"hash":"252670598718038357","title":"Cardiac and hematopoietic development regulation","description":"This cluster centers on developmental processes in heart/muscle (myotube and heart development) and hematopoietic lineages (stem cell proliferation and progenitor differentiation), together with transcriptional control (positive/negative regulation and DNA-templated transcription). A minor signal related to outer dynein arm assembly suggests a broader developmental context. Overall, the set points to developmental regulation in cardiac and hematopoietic lineages with transcriptional control as a shared mechanism.","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0014904","count":1},{"id":"GO:0045944","count":1},{"id":"GO:1902035","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0036158","count":1}]},{"hash":"2189374040674034223","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021756","count":4},{"id":"GO:0006207","count":3},{"id":"GO:0044205","count":3},{"id":"GO:0010107","count":2},{"id":"GO:0051599","count":2}]},{"hash":"2228810300613524831","title":"Intracellular Signaling and Calcium Regulation","description":"The top GO terms cluster around signaling and regulation within the cell, especially involving calcium dynamics (mitochondrial Ca2+ concentration, calcium detection), GTPase activity, and phosphatidylinositol signaling, with supporting roles in transcription regulation, nuclear import, and broader physiological processes like blood pressure and kidney development, suggesting a cohesive theme of intracellular signaling and calcium-driven regulation across cellular compartments.","confidence":"Medium","size":14,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0042144","count":3},{"id":"GO:0043065","count":3},{"id":"GO:0051561","count":3},{"id":"GO:0006607","count":3}]},{"hash":"95203989324687784","title":"Viral Entry, Replication, and Proviral Latency","description":"The dominant GO terms point to viral-like DNA processes: DNA recombination, replication, DNA integration, RNA-templated DNA synthesis, and established integrated proviral latency, along with viral entry into the host nucleus. Additional terms about host apoptosis activation and suppression of RNAi defenses further support a viral genome manipulation and host-interaction program, making this a cohesive viral integration/latency cluster.","confidence":"High","size":14,"edges":17,"triangles":7,"max_degree":8,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":7},{"id":"GO:0006278","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0039651","count":5},{"id":"GO:0015074","count":5}]},{"hash":"1253448519852871790","title":"Golgi-ER vesicle trafficking and mitosis","description":"The cluster is dominated by GO terms for vesicle transport between the ER and Golgi (COPII budding, retrograde ER-Golgi, ER-Golgi transport) and endocytosis, together with mitosis-related terms (mitotic cell cycle, cell division, mitotic spindle assembly) and growth, suggesting a shared function linking membrane trafficking to cell division. ","confidence":"Medium","size":14,"edges":18,"triangles":1,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006890","count":5},{"id":"GO:0008283","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0090307","count":4}]},{"hash":"48898001871814220","title":"Nematode embryogenesis and fertilization","description":"This cluster\u2019s terms cluster around developmental and reproductive processes in nematodes: embryonic morphogenesis and maternal axis specification point to early development; polyspermy prevention and sperm-binding regulation relate to fertilization control; pharyngeal pumping and cuticle/molting terms reflect nematode-specific development and physiology, while phosphatidylinositol signaling and transcription regulation provide supporting signaling and gene expression context. Collectively, they suggest a theme of nematode development and reproductive regulation.","confidence":"Medium","size":14,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035124","count":1},{"id":"GO:0048632","count":1},{"id":"GO:0018996","count":1},{"id":"GO:0006508","count":1},{"id":"GO:0043050","count":1}]},{"hash":"1287116248158657711","title":"Neuronal Ion Transport and cGMP/cAMP Signaling","description":"This cluster centers on GO terms for ion transport (sodium and potassium), potassium homeostasis, and cellular responses to second messengers (cGMP and cAMP), including regulation of receptor guanylyl cyclase signaling. Together with sensory perception of pain, these terms suggest a shared role in neuronal signaling and ionic balance, with protein tetramerization and development terms providing broader structural context.","confidence":"Medium","size":14,"edges":24,"triangles":9,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051262","count":10},{"id":"GO:0007275","count":10},{"id":"GO:0019233","count":10},{"id":"GO:0098719","count":10},{"id":"GO:0071805","count":10}]},{"hash":"1180437833617319703","title":"Genome Mobility and Cell Division","description":"The cluster gathers terms centered on genome dynamics (DNA integration, DNA transposition, proviral latency, chromosome segregation) and cell-cycle processes (cell cycle, cell division), with supporting roles from translation and cytoskeletal/developmental processes that enable growth and movement. The strongest unifying theme is genome mobility during division and replication, hence this label.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0015074","count":1},{"id":"GO:0006313","count":1},{"id":"GO:0007049","count":1},{"id":"GO:0007059","count":1}]},{"hash":"2285076870614525527","title":"Calcium signaling and PKC/NFAT regulation","description":"The Top Terms are centered on calcium-related signaling (detection and regulation of calcium ions, phosphatidylinositol signaling) and downstream regulation of protein kinase activity and the calcineurin-NFAT pathway, pointing to a cohesive calcium-PKC-NFAT signaling theme, despite a few outliers like cell cycle or development terms.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0048015","count":1},{"id":"GO:0005513","count":1},{"id":"GO:0072221","count":1}]},{"hash":"2248233566698184586","title":"Ubiquitin-Proteasome\u2013Mediated Degradation","description":"This cluster is driven by GO terms for ubiquitin-dependent protein catabolic processes, protein polyubiquitination, autoubiquitination, and SCF-dependent proteasomal degradation, indicating proteasome-mediated turnover. There is also a signal for circadian rhythm regulation, which is often controlled by ubiquitin-mediated degradation of clock proteins, suggesting a coherent theme of regulated protein turnover. Other terms point to broader regulatory contexts (synapse assembly, responses to metals), but the core connection across proteins appears to be ubiquitin tagging and proteasomal degradation.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":6},{"id":"GO:0000209","count":4},{"id":"GO:0042752","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0060386","count":2}]},{"hash":"1571332763122180563","title":"Unknown","description":"There are no shared GO terms or functional signals to define a common theme for this cluster (Top Terms are empty, and there are no edges or triangles). Without a coherent functional signal, a meaningful label cannot be assigned beyond Unknown.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1154640802378891009","title":"Mitochondrial respiration and metabolism","description":"Top terms center on mitochondrial energy production: mitochondrial electron transport, proton transmembrane transport, and aerobic respiration, pointing to a mitochondrial metabolism theme. Other terms touch on metabolic regulation and aging (trehalose metabolism, lifespan determination, proteolysis), suggesting the cluster broadly covers metabolic processes with energy-homeostasis ties.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071432","count":1},{"id":"GO:0006122","count":1},{"id":"GO:0045861","count":1},{"id":"GO:0008340","count":1},{"id":"GO:0042447","count":1}]},{"hash":"29501789756181138","title":"RNA Pol II Transcription Regulation","description":"Most top GO terms point to transcription control by RNA polymerase II (DNA-templated transcription, negative regulation of Pol II activity, and related DNA-binding regulation). A few entries touch on redox/ER stress roles, but the core signal is nuclear transcription regulation, so the label captures the cluster's likely function.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0000122","count":2},{"id":"GO:1903206","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0080058","count":2}]},{"hash":"1467314221464341967","title":"Unknown","description":"The top GO terms are diverse, spanning microtubule dynamics (cytoskeleton), membrane transport, signaling, transcription regulation, and neural signaling, with no single cohesive function tying all proteins together. This lack of a clear shared function justifies labeling the cluster as Unknown.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001578","count":1},{"id":"GO:0046785","count":1},{"id":"GO:0032973","count":1},{"id":"GO:1990034","count":1},{"id":"GO:0034968","count":1}]},{"hash":"1809825440208564383","title":"Lipid biosynthesis and adipogenesis","description":"The cluster\u2019s top GO terms cluster around lipid metabolism and adipocyte development, including monounsaturated fatty acid biosynthesis, cholesterol esterification, sphingosine biosynthesis, and white fat cell differentiation. Although some terms are obsolete, the recurring lipid-related processes strongly tie the proteins to lipid formation and adipogenesis, supporting this label.","confidence":"High","size":14,"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:0010873","count":2},{"id":"GO:0070542","count":2},{"id":"GO:0034435","count":2}]},{"hash":"526287300625215028","title":"Unknown","description":"The GO terms are highly diverse, spanning carbohydrate metabolism (UDP-galactose/Leloir pathway), redox processes, neuronal development (Purkinje cell differentiation), liver-related functions (regeneration, hepatocyte proliferation), fibrinolysis, a PTM (deglutamylation), blood pressure regulation (angiotensin), heat response, and insulin processing. With no clear shared pathway or function and no edges connecting members, there isn\u2019t a cohesive theme to name a specific cluster function.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033499","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0021702","count":1},{"id":"GO:0097421","count":1},{"id":"GO:2000346","count":1}]},{"hash":"1193578566674138531","title":"Unknown","description":"The terms span RNA processing, transcription, nuclear and cytoskeletal assembly, plus a mix of developmental processes (neurogenesis, oogenesis, spermatid elongation, chaeta development, synaptic target recognition). There is no single cohesive function connecting these terms, so a meaningful shared label cannot be determined.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000245","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0051017","count":1},{"id":"GO:0007290","count":1},{"id":"GO:0008039","count":1}]},{"hash":"2261154203368464130","title":"Unknown","description":"Top terms are a mixed bag (neural tube development, uterine gland development, biofilm regulation, glucose signaling, various metabolic and transcription-related processes, plus several obsolete terms), with no clear shared function and no edges or interactions among proteins, so there is no coherent theme to label\u2014Unknown.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021915","count":2},{"id":"GO:1903709","count":1},{"id":"GO:1900189","count":1},{"id":"GO:1902661","count":1},{"id":"GO:0044109","count":1}]},{"hash":"1065098712259390433","title":"Unknown","description":"The top GO terms are highly heterogeneous, covering chloroplast movement, ABA homeostasis, sensory organ precursor division, nuclear migration along microfilaments, calcium binding, metanephric tubule development, bioluminescence, calcineurin-NFAT signaling, and tight junction localization. There is no clear, single biological theme linking these terms, and with 0 edges among 14 proteins, a common function or pathway is not evident. Therefore this cluster is best labeled Unknown with no confidence in a unifying function.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009903","count":1},{"id":"GO:1902265","count":1},{"id":"GO:0045035","count":1},{"id":"GO:0031022","count":1},{"id":"GO:0005513","count":1}]},{"hash":"1525039085551232713","title":"Cell cycle regulation and stress signaling","description":"This cluster is dominated by GO terms related to controlling cell growth and division (negative regulation of proliferation, G1/S transition, meiotic spindle organization) and stress-response pathways (p53 mediator regulation, cellular response to virus), suggesting a theme of growth control and cellular stress signaling. Exocytosis and ion transport terms are present but not central, so the core label centers on growth regulation and stress response.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008285","count":2},{"id":"GO:0045956","count":2},{"id":"GO:0016242","count":1},{"id":"GO:2000727","count":1},{"id":"GO:0010765","count":1}]},{"hash":"133318173123311314","title":"Virus-host Interaction and Translation Machinery","description":"The top GO terms point to viral infection processes (viral life cycle, virion assembly, fusion with host membrane, host entry) and host responses (leukocyte migration), alongside core cellular functions like translation, ribosome biogenesis, and protein folding. This suggests a cluster centered on virus-host interactions that co-opt host translation and protein processing machinery. Confidence: Medium","confidence":"","size":13,"edges":69,"triangles":203,"max_degree":12,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0042254","count":4},{"id":"GO:0010849","count":3},{"id":"GO:2000276","count":3},{"id":"GO:0019064","count":3}]},{"hash":"869590176623123550","title":"Transcription-coupled DNA repair and RNA processing","description":"Core signals are TC-NER and DNA damage recognition, with links to transcriptional control, chromatin silencing, RNA processing, and mRNA decay. This suggests a cluster of proteins coordinating transcription, chromatin state, and RNA fate during genome maintenance.","confidence":"Medium","size":13,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006283","count":3},{"id":"GO:0090054","count":2},{"id":"GO:0000715","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0000973","count":2}]},{"hash":"596936219985794769","title":"Cytoplasmic and Mitochondrial Translation Machinery","description":"The top GO terms are centered on translation and ribosome-related processes, including general translation, translational termination, mitochondrial translation, ribosomal large subunit assembly, and regulation of cytoplasmic translation. This indicates the cluster predominantly represents components of the protein synthesis machinery spanning both cytosolic and mitochondrial contexts, with an ancillary link to mRNA decay and a minor outlier related to glial proliferation. ","confidence":"High","size":13,"edges":24,"triangles":21,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006415","count":2},{"id":"GO:0032543","count":1},{"id":"GO:0000027","count":1},{"id":"GO:0002184","count":1}]},{"hash":"1971574116504250822","title":"Cellular stress response and signaling","description":"The top terms indicate responses to various stimuli (xenobiotics, hydrogen peroxide) and signaling-related processes (peptide hormone stimulus) as well as post-transcriptional regulation (mRNA stability). Some terms are obsolete or less coherent with stress signaling (aging, DNA demethylation), suggesting a mixed set, but the core theme centers on cellular stress responses and signaling. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0007568","count":6},{"id":"GO:0080111","count":5},{"id":"GO:0090502","count":5},{"id":"GO:0014912","count":5},{"id":"GO:0042493","count":5}]},{"hash":"41902696534228450","title":"Unknown","description":"The terms span neural development, metabolism, DNA replication and cell-cycle processes, microtubule localization, amino acid starvation response, innate immunity, and TOR signaling, with no single clear theme linking them all. This makes a cohesive, specific label difficult to justify.","confidence":"","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0008542","count":5},{"id":"GO:0006695","count":5},{"id":"GO:0021997","count":4},{"id":"GO:0006260","count":3},{"id":"GO:0035372","count":3}]},{"hash":"2244787887914129571","title":"Telomere maintenance and telomere region localization","description":"The cluster is dominated by GO terms about telomere maintenance (via telomerase, telomere capping) and localization to the telomeric region, with related terms on telomeric cohesion and chromatid dynamics, plus ADP-ribosylation activities (PARP). This points to a cohesive telomere-focused function rather than unrelated processes.","confidence":"High","size":13,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0070213","count":2},{"id":"GO:1904743","count":2},{"id":"GO:1904357","count":2},{"id":"GO:0032212","count":2},{"id":"GO:1904908","count":2}]},{"hash":"1215832145560204136","title":"Endomembrane Trafficking and Signaling","description":"The top GO terms cluster around endomembrane system processes\u2014endosomal transport, endosomal vesicle fusion, Golgi to lysosome transport, and endomembrane organization\u2014with accompanying signaling roles in the TGF-\u03b2 (SMAD) pathway and TLR3 signaling. Additional terms point to actin-driven vesicle dynamics (filopodium assembly) and lipid signaling (PI(5)P), all suggesting a module that links vesicle trafficking with signaling pathways.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016197","count":1},{"id":"GO:0034058","count":1},{"id":"GO:0034141","count":1},{"id":"GO:0048549","count":1},{"id":"GO:0007179","count":1}]},{"hash":"918023424119263841","title":"Viral entry, integration, and latency","description":"This cluster is characterized by terms about viral entry into host cells and nuclei, integration of viral DNA into the host genome, proviral latency, and RNA-templated DNA synthesis, pointing to retroviral-like replication and genome integration; thus 'Viral entry, integration, and latency' aptly summarizes the shared function.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0090502","count":7},{"id":"GO:0006310","count":6},{"id":"GO:0006278","count":5},{"id":"GO:0075713","count":5},{"id":"GO:0075732","count":5}]},{"hash":"797761254925079051","title":"Signaling Regulation and Cell Cycle Control","description":"The top terms center on regulating signaling pathways (GTPase activity, kinase activity, autophosphorylation) and cell cycle processes (mitosis, cytokinesis, proliferation, development). Additional terms like mRNA transport and cellular responses (e.g., hypoxia, visual perception) suggest broader regulatory roles but still connect to controlling cellular growth and division. Overall, the cluster seems to group proteins that modulate signaling to drive cell cycle progression and development.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0071456","count":5},{"id":"GO:0031954","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0071902","count":5}]},{"hash":"312567560751917794","title":"Nucleic acid metabolism and host\u2013microbe interactions","description":"The GO terms show a focus on nucleic acid processes (DNA recombination, DNA replication, RNA-templated DNA biosynthesis, mRNA stability regulation) alongside host-microbe interaction activities (symbiont entry/activation of host apoptosis, viral nuclear entry). The mix suggests a cluster of proteins involved in nucleic acid biology that also participate in intracellular microbe\u2013host interactions, making this a coherent, if broad, theme.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":4},{"id":"GO:0017000","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0090502","count":3},{"id":"GO:0039651","count":3}]},{"hash":"368102681990192059","title":"Retroviral integration and latency","description":"The top GO terms center on proviral DNA integration, establishment of integrated proviral latency, reverse transcription (RNA-templated DNA biosynthesis), and DNA replication, which are hallmark steps of the retroviral life cycle. Additional terms about symbiont entry into host cells and symbiont-mediated activation of host apoptosis align with viral entry and host-pathogen interactions, while translation and cell-cycle-related terms support viral replication and propagation. Overall, the cluster appears to reflect retroviral infection, genome integration, and latency within host cells.","confidence":"High","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":3},{"id":"GO:0075713","count":3},{"id":"GO:0046718","count":3},{"id":"GO:0007049","count":2},{"id":"GO:0051301","count":2}]},{"hash":"880460014662717812","title":"Nuclear RNA processing and cell cycle regulation","description":"The top terms point to nucleus-centered activity: nuclear-transcribed mRNA decay, nuclear import, and ribosomal subunit export, alongside ubiquitination and cell cycle processes. Although some membrane transport terms appear, they are less represented; the dominant pattern ties to nuclear RNA handling and cell cycle control, with ubiquitination likely reflecting regulated protein turnover. ","confidence":"Medium","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000288","count":2},{"id":"GO:0000060","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0071260","count":2}]},{"hash":"847955901185757593","title":"Protein Localization and Vesicle Trafficking","description":"The terms cluster around where proteins are localized within cellular compartments and transported between compartments\u2014ER localization, endosomal transport, vesicle docking, and targeted protein/mRNA localization\u2014spanning several contexts (plants, yeast, animals). The scattered terms suggest a unifying theme of intracellular transport and localization rather than a single pathway, hence a label capturing both localization and trafficking.","confidence":"Medium","size":13,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051643","count":1},{"id":"GO:1903480","count":1},{"id":"GO:0009903","count":1},{"id":"GO:0045856","count":1},{"id":"GO:0032439","count":1}]},{"hash":"81130001068321792","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":14,"triangles":3,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0030260","count":3},{"id":"GO:0019068","count":3},{"id":"GO:0039651","count":3},{"id":"GO:0015074","count":3},{"id":"GO:0075713","count":3}]},{"hash":"512553251713925208","title":"Ubiquitin-Dependent Proteolysis and Chromatin Regulation","description":"Most of the top GO terms center on ubiquitination and proteasomal degradation (ubiquitin-dependent protein catabolic process; protein polyubiquitination; protein K6-linked ubiquitination; protein autoubiquitination) and on histone turnover (histone catabolic process; histone H4-K20 methylation). This points to a functional cluster focused on protein turnover via the ubiquitin-proteasome system and associated chromatin regulation. Less dominant terms like V(D)J recombination and TNF signaling may reflect chromatin remodeling and immune signaling contexts in which these ubiquitin processes operate, but they are not the primary drivers of the cluster. Together, the proteins likely participate in targeted proteolysis and chromatin-associated regulation.","confidence":"High","size":13,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0000209","count":3},{"id":"GO:0033151","count":3},{"id":"GO:0009048","count":3},{"id":"GO:0085020","count":3}]},{"hash":"1046390777731260194","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000480","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0000472","count":1},{"id":"GO:1903645","count":1},{"id":"GO:1903638","count":1}]},{"hash":"1082277950301379629","title":"Unknown","description":"There are no GO terms or connectivity to tie the proteins into a shared function, and with a max degree of 0 and no edges or triangles the cluster appears as isolated proteins, so a representative label cannot be inferred.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1140002544581710938","title":"Nucleic Acid Repair and RNA Processing","description":"This cluster is dominated by GO terms related to DNA repair (DNA repair, DNA alkylation repair) and RNA metabolism (RNA repair, tRNA wobble uridine modification, mRNA processing, regulation of translational initiation by tRNA modification). A few terms touch on mitochondrial membrane permeability and programmed cell death, suggesting a broader link to cell fate, but the strongest shared theme is maintenance of nucleic acid integrity and associated RNA modification/processing that influence translation.","confidence":"High","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042245","count":1},{"id":"GO:0002098","count":1},{"id":"GO:1990983","count":1},{"id":"GO:0035552","count":1},{"id":"GO:0012501","count":1}]},{"hash":"541344605266812061","title":"Nitrogen Utilization and Ammonium Transport","description":"Most of the GO terms converge on nitrogen handling: regulation of nitrogen utilization, nitrogen utilization, and various ammonium/methylammonium transport processes (including transepithelial transport). The presence of related growth-response terms (pseudohyphal and invasive growth under nutrient limitation, lateral root branching) supports a broader nutrient-sensing/wage-growth theme, but the core signal is nitrogen metabolism and ammonium transport across membranes, making this a cohesive label.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006808","count":1},{"id":"GO:0007124","count":1},{"id":"GO:0060586","count":1},{"id":"GO:0015843","count":1},{"id":"GO:0015670","count":1}]},{"hash":"623024556315359500","title":"Redox Metabolism and Xenobiotic Response","description":"This cluster is dominated by redox (oxidation-reduction) processes and core metabolic pathways (glycolysis and TCA cycle), with additional signals of environmental stress responses (lipopolysaccharide and xenobiotic stimulus) and some secondary metabolite biosynthesis. The cohesive theme appears to be metabolic activity linked to redox balance alongside stress-responsive behavior, though the term mix suggests broad, cross-species annotations rather than a single specific pathway.","confidence":"Medium","size":13,"edges":9,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0042572","count":4},{"id":"GO:0042619","count":4},{"id":"GO:0032496","count":3},{"id":"GO:0006541","count":3}]},{"hash":"1505790202357584877","title":"Telomere maintenance and telomeric chromosome localization","description":"The top GO terms are dominated by telomere-related processes (maintenance via telomerase, telomere capping, and localization to telomeres) as well as localization to the telomeric region, suggesting a core theme around telomere biology and chromosome integrity. Peripheral terms like spindle assembly and certain signaling pathways may reflect broader cell-cycle or regulatory connections but do not override the central telomere-centric theme.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":6},{"id":"GO:1900383","count":6},{"id":"GO:0070198","count":6},{"id":"GO:0051225","count":6},{"id":"GO:0007205","count":6}]},{"hash":"423827162440920094","title":"Unknown","description":"There are no shared GO terms or network connections in this cluster (no edges, no triangles, max degree 0), and although proteins were re-added by ReCIPE, there is no functional signal to bind them into a common process. Without a clear theme, the cluster cannot be confidently named.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2137984325269772685","title":"Unknown","description":"The GO terms cover diverse processes (ubiquitin-dependent protein catabolism, glucocorticoid signaling, interferon response, cilium assembly, prostate development, sex differentiation, protein oligomerization, oxidative stress, and morphine response) with no clear shared function or pathway, and there are no edges connecting proteins, making a cohesive label unlikely.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903071","count":1},{"id":"GO:2000324","count":1},{"id":"GO:0071357","count":1},{"id":"GO:1905515","count":1},{"id":"GO:0030850","count":1}]},{"hash":"980690151470881242","title":"DNA Damage Response & Cell Cycle","description":"These proteins cluster around genome maintenance and chromosome dynamics, as reflected by GO terms for DNA damage checkpoint regulation, G1/S transition, nucleotide-excision repair, meiotic sister chromatid movement, and meiotic spindle elongation, plus histone H2A monoubiquitination. While a few terms point to developmental or cytoskeletal processes, the dominant theme is genome stability and cell-cycle progression during replication and meiosis.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035518","count":1},{"id":"GO:2000001","count":1},{"id":"GO:0051759","count":1},{"id":"GO:0000082","count":1},{"id":"GO:0040016","count":1}]},{"hash":"1263091981084307185","title":"LDL receptor catabolic pathway","description":"This cluster is dominated by GO terms related to LDL receptor-mediated endocytosis and processing, including multiple entries for LDL receptor catabolic processes and their regulation. While there are a few other terms (bone resorption, insulin processing, nerve growth factor production, renin secretion), the recurring theme centers on LDL receptor trafficking and degradation, suggesting the proteins share involvement in lipid uptake and receptor recycling pathways.","confidence":"Medium","size":13,"edges":19,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0045453","count":4},{"id":"GO:1902349","count":4},{"id":"GO:0032902","count":2},{"id":"GO:0002001","count":2},{"id":"GO:0032804","count":2}]},{"hash":"2104055739082872177","title":"Endosome-Lysosome Trafficking and Vesicle Exocytosis","description":"The top terms cluster around vesicle trafficking and lysosome-related processes: endosome to melanosome transport, lysosomal membrane organization, cytoplasm-to-vacuole targeting, MVB size regulation, and regulation of synaptic vesicle exocytosis. These point to a cohesive function in intracellular trafficking and vesicle dynamics, with a few unrelated terms likely reflecting broader roles or annotation noise.","confidence":"Medium","size":13,"edges":3,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0034198","count":8},{"id":"GO:0031384","count":6},{"id":"GO:0007420","count":6},{"id":"GO:0010796","count":6},{"id":"GO:2000300","count":6}]},{"hash":"1185588073223721359","title":"Mitochondrial transport and membrane dynamics","description":"The cluster shows strong enrichment for mitochondrial-focused functions: membrane fission, various transport processes into or across the mitochondrial membranes (alpha-ketoglutarate, ornithine, ATP, pyrimidine nucleotides), and regulation of membrane permeability, plus links to adaptive thermogenesis. These collectively point to mitochondrial metabolism and membrane dynamics as the core theme, with a note that a couple of terms are obsolete annotations. ","confidence":"High","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090149","count":6},{"id":"GO:0000002","count":6},{"id":"GO:0046902","count":6},{"id":"GO:0097274","count":6},{"id":"GO:0015742","count":5}]},{"hash":"1177426125823672246","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":1},{"id":"GO:1902039","count":1},{"id":"GO:0000472","count":1},{"id":"GO:0000288","count":1},{"id":"GO:0001308","count":1}]},{"hash":"628621486718780305","title":"Nuclear mRNA decay and processing","description":"This cluster is dominated by GO terms tied to deadenylation-dependent and -independent mRNA decay and general mRNA catabolic processes, suggesting a core role in nuclear RNA turnover. Additional terms for mRNA splicing hint at broader RNA processing involvement. The presence of a couple of oxidative stress response terms may reflect how RNA turnover changes under stress, but the prevailing theme is nuclear RNA metabolism and processing.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000290","count":1},{"id":"GO:0000288","count":1},{"id":"GO:1901919","count":1},{"id":"GO:0000012","count":1},{"id":"GO:0045292","count":1}]},{"hash":"543992861238016562","title":"Ubiquitin-Dependent Regulation of Gene Expression","description":"This cluster is dominated by deubiquitination activities (K48-, K11-, and linear-linked) alongside transcription-related processes (DNA-templated transcription and spliceosomal assembly), suggesting a shared role in regulating gene expression via ubiquitin remodeling. Some terms are peripheral (necroptosis-related assembly, ethanol-related behavior), but the core theme centers on ubiquitin-mediated control of transcription/RNA processing.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":1},{"id":"GO:0000245","count":1},{"id":"GO:0071108","count":1},{"id":"GO:1990108","count":1},{"id":"GO:1903070","count":1}]},{"hash":"713558272930364010","title":"Protein and rRNA methylation","description":"This cluster is dominated by methylation-related GO terms\u2014N-terminal peptidyl-glycine methylation, peptidyl-lysine methylation (dimethyl/trimethyl), peptidyl-arginine methylation, and rRNA methylation\u2014with an additional hint of rDNA heterochromatin formation, suggesting a methyltransferase-centric module that modulates both proteins and RNA and may couple to chromatin regulation around rRNA genes.","confidence":"High","size":13,"edges":9,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0018013","count":2},{"id":"GO:0018023","count":2},{"id":"GO:0031167","count":2},{"id":"GO:0019919","count":2},{"id":"GO:0000183","count":2}]},{"hash":"868178738616117049","title":"Unknown","description":"The GO terms cover several unrelated themes (central metabolism like the TCA and urea cycles, polyamine biosynthesis, xenobiotic and oxidative stress responses, collagen/ECM biosynthesis, and various signaling and growth responses). There is no clear, single functional thread linking the proteins, and with no edges among them this cluster appears heterogeneous rather than a cohesive module.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":2},{"id":"GO:0033388","count":1},{"id":"GO:0008295","count":1},{"id":"GO:0042493","count":1},{"id":"GO:0032964","count":1}]},{"hash":"81924299374116000","title":"Transcriptional control of differentiation and vasculogenesis","description":"These proteins cluster around transcriptional regulation, highlighted by DNA-templated transcription and negative regulation of transcription from RNA Pol II. They also connect to differentiation and development\u2014positive regulation of myoblast differentiation and vasculogenesis\u2014plus Notch signaling regulation. A few outlier terms (menaquinone biosynthesis and outdated hydroxylation terms) likely reflect annotation noise. Overall, the group appears to be transcriptional regulators guiding differentiation and vascular developmental processes.","confidence":"Medium","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0061428","count":3},{"id":"GO:0045746","count":3},{"id":"GO:2001214","count":3},{"id":"GO:0036138","count":3}]},{"hash":"738319780195115488","title":"Unknown","description":"The GO terms span cell cycle, epithelial polarity, apoptosis in immune and liver cells, telomere maintenance, endocytosis, innate immune signaling, and sensory temperature perception, with no single unifying function. With no edges and a broad mix of processes, there isn't a cohesive theme to name the cluster beyond Unknown.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":4},{"id":"GO:0090162","count":4},{"id":"GO:0033028","count":4},{"id":"GO:0097284","count":4},{"id":"GO:2000171","count":4}]},{"hash":"1161130701634405856","title":"Unknown","description":"The terms span xenobiotic and nutrient responses alongside RNA modification and tRNA/rRNA processing, with no single cohesive function tying all proteins together; thus there isn\u2019t a confident, representative label.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":3},{"id":"GO:0009877","count":2},{"id":"GO:0007584","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0002943","count":1}]},{"hash":"966175261128820909","title":"Unknown","description":"The cluster has no GO terms, no edges, and no apparent functional signal to connect the members, so there is no clear common theme to name it; label as Unknown.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2280682949263843388","title":"Vesicle trafficking and organelle transport","description":"The top terms cluster around intracellular transport of cargo via vesicles, including endosome-to-melanosome transport, endosomal vesicle fusion, cytoplasm-to-vacuole targeting, and transmembrane transport, indicating a shared vesicle- and organelle- trafficking function despite some peripheral terms. Medium","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021762","count":2},{"id":"GO:0051457","count":1},{"id":"GO:0042517","count":1},{"id":"GO:1903542","count":1},{"id":"GO:0071806","count":1}]},{"hash":"1966139331960800866","title":"Neural and Developmental Processes","description":"The top GO terms center on brain and neural development (brain development, forebrain development, neural tube closure) and broader developmental processes (multicellular organism development, skeletal system development). Although there are a few terms related to stress responses and DNA replication, the dominant signal is neural and developmental biology, justifying this label.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0075713","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0050830","count":2}]},{"hash":"1508938344975418124","title":"Calcium signaling and insulin secretion","description":"Top GO terms indicate Ca2+-dependent signaling and release (ryanodine receptor regulation, sarcoplasmic reticulum calcium release), along with insulin secretion and its glucose-responsive regulation. These collectively point to a calcium-regulated secretory/endocrine function as the core theme of this cluster, with a few less-connected terms (e.g., prostate development, amyloid formation) acting as background noise. ","confidence":"High","size":13,"edges":42,"triangles":61,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0060315","count":2},{"id":"GO:1901710","count":2},{"id":"GO:0030850","count":2},{"id":"GO:0035584","count":2},{"id":"GO:0014808","count":2}]},{"hash":"1032472516367562396","title":"Nematode Development and Reproduction","description":"The GO terms are largely centered on nematode biology\u2014molting and cuticle formation, pharyngeal pumping, and reproductive regulation (polyspermy prevention, sperm binding regulation), plus maternal axis specification during early development. This pattern points to lifecycle progression and reproductive processes typical of nematodes, despite a few broader annotations. Confidence: Medium","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046718","count":2},{"id":"GO:0035124","count":2},{"id":"GO:0048632","count":2},{"id":"GO:0018996","count":2},{"id":"GO:0006508","count":2}]},{"hash":"2081199092428500553","title":"Nucleotide and Cofactor Metabolism","description":"The top GO terms cluster around catabolic and biosynthetic processes for nucleotides (dGDP, dADP, IDP, diadenosine hexaphosphate) and cofactors (coenzyme A), plus related biosynthesis (folic acid, DMAPP); a few RNA-related processes (snoRNA catabolic, adenosine-to-inosine editing) are present but likely secondary. This breadth points to a functional theme of nucleotide/cofactor turnover and small-molecule metabolism.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046656","count":1},{"id":"GO:0046067","count":1},{"id":"GO:0016077","count":1},{"id":"GO:0071544","count":1},{"id":"GO:0046057","count":1}]},{"hash":"1414064639893393320","title":"Arthropod Cuticle Development and Molting","description":"This cluster is dominated by GO terms tied to chitin-based cuticle development (GO:0040003), ecdysis (GO:0018990), and polysaccharide catabolic processes (GO:0000272), which together point to cuticle formation and molting in arthropods. Additional terms such as synapse organization and interleukin responses appear but are less central to the core function; they may reflect broader roles of the proteins or annotation noise. Overall, the strongest common theme is cuticle biosynthesis/remodeling and molting processes.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008285","count":2},{"id":"GO:0050808","count":2},{"id":"GO:0071347","count":2},{"id":"GO:0009612","count":2},{"id":"GO:0000272","count":2}]},{"hash":"883218484807806314","title":"Serine/threonine kinase signaling regulation","description":"The top GO terms point to regulation and activation of serine/threonine phosphorylation and kinase activity, including positive and negative regulation of protein serine/threonine kinase activity and phosphorylation events. Other terms touch on cell cycle control (G1/S) and autophagy/starvation responses, suggesting a kinase-centered signaling module that modulates growth, stress response, and cell-cycle progression.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033138","count":1},{"id":"GO:0031139","count":1},{"id":"GO:0010506","count":1},{"id":"GO:0071901","count":1},{"id":"GO:0009267","count":1}]},{"hash":"178176135226872582","title":"Folate and riboflavin metabolism","description":"Top GO terms include tetrahydrofolate biosynthetic process and interconversion, and a response to vitamin B2, suggesting a shared role in folate metabolism with riboflavin-dependent cofactors. Some terms are obsolete and there are no edges, but the recurring folate-related processes provide a plausible unifying theme. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0009820","count":1},{"id":"GO:0033274","count":1},{"id":"GO:0009086","count":1},{"id":"GO:0046654","count":1}]},{"hash":"233601912118325007","title":"Heat-stress signaling with telomere localization","description":"This cluster is dominated by intracellular signal transduction terms and several temperature/chemical stimulus responses (thermoception, response to capsazepine, heat-stress transcription), suggesting a module of stress-responsive signaling. The presence of telomere maintenance and telomeric region localization terms provides a secondary link to telomere biology, but overall the set appears to reflect diverse stress- and signaling-related roles rather than a single pathway, hence the heat-stress signaling label with moderate confidence.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":3},{"id":"GO:0032212","count":2},{"id":"GO:0048549","count":2},{"id":"GO:0070427","count":2},{"id":"GO:0050955","count":2}]},{"hash":"576291001486354836","title":"Cardiac function regulation cluster","description":"The top terms show emphasis on heart rate regulation, cardiac conduction, and cardiac muscle cell proliferation, with a cGMP response, pointing to cardiac signaling/regulation. The remaining terms suggest broader transcriptional and metabolic regulation, indicating some heterogeneity beyond cardiac-specific functions.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002027","count":2},{"id":"GO:0060038","count":1},{"id":"GO:0071321","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0045013","count":1}]},{"hash":"1963405078383903049","title":"Unknown","description":"The top GO terms span plant development, microbial metabolism, and neuronal components, with no unifying biological process or cellular localization linking the proteins. The set includes seed germination and seed coat development (plant), various metabolic pathways (fermentation to acetate, phenylpropanoid metabolism, menaquinone biosynthesis), siderophore biosynthesis (bacteria), and even microtubule localization or postsynaptic density clustering (neural). This suggests annotation noise or a highly heterogeneous collection rather than a single cohesive function, so no confident single-label theme can be assigned.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035372","count":1},{"id":"GO:1902897","count":1},{"id":"GO:0010030","count":1},{"id":"GO:0008218","count":1},{"id":"GO:0019654","count":1}]},{"hash":"816667548771376825","title":"Developmental transcription regulation","description":"The terms include multiple development-related GO terms across tissues (myotube development, cerebellar cortex development, uterine gland development, hepatocyte homeostasis) and transcription-related terms (DNA-templated transcription, transcription regulation by RNA polymerase II, histone acetylation). This suggests a broad theme of transcriptional control during development in diverse organs, rather than a single, specific function. Therefore the label Developmental transcription regulation captures the shared concept while remaining concise.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014904","count":1},{"id":"GO:2000134","count":1},{"id":"GO:0045944","count":1},{"id":"GO:2000616","count":1},{"id":"GO:0021695","count":1}]},{"hash":"1660512538940427644","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033260","count":1},{"id":"GO:0006398","count":1},{"id":"GO:0097107","count":1},{"id":"GO:2000303","count":1},{"id":"GO:1904238","count":1}]},{"hash":"1828318675649747909","title":"GPCR-driven cyclic nucleotide signaling and sensory responses","description":"The top GO terms cluster around G protein-coupled receptor signaling pathways (adenylate cyclase and guanylyl cyclase activation, adenosine receptor signaling) and biosynthesis of cAMP and cGMP, plus sensory-related processes like blue light signaling and hypoxia detection, suggesting a cohesive role in GPCR-mediated signal transduction and cyclic nucleotide second messenger production in sensory/environmental responses.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0071880","count":8},{"id":"GO:0070483","count":8},{"id":"GO:0006182","count":8},{"id":"GO:0009785","count":8},{"id":"GO:0001973","count":8}]},{"hash":"54444001468759331","title":"GPCR-driven cyclic nucleotide signaling","description":"This cluster is dominated by GO terms tied to G protein-coupled receptor signaling and production of cyclic nucleotides, including both cAMP and cGMP pathways (adenylate cyclase-activating adrenergic receptor signaling, adenosine receptor signaling, receptor guanylyl cyclase signaling, and cGMP/cAMP biosynthesis). The presence of blue light signaling and hypoxia detection terms suggests broader signaling contexts but still points to GPCR- and second-messenger\u2013mediated communication. Therefore, a concise label focusing on GPCR-driven cyclic nucleotide signaling captures the core functional theme of this cluster.","confidence":"Medium","size":12,"edges":3,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0071880","count":3},{"id":"GO:0070483","count":3},{"id":"GO:0006182","count":3},{"id":"GO:0009785","count":3},{"id":"GO:0001973","count":3}]},{"hash":"2051792572171332464","title":"Stomatal CO2 and Blue-Light Signaling","description":"The top terms point to plant-specific signaling responses to carbon dioxide and blue light, including cellular CO2 response, blue light pathways, and regulation of stomatal development, with supporting cGMP and GPCR/receptor signaling components and transcriptional regulation. This combination suggests a cohesive theme of stomatal signaling and development modulated by CO2 and light cues.","confidence":"High","size":12,"edges":20,"triangles":9,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0015976","count":3},{"id":"GO:2000122","count":3},{"id":"GO:0071244","count":3},{"id":"GO:0071880","count":2},{"id":"GO:0070483","count":2}]},{"hash":"902106448454161904","title":"Lipid biosynthesis and redox homeostasis","description":"This cluster shows a clear emphasis on lipid metabolism (unsaturated fatty acid biosynthesis, sphingolipid metabolism via mannosyl-inositol phosphorylceramide) as well as functions tied to lipid-rich tissues (sebaceous gland differentiation, CNS myelin maintenance). In addition, several terms relate to redox balance and detoxification (cellular oxidant detoxification, redox homeostasis) and responses to environmental stresses (ethanol, aluminum, herbicide), suggesting the proteins coordinate lipid biosynthesis with oxidative stress management. Confidence: Medium","confidence":"","size":12,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001949","count":3},{"id":"GO:0032286","count":3},{"id":"GO:0006675","count":3},{"id":"GO:0098869","count":2},{"id":"GO:0010044","count":2}]},{"hash":"1534837929157523950","title":"TGF-beta/BMP signaling regulation","description":"The top GO terms point to regulation of TGF-beta/BMP signaling, including negative regulation of BMP signaling and TGF-beta receptor signaling, plus cellular responses to TGF-beta and SMAD-related references. The presence of peptidyl-threonine dephosphorylation suggests phosphatases modulating this pathway. While some plant-specific terms appear, the dominant theme is modulation of TGF-beta/BMP signaling.","confidence":"High","size":12,"edges":10,"triangles":1,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0035970","count":5},{"id":"GO:0046827","count":4},{"id":"GO:0030514","count":4},{"id":"GO:0071560","count":4},{"id":"GO:0010991","count":4}]},{"hash":"956559249142574189","title":"Unknown","description":"There are no GO terms or network connections to define a shared function, and the cluster shows no edges or triangles, making it impossible to infer a coherent theme. The proteins were re-added by ReCIPE, but without functional signals, a reliable label cannot be assigned.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1953092718766051912","title":"Unknown","description":"No common functional theme can be inferred: the cluster has 12 proteins with no reported edges or GO terms (Top Terms is empty; Max Degree 0; Triangles 0), and although ReCIPE added 20 proteins, they do not connect into a coherent function group. Therefore label is Unknown.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"490330978266069574","title":"Retroviral integration and latency","description":"Top GO terms center on reverse transcription (RNA-templated DNA biosynthesis), DNA replication and integration, viral entry into host cells and penetration into the nucleus, and the establishment of integrated proviral latency. Together these indicate a retroviral-like life cycle with proviral latency, and the label captures the dominant theme of the cluster.","confidence":"High","size":12,"edges":5,"triangles":2,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006278","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0039651","count":3},{"id":"GO:0015074","count":3},{"id":"GO:0075713","count":3}]},{"hash":"1811788117635857576","title":"Ribosome Biogenesis and Assembly","description":"The top GO terms are dominated by ribosome production processes, including ribosome biogenesis, maturation of LSU-rRNA, cytosolic ribosome assembly, and preribosome assembly for the large subunit, pointing to a cohesive role in assembling and maturing ribosomes. Peripheral terms like protein ubiquitination and proteasome assembly may reflect broader protein homeostasis rather than a core function of the cluster.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0042256","count":2},{"id":"GO:1902626","count":2},{"id":"GO:0009409","count":2}]},{"hash":"724868647191538328","title":"LPS Core and Lipid Biosynthesis","description":"The top GO terms are dominated by lipopolysaccharide biosynthetic processes (LPS core, O antigen) and related lipid pathways (CDP-diacylglycerol, phosphatidylinositol remodeling; GDP-mannose and ADP-L-glycero-beta-D-manno-heptose biosynthesis). Although some terms appear unrelated and there are no observed edges, the cohesive theme centers on bacterial LPS assembly and lipid biosynthesis, suggesting a bacterial envelope biosynthesis function for this cluster.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007274","count":2},{"id":"GO:0016024","count":1},{"id":"GO:0060217","count":1},{"id":"GO:0036149","count":1},{"id":"GO:0009244","count":1}]},{"hash":"947070110557054534","title":"Negative regulation of signaling pathways","description":"The cluster shows a clear enrichment for GO terms involving downregulation of signaling processes (BMP signaling, TGF-beta receptor signaling, SMAD complex regulation, and non-canonical NF-kappaB). Added terms point to related regulatory activities like nuclear export and peptidyl-threonine dephosphorylation, suggesting a theme of controlling signaling and intracellular trafficking. Some terms are organism-specific (meristem identity, photosystem adjustments), but the dominant pattern is negative regulation of signaling, making this label appropriate.","confidence":"Medium","size":12,"edges":15,"triangles":8,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":5},{"id":"GO:0030514","count":4},{"id":"GO:0071560","count":4},{"id":"GO:0035970","count":4},{"id":"GO:0010991","count":4}]},{"hash":"2142313380719987741","title":"Spindle assembly and chromosome segregation","description":"Based on the top GO terms, the cluster is dominated by mitotic spindle\u2013related processes (assembly, elongation, orientation, microtubule-kinetochore attachment) and cytokinesis, pointing to spindle dynamics driving chromosome separation during cell division (mitosis/meiosis). Some terms may be peripheral or noisy (e.g., chloroplast movement, Purkinje cell layer organization), but the core theme is clearly spindle-mediated chromosome segregation.","confidence":"High","size":12,"edges":64,"triangles":200,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0000743","count":11},{"id":"GO:1990942","count":11},{"id":"GO:0021693","count":11},{"id":"GO:0000022","count":11},{"id":"GO:0051296","count":11}]},{"hash":"1458477299643549930","title":"Unknown","description":"The top GO terms are highly diverse, spanning cell migration, muscle stretch response, cell cycle regulation, RNA processing, telomere maintenance, adipogenesis, epithelial polarity, and apoptosis. There are no clear, single pathways tying these proteins together, and with no edges among them, a cohesive functional label is not supported.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":9},{"id":"GO:0035994","count":8},{"id":"GO:0045736","count":8},{"id":"GO:0006397","count":8},{"id":"GO:0032212","count":8}]},{"hash":"2041694357910408767","title":"Nucleotide Biosynthesis and DNA Replication","description":"This cluster is dominated by GO terms for nucleotide metabolism and biosynthesis (AMP salvage, purine interconversion, ADP/CDP/ITP-related phosphorylation) alongside DNA replication, pointing to a core function in nucleotide production used for DNA synthesis. The brain and liver development terms likely reflect broader tissue-context annotations rather than a primary function, so the dominant theme remains nucleotide metabolism plus replication in proliferating cells.","confidence":"Medium","size":12,"edges":50,"triangles":105,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0044209","count":8},{"id":"GO:0007420","count":8},{"id":"GO:0046939","count":7},{"id":"GO:0015951","count":7},{"id":"GO:0046041","count":7}]},{"hash":"375371648111656984","title":"Biosynthesis and Metabolism","description":"The top GO terms are dominated by biosynthetic and metabolic processes (cholesterol biosynthetic process, lipopolysaccharide core region biosynthetic process, glucose metabolic process), suggesting the cluster centers on biomolecule synthesis and energy metabolism. There are a few signaling/regulatory terms (T cell receptor signaling, Wnt pathway regulation) that appear less central, indicating these may be secondary roles within a broader metabolic context.","confidence":"Medium","size":12,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006695","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0009244","count":2},{"id":"GO:0050852","count":2},{"id":"GO:0060716","count":2}]},{"hash":"916884394976276699","title":"Transcription and RNA Processing Regulation","description":"The cluster shows a clear emphasis on gene expression control, with GO terms centered on transcription (DNA-templated transcription, transcription antitermination, termination regulation) and RNA processing/stability (pre-miRNA processing, miRNA catabolic process, CRD-mediated mRNA stabilization), plus related developmental signals. This suggests a cohesive theme of regulating transcription and post-transcriptional RNA maturation and stability.","confidence":"Medium","size":12,"edges":17,"triangles":3,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0031054","count":1},{"id":"GO:1902219","count":1},{"id":"GO:0060567","count":1},{"id":"GO:1901724","count":1}]},{"hash":"70517770793789796","title":"T cell activation and signaling","description":"The cluster\u2019s terms cluster around immune signaling and T cell activation, notably T cell activation via TCR-MHC interactions (GO:0002291) and integrin-mediated signaling (GO:0007229), with accompanying signaling dynamics such as cAMP response and peptide hormone stimulus. Also present are apoptosis regulation and extracellular matrix-related processes (hyaluronan metabolism), which can accompany lymphocyte activation and adhesion. Together, these point to a cohesive theme of immune cell signaling and activation, with ECM context. ","confidence":"Medium","size":12,"edges":20,"triangles":11,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0019233","count":2},{"id":"GO:0071320","count":2},{"id":"GO:0051262","count":2},{"id":"GO:0071375","count":2}]},{"hash":"1089924876839210443","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":18,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000380","count":2},{"id":"GO:0030260","count":2},{"id":"GO:0019068","count":2},{"id":"GO:0039651","count":2},{"id":"GO:0015074","count":2}]},{"hash":"1010012474387750862","title":"Regulation of mRNA splicing and ncRNA silencing","description":"The cluster is dominated by terms linking mRNA splicing, spliceosome function, and splice site recognition (positive/negative regulation of splicing, cis splicing via spliceosome), along with regulatory ncRNA\u2013mediated gene silencing, indicating a core theme of RNA processing and ncRNA-driven regulation. A minor term related to translation initiation factor complex assembly is compatible with RNA-protein regulatory complexes.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":2},{"id":"GO:0048026","count":2},{"id":"GO:1902625","count":2},{"id":"GO:0075525","count":2},{"id":"GO:1905663","count":2}]},{"hash":"564642800315938872","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0097500","count":1},{"id":"GO:0070121","count":1},{"id":"GO:0060271","count":1},{"id":"GO:0042755","count":1},{"id":"GO:0032402","count":1}]},{"hash":"328484827551030800","title":"Proteostasis via ubiquitin-proteasome and ERAD","description":"The top terms point to protein quality control and degradation, including ubiquitin-dependent ERAD, nuclear quality control by the ubiquitin-proteasome system, and misfolded protein transport. While some terms are obsolete or unrelated (DNA replication, mesoderm formation), the prevailing theme is proteostasis and targeting misfolded proteins for degradation.","confidence":"Medium","size":12,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":5},{"id":"GO:0006260","count":4},{"id":"GO:0097428","count":4},{"id":"GO:0032781","count":4},{"id":"GO:0001707","count":4}]},{"hash":"1372761908933590882","title":"RNA splicing and translation initiation","description":"Top terms indicate a focus on RNA metabolism: spliceosome-mediated mRNA splicing (including positive/negative regulation) and assembly of the eIF4F translation initiation complex, with supporting RNA silencing regulation. This suggests the cluster centers on RNA processing and translation initiation control.","confidence":"High","size":12,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1902455","count":1},{"id":"GO:0031047","count":1},{"id":"GO:0048026","count":1},{"id":"GO:1902625","count":1},{"id":"GO:0075525","count":1}]},{"hash":"648703958970269765","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030260","count":1},{"id":"GO:0019068","count":1},{"id":"GO:0039651","count":1},{"id":"GO:0015074","count":1},{"id":"GO:0075713","count":1}]},{"hash":"744288655139034513","title":"Apoptosis and DNA Damage Response Regulation","description":"The terms point to signaling that governs cell fate decisions, with strong emphasis on apoptosis regulation (positive regulation of apoptotic process; mitochondrial fragmentation in apoptosis) and DNA damage response/checkpoints (negative regulation of intrinsic apoptotic signaling in response to DNA damage; positive regulation of DNA damage checkpoint) as well as transcription regulation linked to DNA-templated processes. While a few terms touch on other regulatory processes like Wnt signaling and ion homeostasis, the overall theme is coordinated control of apoptosis and DNA damage\u2013related signaling.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043065","count":2},{"id":"GO:0090311","count":1},{"id":"GO:1902230","count":1},{"id":"GO:2000003","count":1},{"id":"GO:0030308","count":1}]},{"hash":"1887080342602934528","title":"Negative Regulation of Autophagy, Glycogen Metabolism, and Signaling","description":"The terms show regulatory roles across autophagy, glycogen metabolism, calcium signaling, and CDK activity, with no inferred interactions, suggesting these proteins function mainly as regulators of these processes rather than core enzymes.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042144","count":1},{"id":"GO:0016242","count":1},{"id":"GO:0005981","count":1},{"id":"GO:0005979","count":1},{"id":"GO:0050849","count":1}]},{"hash":"1651083665968522311","title":"Calcium signaling and NFAT regulation","description":"The cluster shows several GO terms centered on calcium signaling and its downstream transcriptional effects (phosphatidylinositol-mediated signaling, detection/handling of calcium ions, and regulation of the calcineurin-NFAT cascade, plus negative regulation of calcium import and protein kinase activity). This suggests a cohesive theme of calcium-dependent signaling and transcriptional control, with a few outliers likely due to annotation noise or broader protein roles. ","confidence":"Medium","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0048015","count":1},{"id":"GO:0045944","count":1},{"id":"GO:0005513","count":1},{"id":"GO:0072221","count":1},{"id":"GO:0060316","count":1}]},{"hash":"588154768993315312","title":"Muscle regeneration and calcium signaling","description":"The cluster centers on skeletal muscle development and regeneration, with terms like myoblast fusion and satellite cell activation repeatedly pointing to muscle repair processes, alongside positive regulation of calcium release into the cytosol, which is key to muscle signaling and contraction. Some outlying terms exist, but the core theme is muscle regeneration and calcium-mediated signaling.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001666","count":1},{"id":"GO:0051281","count":1},{"id":"GO:0016540","count":1},{"id":"GO:0097264","count":1},{"id":"GO:0007520","count":1}]},{"hash":"1106725979576340541","title":"Retroviral DNA Integration and Latency","description":"The GO terms cluster around reverse transcription, DNA replication/recombination, DNA integration, proviral latency, and viral or symbiont entry into the host nucleus, all characteristic of retroviral life cycle steps and host genome integration. This suggests the proteins participate in retroviral replication and proviral establishment within the host. ","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0006310","count":5},{"id":"GO:0006278","count":4},{"id":"GO:0039651","count":4},{"id":"GO:0015074","count":4}]},{"hash":"587967367707777742","title":"Diverse Metabolic Pathways","description":"This cluster features GO terms covering lipid biosynthesis and oxidation, various sugar and amino acid catabolic processes, and specialized metabolite pathways (retinoic acid, lignin), along with a lipopolysaccharide response and respiration. The shared theme is broad metabolic activity and energy-related processes rather than a single, cohesive function, so a label like \u201cDiverse Metabolic Pathways\u201d best captures the aggregate function of these proteins.","confidence":"Medium","size":12,"edges":40,"triangles":54,"max_degree":11,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0006633","count":7},{"id":"GO:0009809","count":5},{"id":"GO:0006069","count":5},{"id":"GO:0019595","count":5},{"id":"GO:0010430","count":5}]},{"hash":"1448304864954441607","title":"Apoptosis and cell cycle regulation","description":"This cluster is dominated by GO terms for apoptotic process, p53-mediated regulation, and cell cycle transitions (G1/S) as well as spindle organization/checkpoint signaling, suggesting a core theme of cellular stress responses that govern apoptosis and cell cycle control, with some related stress responses such as viral response and neuron death regulation.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006915","count":5},{"id":"GO:0016242","count":3},{"id":"GO:2000727","count":3},{"id":"GO:0010765","count":3},{"id":"GO:0000082","count":3}]},{"hash":"1180171370206198836","title":"Nuclear DNA metabolism, RNA surveillance, and protein import","description":"These terms cluster around nuclear functions: DNA replication and recombination, mRNA quality control via nonsense-mediated decay, and import/targeting of proteins into the nucleus. The presence of developmental and viral process terms likely reflects broader roles or pleiotropy, but the dominant theme is nuclear genome maintenance, RNA surveillance, and protein trafficking. ","confidence":"Medium","size":12,"edges":7,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0006605","count":2},{"id":"GO:0000184","count":2},{"id":"GO:0048701","count":2},{"id":"GO:0006310","count":2}]},{"hash":"543515300899763742","title":"SNARE-Driven Vesicle Trafficking in Neurons","description":"This cluster centers on vesicle trafficking and exocytosis in the secretory pathway, highlighted by SNARE complex assembly, intra-Golgi transport, vesicle fusion with the Golgi, exocytic insertion of neurotransmitter receptors, Golgi ribbon formation, and plasma membrane organization, all of which are tied to synaptic receptor trafficking and long-term potentiation.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071470","count":3},{"id":"GO:0034605","count":3},{"id":"GO:0010972","count":3},{"id":"GO:0007009","count":3},{"id":"GO:0090161","count":2}]},{"hash":"1876020698382076193","title":"Chromatin remodeling and chromosome segregation","description":"The top GO terms cluster around chromatin dynamics and genome maintenance, including histone acetylation, chromatin organization, and homologous chromosome segregation, pointing to roles in DNA packaging and proper chromosome partitioning. A few terms (e.g., phagolysosome assembly, growth hormone response) are more distant, which may reflect broader annotation signals or multifunctional proteins. With no observed edges, the core theme remains chromatin-related. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043981","count":3},{"id":"GO:0000747","count":2},{"id":"GO:0050679","count":2},{"id":"GO:1902510","count":2},{"id":"GO:0001845","count":2}]},{"hash":"2111923932044590466","title":"Diverse small-molecule metabolism","description":"The listed GO terms point to a mix of catabolic and biosynthetic processes affecting a variety of small organic molecules and secondary metabolites (alkaloids, stilbenes, antibiotics, strigolactones, menaquinone biosynthesis, poly-hydroxybutyrate, etc.). There isn\u2019t a single unified pathway apparent; instead, the cluster seems to represent a broad, shared involvement in processing diverse small molecules.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019260","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0017000","count":1},{"id":"GO:0097755","count":1},{"id":"GO:1902348","count":1}]},{"hash":"461473531103941280","title":"Lipid metabolism and steroid biosynthesis","description":"The GO terms with strongest signal are fatty-acyl-CoA biosynthetic process, fatty acid beta-oxidation using acyl-CoA dehydrogenase, and steroid biosynthetic process, indicating the proteins in this cluster are predominantly involved in lipid metabolism and related biosynthetic pathways. Other terms are more peripheral, so this label best captures the core theme of the cluster.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006355","count":1},{"id":"GO:0030224","count":1},{"id":"GO:0019439","count":1},{"id":"GO:0032286","count":1}]},{"hash":"2034109503313755075","title":"ER Stress and Protein Quality Control","description":"The top GO terms cluster around responses to misfolded proteins in the endoplasmic reticulum, ER-associated degradation, ubiquitin-related protein turnover, and ATP-dependent energy processes, all pointing to ER quality control and proteostasis mechanisms. Although a few terms touch on DNA replication and peroxisomal import, the dominant theme is ER stress\u2013driven protein quality control and degradation pathways, supported by ubiquitin-protease activity and ATP metabolism.","confidence":"Medium","size":12,"edges":7,"triangles":2,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0071218","count":3},{"id":"GO:0061166","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0046034","count":3},{"id":"GO:0070407","count":3}]},{"hash":"1091612136741510389","title":"Cellular stress response and signaling","description":"The GO terms cluster around responses to external stimuli (xenobiotic, hydrogen peroxide, peptide hormone) and related signaling/post-transcriptional regulation (mRNA stability, phosphatidylinositol dephosphorylation), suggesting proteins involved in sensing stress and mediating downstream signaling rather than a single specific function.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0080111","count":5},{"id":"GO:0090502","count":5},{"id":"GO:0014912","count":5},{"id":"GO:0042493","count":5},{"id":"GO:0070301","count":5}]},{"hash":"1937263578223540880","title":"Diverse biosynthesis of lipids, pigments, and hormones","description":"These proteins are tied to multiple biosynthetic processes across different molecule classes (lipids like mycolic acids, pigments such as melanin, hormones like androgens/estrogens, and other biosynthetic pathways). The lack of a single cohesive pathway, plus no interactions within the cluster, supports a broad biosynthetic theme rather than a specific function. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0071768","count":6},{"id":"GO:0055114","count":6},{"id":"GO:0017000","count":6},{"id":"GO:0042438","count":6},{"id":"GO:0042619","count":6}]},{"hash":"827042320563039942","title":"Ciliary motility and snoRNP assembly","description":"The cluster includes GO:0060285 cilium-dependent cell motility and GO:0070286 axonemal dynein complex assembly, indicating involvement in ciliary motility. It also features snoRNP- and snoRNA-related terms (Box C/D snoRNP assembly, snoRNA localization), pointing to nucleolar RNA-processing roles. Additional terms touch on nucleolar rRNA transcription by RNA polymerase I and TORC1 signaling, suggesting links to growth-related regulation of ribosome biogenesis. Overall, the proteins seem to connect ciliary machinery with nucleolar RNA processing rather than a single cohesive function.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060285","count":1},{"id":"GO:1901838","count":1},{"id":"GO:1904263","count":1},{"id":"GO:2000619","count":1},{"id":"GO:0000492","count":1}]},{"hash":"1115490061898071724","title":"Sterol biosynthesis and lipid metabolism","description":"The top GO terms overwhelmingly point to lipid and sterol pathways\u2014cholesterol/ergosterol biosynthesis, various sterol oxidations, fatty acid and ether lipid metabolism\u2014which together define a lipid-metabolism-centric group. Some terms relate to lipid-rich tissues (CNS myelin maintenance, sebaceous gland differentiation), with a couple peripheral terms (e.g., B cell chemotaxis) likely reflecting membrane-associated roles rather than core function. ","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080064","count":2},{"id":"GO:0033490","count":2},{"id":"GO:0032286","count":2},{"id":"GO:0006675","count":2},{"id":"GO:0001949","count":2}]},{"hash":"365445400049440045","title":"Proteostasis and Ubiquitin-Proteasome Quality Control","description":"The cluster is enriched for protein quality control and degradation functions, including nuclear quality control by the ubiquitin-proteasome system, misfolded protein transport, and ubiquitin-dependent ERAD, with related terms pointing to proteostasis rather than a single development or replication process.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001707","count":3},{"id":"GO:0006260","count":2},{"id":"GO:0097428","count":2},{"id":"GO:0032781","count":2},{"id":"GO:0006469","count":2}]},{"hash":"1889692090947383278","title":"Unknown","description":"These proteins span a mix of processes (budding growth, hormone signaling, apoptosis, drug/toxic responses, cholesterol biosynthesis, autophagy regulation, cardiac differentiation, and ion transport) with little overlap and only minimal network connectivity. There isn\u2019t a clear shared function to define a cohesive label, so a generic Unknown category is most appropriate.","confidence":"","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0007118","count":4},{"id":"GO:0071375","count":4},{"id":"GO:0008285","count":4},{"id":"GO:0006915","count":4},{"id":"GO:0009636","count":4}]},{"hash":"505876476415961406","title":"GPCR-driven cAMP/cGMP Signaling in Sensory Pathways","description":"The proteins cluster around G protein-coupled receptor signaling (adrenergic and adenosine receptors), receptor guanylyl cyclase signaling, and biosynthesis of cAMP and cGMP, along with sensory-related processes (blue light signaling, hypoxia detection) and transcription regulation. This points to a coherent module where GPCR activity modulates cyclic nucleotide second messengers to influence gene expression in sensory/environmental responses.","confidence":"High","size":11,"edges":7,"triangles":0,"max_degree":6,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0071880","count":4},{"id":"GO:0070483","count":4},{"id":"GO:0006182","count":4},{"id":"GO:0009785","count":4},{"id":"GO:0001973","count":4}]},{"hash":"1747444116449498317","title":"Unknown","description":"The cluster has no shared GO terms listed (Top Terms is empty), and with only 11 proteins and 8 edges, plus no triangles, there is insufficient functional signal to infer a unifying biological role. The ReCIPE note indicates network refinement rather than functional annotation, so a specific, representative label cannot be confidently assigned.","confidence":"","size":11,"edges":8,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[]},{"hash":"1766658132448298841","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":53,"triangles":148,"max_degree":10,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006369","count":9},{"id":"GO:0045944","count":6},{"id":"GO:0006260","count":6},{"id":"GO:0034475","count":6},{"id":"GO:0048026","count":6}]},{"hash":"151985459443404339","title":"Nucleolar Transcription and Ribosome Biogenesis","description":"This cluster centers on transcriptional activity within the nucleolus and the production of ribosomes, as shown by GO terms for RNA polymerases I\u2013III, ribosome biogenesis, nucleologenesis, and nucleolar transcription, along with Pol II transcription and regulatory ncRNA-related chromatin processes. A couple of outliers (neuronal crest migration and oxidative stress) appear less central to this theme and may reflect broader annotation noise, but the core signal strongly indicates nucleolar transcription coupled to ribosome assembly.","confidence":"High","size":11,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042797","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0017126","count":1},{"id":"GO:0001172","count":1},{"id":"GO:0042790","count":1}]},{"hash":"870548189386306917","title":"RNA processing and transcription regulation cluster","description":"The cluster\u2019s top GO terms cluster around RNA metabolism and gene expression control, including translation, tRNA modification, pre-miRNA processing, transcription activities, transcription termination regulation, transcription antitermination, miRNA catabolic processes, and CRD-mediated mRNA stabilization. This suggests a shared theme of RNA processing and regulation of transcription rather than a single signaling pathway. A few terms related to kidney development and osmotic-stress\u2013related apoptosis are represented by single instances and may reflect broader cellular context rather than a core function of the cluster.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006400","count":2},{"id":"GO:0031054","count":1},{"id":"GO:0006351","count":1},{"id":"GO:1902219","count":1}]},{"hash":"470988401662215001","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006620","count":1},{"id":"GO:0051083","count":1},{"id":"GO:0000466","count":1},{"id":"GO:0000463","count":1},{"id":"GO:0000055","count":1}]},{"hash":"811559580001771446","title":"T Cell Immune Regulation","description":"This cluster is best described by signals related to T cell biology: regulation of T cell proliferation, T cell homeostasis, and negative regulation of IL-2 production, along with cellular responses to glucocorticoid stimulus\u2014all classic aspects of T cell immune modulation. Some polyadenylation-related terms and a few other signals (antibiotic response, chorio-allantoic fusion) appear weak or noisy, not tying the set into a single cohesive theme, so the immune-regulatory T cell connection is the strongest common thread.","confidence":"Medium","size":11,"edges":48,"triangles":112,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0098789","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0071385","count":1},{"id":"GO:0045085","count":1}]},{"hash":"711983724287418285","title":"Cell cycle regulation and p53 signaling","description":"This cluster centers on mitosis and cell-cycle control (G1/S transition, centrosome separation, meiotic spindle organization), together with nuclear transport and p53-mediated stress/damage signaling. While a few terms touch on viral response or differentiation signals, the dominant theme links cell division control and p53 pathway regulation.","confidence":"High","size":11,"edges":12,"triangles":1,"max_degree":6,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0046827","count":8},{"id":"GO:0007100","count":8},{"id":"GO:0016242","count":7},{"id":"GO:2000727","count":7},{"id":"GO:0010765","count":7}]},{"hash":"411940606585720495","title":"Mitotic cell cycle control and p53 signaling","description":"The top GO terms cluster around regulation of cell cycle progression (G1/S transition, meiotic spindle organization/checkpoint) and p53-mediated signaling, with an additional link to receptor serine/threonine kinase pathways. This suggests a coherent theme of cell cycle regulation intertwined with p53-dependent stress signaling, despite some ancillary terms. Confidence: High","confidence":"","size":11,"edges":6,"triangles":0,"max_degree":3,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0016242","count":11},{"id":"GO:2000727","count":11},{"id":"GO:0010765","count":11},{"id":"GO:0000082","count":11},{"id":"GO:0000212","count":11}]},{"hash":"276765841907485642","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000463","count":5},{"id":"GO:0000462","count":5},{"id":"GO:0000398","count":5},{"id":"GO:0000466","count":5},{"id":"GO:0042273","count":5}]},{"hash":"357633982520847523","title":"ER protein quality control and degradation","description":"The cluster is dominated by GO terms for cellular response to misfolded protein, ER-associated degradation, and energy-dependent proteostasis (ATP-driven degradation and ubiquitin-specific protease regulation), pointing to ER quality control and proteasomal turnover. A few terms like DNA replication and gas vesicle organization appear incidental, likely annotation noise or multifunctional proteins, but the core theme centers on ERAD and ATP-dependent protein turnover.","confidence":"Medium","size":11,"edges":7,"triangles":3,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0071218","count":7},{"id":"GO:0061166","count":7},{"id":"GO:0006260","count":7},{"id":"GO:0046034","count":7},{"id":"GO:0070407","count":7}]},{"hash":"225096396644529451","title":"Transsulfuration and serine/cysteine metabolism","description":"The top GO terms center on sulfur-containing amino acid metabolism, including transsulfuration, cysteine biosynthesis, hydrogen sulfide production, and related serine/threonine/pyruvate pathways, indicating a cohesive theme of sulfur amino acid biosynthesis and interconversion.","confidence":"High","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006565","count":10},{"id":"GO:0019499","count":8},{"id":"GO:0070689","count":8},{"id":"GO:0070814","count":8},{"id":"GO:0046360","count":8}]},{"hash":"1188029185544676872","title":"MAPK-Related Immune and Neural Signaling","description":"The cluster is enriched in signaling pathways: ERK1/ERK2 cascade, JNK cascade, ephrin receptor signaling, T cell receptor signaling, and dopamine response, all pointing to receptor-driven MAPK and related pathways. While mitotic cell cycle terms appear, the dominant pattern is signaling processes with immune and neural contexts, suggesting these proteins participate in MAPK-mediated signaling across cell types and development. Confidence: Medium","confidence":"Medium","size":11,"edges":7,"triangles":0,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0070374","count":3},{"id":"GO:0050852","count":3},{"id":"GO:0046330","count":3}]},{"hash":"2273802122288168439","title":"Ubiquitin-dependent proteostasis and autophagy","description":"The cluster is enriched for ubiquitin-related processes (protein autoubiquitination, ubiquitin-dependent ERAD, and sumoylation) and autophagy/mitophagy pathways (mitophagy, autophagosome maturation regulation, and ER stress\u2013linked apoptotic signaling), suggesting a core theme of protein quality control and turnover. The ribosome biogenesis terms (small subunit assembly and SSU rRNA maturation) may reflect coordination between protein synthesis capacity and proteostasis. Overall, these proteins likely function in maintaining protein homeostasis via ubiquitin signaling and autophagy.","confidence":"High","size":11,"edges":51,"triangles":135,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":10},{"id":"GO:0030433","count":10},{"id":"GO:0016925","count":10},{"id":"GO:1903071","count":9},{"id":"GO:0000423","count":9}]},{"hash":"983490360741760725","title":"Unknown","description":"The GO terms span across plant defense signaling (jasmonic acid/ethylene-dependent systemic resistance), animal muscle adaptation, general transcription and chromatin-related processes, and even angiogenesis/migration and glycolysis, with several terms marked obsolete. There is no clear, cohesive biological function or pathway uniting these terms, suggesting the cluster may reflect mixed or non-specific annotations rather than a single module. ","confidence":"","size":11,"edges":26,"triangles":21,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0009861","count":1},{"id":"GO:0014894","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0030702","count":1},{"id":"GO:0001308","count":1}]},{"hash":"660375092687280788","title":"Cellular stress response and metabolic regulation","description":"The top GO terms cluster around sensing environmental conditions (hypoxia detection) and nutrient status, plus regulation of glucose and fatty acid metabolism and fatty acid biosynthesis, with an apoptosis pathway linked to p53. These points suggest proteins acting in stress sensing and metabolic adaptation rather than a single enzymatic function. Some growth-related terms (DNA replication, cell size) may be linked to cellular state under stress. Confidence: Medium.","confidence":"","size":11,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0017006","count":1},{"id":"GO:0070483","count":1},{"id":"GO:0071398","count":1},{"id":"GO:0006261","count":1},{"id":"GO:0045793","count":1}]},{"hash":"228480709294353439","title":"Eye development and photoreceptor ciliogenesis","description":"The top GO terms cluster around retina and camera-type eye development and cilium-related receptor localization, suggesting a shared role in eye development and photoreceptor ciliary biology. The concurrent translation-related terms likely reflect annotation noise or dual-purpose factors and do not substantially shift the main theme. Overall, the theme points to eye development with a focus on photoreceptor ciliogenesis.","confidence":"Medium","size":11,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0060041","count":2},{"id":"GO:0075525","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0075522","count":2},{"id":"GO:0002188","count":2}]},{"hash":"1535964437646007541","title":"RNA Polymerase Transcription Initiation","description":"The majority of GO terms center on transcription initiation and promoter engagement by RNA polymerase II and III (e.g., preinitiation complex assembly, open complex formation, promoter binding, and transcription initiation at promoters), indicating this cluster reflects the transcription initiation machinery. A couple of terms relate to splicing or viral transcription as minor outliers.","confidence":"High","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":1},{"id":"GO:0006367","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0001113","count":1}]},{"hash":"208709444211768568","title":"DNA replication and chromosome maintenance","description":"The top GO terms cluster around DNA replication (DNA-templated replication, mitotic DNA replication, replication fork progression), chromosome segregation (sister chromatid segregation, chromosome separation), recombination/repair, and telomere maintenance. This combination points to a cohesive theme of genome duplication and chromosome stability, justifying the label DNA replication and chromosome maintenance.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030263","count":1},{"id":"GO:0051304","count":1},{"id":"GO:0000712","count":1},{"id":"GO:0006261","count":1},{"id":"GO:0000819","count":1}]},{"hash":"1047863031140183060","title":"Nuclear transport and cell cycle regulation","description":"The GO terms cluster around nucleus-related processes (nuclear pore complex assembly, ribosomal protein import into nucleus) plus chromosome dynamics (mitotic sister chromatid separation, centromeric cohesion) and DNA replication regulation, with additional signals from ciliary basal body docking and post-translational modification control. This combination suggests a cluster of proteins involved in nuclear transport, chromosome segregation/ replication control, and centrosome/cilium-related regulation, i.e., cell cycle\u2013 and nucleus-oriented functions.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051306","count":2},{"id":"GO:0070262","count":2},{"id":"GO:0097711","count":2},{"id":"GO:0006275","count":2},{"id":"GO:0060188","count":2}]},{"hash":"1143066783828051354","title":"Nucleic acid processing and stress response","description":"Top GO terms indicate nucleic acid metabolism (RNA phosphodiester bond hydrolysis, DNA recombination, regulation of mRNA stability) and related DNA demethylation, complemented by stress-response terms (response to xenobiotic stimulus, cellular response to hydrogen peroxide). The mixture suggests a cluster of proteins involved in nucleic acid processing with ancillary roles in cellular stress signaling, though some terms (e.g., regulation of smooth muscle cell migration, obsolete GO terms) reflect annotation noise. Overall I label it as nucleic acid processing with stress response due to the strongest coherence around nucleic acid metabolism and stress cues.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0090502","count":4},{"id":"GO:0006310","count":4},{"id":"GO:0080111","count":3},{"id":"GO:0014912","count":3},{"id":"GO:0042493","count":3}]},{"hash":"1848154052165899792","title":"Unknown","description":"There are no Top Terms reported for this cluster, and with only a single edge and no triangles, there is no shared GO signal to bind these proteins to a common function. The lack of functional terms from the data means a meaningful label cannot be assigned beyond Unknown.","confidence":"","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[]},{"hash":"1138962221346494083","title":"Unknown","description":"The terms reflect a very diverse set of processes (RNA modification, translation-related modifications, spindle organization, hormone and nodulation biosynthesis), with little overlap, and no shared functional theme evident from GO terms alone; thus no coherent function characterizes the cluster.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071891","count":1},{"id":"GO:0035902","count":1},{"id":"GO:0002098","count":1},{"id":"GO:0007051","count":1},{"id":"GO:1901052","count":1}]},{"hash":"561809029140626256","title":"Mitochondrial respiration and ETC assembly","description":"These proteins primarily relate to mitochondrial energy production, with GO terms for respiratory chain complex IV assembly and cytochrome-c oxidase activity, pointing to oxidative phosphorylation. A single term on glucokinase regulation suggests broader energy metabolism context but does not override the mitochondrial theme. Overall, the cluster most coherently reflects mitochondrial respiration and ETC assembly.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0033132","count":1},{"id":"GO:1904960","count":1},{"id":"GO:0008535","count":1}]},{"hash":"1722340599494091932","title":"RNA processing and translational control","description":"The cluster includes mRNA splicing and polyadenylation, translation initiation/reinitiation, and regulatory ncRNA-mediated silencing, suggesting a shared theme of post-transcriptional regulation of gene expression.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":2},{"id":"GO:0051209","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0002188","count":2}]},{"hash":"1360547385499540871","title":"Retroviral DNA integration and latency","description":"This cluster centers on steps of viral infection and proviral genome integration: entry into the host cell, trafficking to the nucleus, reverse transcription and DNA synthesis, DNA replication and recombination, and establishment of integrated proviral latency; it also includes themes of host antiviral defense suppression (siRNA processing) and virus-induced host apoptosis, all characteristic of retroviral life cycles.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0015074","count":9},{"id":"GO:0075713","count":9},{"id":"GO:0046718","count":9},{"id":"GO:0006278","count":8},{"id":"GO:0006260","count":8}]},{"hash":"2123516991719619744","title":"Unknown","description":"The terms span transcription regulation, ubiquitination, ribosomal export, neuronal apoptosis, development, and GTPase activity with no clear single function linking the cluster; several terms are archaic/obsolete, and there is little connectivity, so a cohesive label isn\u2019t supported.","confidence":"","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019089","count":1},{"id":"GO:0045944","count":1},{"id":"GO:0035519","count":1},{"id":"GO:2000203","count":1},{"id":"GO:0043525","count":1}]},{"hash":"170811263222332278","title":"Diverse Biosynthesis Pathways","description":"The Top Terms include several distinct biosynthetic processes (molybdopterin cofactor biosynthesis, phospholipid biosynthesis, polysaccharide biosynthesis, pantothenate biosynthesis) and related metabolic activities, indicating a metabolic/biosynthesis-focused cluster rather than a single, cohesive pathway. There are some outliers (peroxisomal protein import, TNF-related signaling), but the shared functional thrust is biosynthesis across multiple compounds.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006777","count":1},{"id":"GO:0008654","count":1},{"id":"GO:0060373","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0016558","count":1}]},{"hash":"391673949897839106","title":"Retroviral Integration and Latency","description":"The cluster is dominated by terms tied to retroviral life cycles: reverse transcription (RNA-templated DNA biosynthetic process), DNA integration and recombination, and establishment of integrated proviral latency, plus viral entry/penetration into the host nucleus and host apoptosis modulation. These collectively point to retroviral infection, genome integration, and latency as the core theme.","confidence":"High","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0006278","count":5},{"id":"GO:0039651","count":4},{"id":"GO:0015074","count":4},{"id":"GO:0075713","count":4}]},{"hash":"2033104250565740939","title":"Nucleic acid metabolism and stress response","description":"The top terms cluster around nucleic acid processes (DNA replication and recombination, RNA cleavage) and cellular stress responses (response to xenobiotics, hydrogen peroxide), with a few host-pathogen interaction annotations. The common thread appears to be nucleic acid metabolism intertwined with stress response pathways, though some terms reflect broader host-pathogen interactions. ","confidence":"Medium","size":11,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0090502","count":5},{"id":"GO:0006310","count":5},{"id":"GO:0006260","count":3},{"id":"GO:0080111","count":3},{"id":"GO:0014912","count":3}]},{"hash":"1039507951892977397","title":"Transcriptional Regulation and Cell Cycle Control","description":"The top GO terms cluster around transcriptional regulation (DNA-templated transcription, RNA Pol II regulation, galactose-induced transcription) and cell-cycle transitions (G1/S, G2/M), with additional signals related to growth/metabolism (ribosome biogenesis, glycogen catabolism) that can tie to proliferation. Some terms are organism-specific (stomatal opening, mammary gland proliferation), but the core theme is gene expression control linked to cell division.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0006351","count":1},{"id":"GO:0016242","count":1},{"id":"GO:0000411","count":1},{"id":"GO:0000122","count":1}]},{"hash":"1813407096521854837","title":"Endosomal trafficking and exosome secretion","description":"The cluster\u2019s top GO terms cluster strongly around endosomal transport between cellular compartments (Golgi to endosome, endosome to lysosome, plasma membrane to endosome) and endosome-associated protein localization, plus exosomal secretion. This points to a cohesive theme of endocytic trafficking and vesicle-mediated cargo release, with a touch of signaling roles linked to endosomal pathways (ephrin signaling, tube formation, plasticity). Confidence that this name captures the cluster\u2019s core function is High.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008333","count":2},{"id":"GO:0014902","count":2},{"id":"GO:0006895","count":2},{"id":"GO:0048227","count":2},{"id":"GO:0048013","count":2}]},{"hash":"2084391072961322585","title":"Neural Development and Apoptosis Regulation","description":"Top GO terms are dominated by neural development and brain formation, including neural tube closure, brain and forebrain development, and dendrite morphogenesis, along with apoptosis-related processes like regulation of apoptotic DNA fragmentation and positive regulation of apoptotic signaling. This pattern suggests the cluster represents neural development with coordinated apoptotic signaling components.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001843","count":2},{"id":"GO:1902510","count":2},{"id":"GO:0010659","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0071560","count":2}]},{"hash":"258820694752225529","title":"Unknown","description":"The proteins are associated with a highly diverse set of GO terms (xenobiotic response, antibiotic biosynthesis, fatty acid metabolism, receptor internalization, plant hormone-related processes) and show no interactions (Edges 0, triangles 0, max degree 0). This scattered functional annotation provides no clear, common theme to bind the cluster, so a reliable concise label cannot be assigned.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008285","count":1},{"id":"GO:0019260","count":1},{"id":"GO:0051791","count":1},{"id":"GO:0042136","count":1},{"id":"GO:0055114","count":1}]},{"hash":"2061745843436532765","title":"Unknown","description":"The GO terms span phosphorylation, DNA replication, complex assembly, biosynthesis, and varied stress/metabolic responses, showing little common function.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006468","count":2},{"id":"GO:0006461","count":1},{"id":"GO:0009236","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0080111","count":1}]},{"hash":"780751888264207252","title":"Unknown","description":"The listed GO terms span diverse biology (catabolic processes for sugars, glycerol, ketones, and lignin; plant cell wall organization; bone resorption; immune signaling; drug response), with no obvious common pathway or function for the cluster. The lack of edges/connectedness also suggests this is a heterogeneous set rather than a cohesive functional group.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097237","count":1},{"id":"GO:0019588","count":1},{"id":"GO:0042182","count":1},{"id":"GO:0046365","count":1},{"id":"GO:0039534","count":1}]},{"hash":"1039913796134907687","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":1},{"id":"GO:0002047","count":1},{"id":"GO:0042823","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0008615","count":1}]},{"hash":"1913913156653594510","title":"Mitochondria-driven Apoptosis and Stress Response","description":"This cluster centers on mitochondrial membrane permeability regulation and apoptotic process, with supporting signals from cell-cycle control and various stress responses (xenobiotic, bacterial motif muramyl dipeptide, peptide hormones). Taken together, the proteins likely participate in mitochondrial-mediated apoptosis linked to cellular stress signaling.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000134","count":2},{"id":"GO:0070940","count":2},{"id":"GO:0046902","count":2},{"id":"GO:0010867","count":2},{"id":"GO:1903740","count":2}]},{"hash":"2024085481875703681","title":"Proteostasis and Ubiquitin-Proteasome System","description":"The GO terms are dominated by proteasome regulatory particle assembly, oxidation-dependent proteolysis, and positive regulation of ubiquitin-specific protease activity, pointing to a core proteostasis/UPS function. Misfolded protein response and protein hexamerization further support this theme, while other terms may reflect broader cellular processes. Overall, this cluster centers on protein quality control and degradation.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070682","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0071218","count":1},{"id":"GO:0061166","count":1}]},{"hash":"1373861579570910695","title":"Mitotic DNA replication machinery","description":"The terms cluster around mitotic DNA replication, including initiation and preinitiation complex assembly (GINS complex), DNA strand elongation in mitosis, and related replication initiation and repair steps. A couple of terms (amino acid biosynthesis and early embryo proliferation) are less central, but the dominant theme is the machinery and steps of mitotic DNA replication.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902983","count":1},{"id":"GO:0071165","count":1},{"id":"GO:1902977","count":1},{"id":"GO:0032508","count":1},{"id":"GO:1902975","count":1}]},{"hash":"1387970123613534419","title":"Unknown","description":"The Top Terms span telomere maintenance, endocytosis, innate immune signaling, thermal sensation and heat-stress responses, cell cycle, synaptic plasticity, chromosomal telomere localization, and calcium signaling, with no single dominant function tying the cluster together. Therefore no cohesive theme is evident.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":2},{"id":"GO:0048549","count":2},{"id":"GO:0070427","count":2},{"id":"GO:0050955","count":2},{"id":"GO:1901594","count":2}]},{"hash":"610731784486744082","title":"Unknown","description":"There are no GO terms, interactions, or other signals to define a shared function for the 11 proteins; the graph has no edges or triangles and the Top Terms field is empty, so a coherent biological theme cannot be inferred from the data provided.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"122110695091995115","title":"Inflammation modulation and redox detoxification","description":"The cluster centers on oxidative stress management (cellular oxidant detoxification, glutathione derivative biosynthetic process, nitric oxide storage) and anti-inflammatory signaling (glucocorticoid response, negative regulation of TNF and IL-1\u03b2 pathways, prostaglandin biosynthesis). The CNS development term appears less central but may reflect tissue-specific expression; overall, the shared theme is regulation of inflammation via redox balance and steroid signaling.","confidence":"High","size":10,"edges":21,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":6},{"id":"GO:0001516","count":5},{"id":"GO:0071385","count":4},{"id":"GO:0010804","count":4},{"id":"GO:0032691","count":4}]},{"hash":"688102138715119919","title":"GPCR Signaling with cAMP and cGMP","description":"This cluster centers on GO terms for G protein-coupled receptor signaling pathways that activate adenylate cyclase and guanylyl cyclase, generating the second messengers cAMP and cGMP (e.g., adenylate cyclase-activating adrenergic receptor signaling, adenosine receptor signaling, receptor guanylyl cyclase signaling). Additional terms like cGMP/cAMP biosynthesis and blue light signaling reinforce the shared theme of GPCR-driven cyclic nucleotide signaling; a few items (e.g., detection of hypoxia, transcription regulation) may reflect downstream or context-specific responses but do not override the core signaling axis. Therefore, a concise label focusing on GPCR-driven cAMP/cGMP signaling is appropriate.","confidence":"High","size":10,"edges":8,"triangles":0,"max_degree":8,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0071880","count":3},{"id":"GO:0070483","count":3},{"id":"GO:0006182","count":3},{"id":"GO:0009785","count":3},{"id":"GO:0001973","count":3}]},{"hash":"1434550417727826735","title":"Ribosome Translation and Spliceosome Machinery","description":"This cluster is dominated by GO terms for translation and ribosome assembly (translation, ribosomal large subunit assembly, ribosome disassembly, and selenium incorporation), plus multiple spliceosome-related terms (spliceosome conformational change, spliceosomal tri-snRNP complex assembly, catalytic spliceosome formation). This suggests a core of protein synthesis machinery plus RNA processing components. A few terms related to brain-derived neurotrophic factor signaling and skeletal muscle contraction may reflect context-dependent roles or multifunctional proteins. ","confidence":"High","size":10,"edges":23,"triangles":25,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0000027","count":2},{"id":"GO:2000767","count":1},{"id":"GO:0000388","count":1},{"id":"GO:0001514","count":1}]},{"hash":"1636358469426988704","title":"Actin cytoskeleton remodeling and cell shape","description":"The top GO terms cluster around actin dynamics: Arp2/3 nucleation, actin filament bundle assembly, and regulation of cell shape/polarity. Additional terms point to muscle fiber adaptability and platelet aggregation, both linked to cytoskeletal remodeling, while brain development and chromatin terms are less central, supporting a primary theme of actin-driven morphology and cytoskeletal organization.","confidence":"Medium","size":10,"edges":28,"triangles":36,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048741","count":9},{"id":"GO:0021762","count":9},{"id":"GO:0051017","count":5},{"id":"GO:0071963","count":5},{"id":"GO:0043981","count":5}]},{"hash":"2293580503296947857","title":"ER proteostasis and vesicle trafficking during cell cycle","description":"The cluster\u2019s top GO terms center on ER-related proteostasis\u2014chaperone-assisted protein folding/refolding, ER-to-Golgi vesicle transport, and responses to misfolded proteins\u2014along with cell cycle signals (DNA replication, cell division) and ER polarization. ATP metabolism supports the energy needs of these processes, suggesting a cohesive theme of protein quality control and trafficking during cell cycle progression. Some terms like gas vesicle organization may be noise, but the dominant signal points to ER proteostasis and vesicle trafficking.","confidence":"Medium","size":10,"edges":24,"triangles":36,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0070389","count":5},{"id":"GO:0006888","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0071218","count":4}]},{"hash":"830776042543845159","title":"Neural Signaling and Development","description":"This cluster centers on GO terms tied to neural signaling and development, including positive regulation of Wnt, ERK1/2, JNK, and ephrin signaling, plus hippocampus development and dopamine response. While there are immune-related signaling terms present (T cell receptor signaling, mast cell degranulation), the prominent neural development and signaling pathways suggest a neural signaling/construction theme best captured by this label.","confidence":"Medium","size":10,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090263","count":8},{"id":"GO:0070374","count":7},{"id":"GO:0050852","count":7},{"id":"GO:0046330","count":7},{"id":"GO:0021766","count":7}]},{"hash":"878615275819053598","title":"Steroid and Prostaglandin Hormone Biosynthesis","description":"The top terms are dominated by prostaglandin biosynthesis and androgen/testosterone biosynthetic processes, pointing to enzymes involved in lipid hormone production. Although there are a few outliers (e.g., endothelial morphogenesis, calcium-channel regulation), the strongest and most recurrent theme is lipid hormone biosynthesis, justifying this label.","confidence":"High","size":10,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":3},{"id":"GO:0008209","count":3},{"id":"GO:0061370","count":3},{"id":"GO:0046677","count":3},{"id":"GO:1902000","count":2}]},{"hash":"1862091729749396561","title":"Ribosome biogenesis and translation regulation","description":"Most of the top GO terms cluster around the core protein synthesis machinery and its control (translation, ribosome biogenesis, initiation/elongation/termination, selenocysteine incorporation, and positive regulation of cytoplasmic translation), with a secondary link to mRNA turnover (deadenylation-dependent decay). This suggests the proteins in this group function together in assembling ribosomes and regulating translation, rather than unrelated processes; a couple of terms (glial cell proliferation, response to antibiotic) appear less central but may reflect context-specific roles. ","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0042254","count":3},{"id":"GO:2000767","count":2},{"id":"GO:0000288","count":2},{"id":"GO:0046677","count":2}]},{"hash":"808263292620944221","title":"RNA Splicing and Translation Regulation","description":"The top GO terms cluster around both spliceosome/rna processing (spliceosome assembly, U4/U6/U5 tri-snRNP, first transesterification, ribosome-related processes) and translation (translation itself, ribosome disassembly, translational termination regulation, selenocysteine incorporation, cytoplasmic translation regulation). This suggests a cohesive theme of post-transcriptional control linking RNA processing and protein synthesis, despite a few context-specific outliers. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000767","count":1},{"id":"GO:0000388","count":1},{"id":"GO:0001514","count":1},{"id":"GO:0032790","count":1},{"id":"GO:0006449","count":1}]},{"hash":"1248124926270278950","title":"Chromatin regulation and mitotic cell cycle","description":"The top GO terms cluster around DNA replication, heterochromatin formation (subtelomeric and silent mating-type cassette), and mitosis-related processes (cell division, mitotic spindle elongation), which together point to chromosome maintenance and progression through cell division. While there are additional processes noted (RNA granule dynamics, ER-Golgi transport, phosphatase activity, and GTPase regulation), the core theme appears to be chromatin organization coupled with cell-cycle control. Confidence: Medium.","confidence":"","size":10,"edges":5,"triangles":0,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0006888","count":3},{"id":"GO:0006348","count":3},{"id":"GO:0035617","count":3},{"id":"GO:0051301","count":3}]},{"hash":"1267770542681558810","title":"Unknown","description":"The cluster shows a mix of GO terms spanning vision, cell cycle, development, metabolism, autophagy regulation, cardiac differentiation, ion transport, spindle organization, and virus response. There isn\u2019t a single clear biological theme connecting these functions, so a coherent, specific label isn\u2019t supported. ","confidence":"","size":10,"edges":7,"triangles":1,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0006006","count":3},{"id":"GO:0016242","count":2}]},{"hash":"1640897301734542775","title":"Gene Expression Regulation and RNA Processing","description":"The top terms cluster around DNA-templated transcription and its regulation (including termination/antitermination) plus RNA processing (pre-miRNA processing, miRNA turnover, CRD-mediated mRNA stabilization) and linked protein turnover (SCF-dependent proteasomal degradation). Although a couple of terms touch on stress/defense, the dominant signal is transcriptional control and post-transcriptional RNA metabolism, with associated proteostasis. Confidence: Medium","confidence":"","size":10,"edges":10,"triangles":1,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0031054","count":1},{"id":"GO:1902219","count":1}]},{"hash":"356089893183641661","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0000472","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0000462","count":3}]},{"hash":"2147271664551286715","title":"Viral Translation Initiation & Reinitiation","description":"This cluster is dominated by GO terms related to translation initiation, preinitiation complex formation, translation reinitiation, and IRES-dependent viral initiation, pointing to a shared function in starting protein synthesis, including viral strategies. A few terms refer to RNA pseudouridine synthesis (tRNA and rRNA) and regulatory RNA processes, which are related to translation but are secondary to the main theme.","confidence":"Medium","size":10,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0075525","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0002188","count":2}]},{"hash":"480506135672538143","title":"Neuronal Signaling and Vesicle Trafficking","description":"The top GO terms cluster around visual perception and synaptic/vesicle processes (visual perception, presynapse assembly, receptor recycling, endosome size) along with signaling-related terms (GTPase activity, Ran signaling), suggesting proteins involved in neuronal signaling and intracellular trafficking, especially in the visual system. Some terms (pheromone response, Hippo signaling, tRNA modification, mitotic cycle) may reflect broader signaling or housekeeping roles captured by the dataset.","confidence":"Medium","size":10,"edges":40,"triangles":87,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":8},{"id":"GO:0043547","count":8},{"id":"GO:0019236","count":8},{"id":"GO:0000278","count":8},{"id":"GO:0002098","count":7}]},{"hash":"1951742965469417373","title":"Small RNA biogenesis and gene silencing","description":"The top GO terms cluster around RNA silencing and small RNA pathways, including pre-miRNA processing, piRNA processing, and RNA interference-related activities such as mRNA cleavage. This points to a theme of small RNA biogenesis and gene-silencing mechanisms, with some additional development-related terms that may reflect broader transcriptional regulation. ","confidence":"Medium","size":10,"edges":6,"triangles":1,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0031054","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0048015","count":2},{"id":"GO:0010492","count":2},{"id":"GO:0033168","count":2}]},{"hash":"913742855697610243","title":"Innate Immune Signaling with LPS and dsRNA","description":"The top terms cluster around innate immune response, defense against Gram-positive bacteria, LPS signaling, and dsRNA response, pointing to a cohesive theme of innate immune activation. Some terms (ubiquitination, DNA replication) reflect general cellular processes, and dopamine/synapse terms may indicate neuronal signaling cross-talk rather than core cluster function. Overall, the dominant theme is innate immune signaling.","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0006260","count":2},{"id":"GO:1903351","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0045087","count":2}]},{"hash":"920724789084712321","title":"Spliceosome-regulated mRNA processing","description":"The top GO terms center on mRNA splicing regulation via the spliceosome and related mRNA processing (positive and negative regulation of splicing, cis splicing), indicating proteins that coordinate spliceosomal processing and maturation of mRNA, with a minor note of translation-initiation factor assembly. ","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":4},{"id":"GO:0031047","count":3},{"id":"GO:0048026","count":3},{"id":"GO:1902625","count":3},{"id":"GO:0075525","count":3}]},{"hash":"379644363662024377","title":"Transcription and RNA processing in development","description":"These terms cluster around RNA biogenesis (pre-miRNA processing, miRNA catabolic process), transcriptional control (DNA-templated transcription, transcription antitermination, termination regulation), and mRNA stability, with several development-related terms (kidney development, EMT, trophoblast differentiation). Together they suggest a cluster of proteins involved in RNA-based regulation of gene expression during development.","confidence":"Medium","size":10,"edges":18,"triangles":16,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0031054","count":1},{"id":"GO:0006351","count":1},{"id":"GO:1902219","count":1},{"id":"GO:0060567","count":1},{"id":"GO:1901724","count":1}]},{"hash":"2164261198186294349","title":"RNA splicing regulation and spliceosome assembly","description":"The top terms revolve around mRNA splicing, spliceosome components, and splice site recognition, with additional signals for regulatory ncRNA-mediated gene silencing and translation initiation factor complex assembly, suggesting a cluster of proteins involved in RNA processing and regulation at the splicing level and related translation initiation processes.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":1},{"id":"GO:0048026","count":1},{"id":"GO:1902625","count":1},{"id":"GO:0075525","count":1},{"id":"GO:1905663","count":1}]},{"hash":"2112417370368307675","title":"Developmental signaling and glycosylation","description":"The terms point to developmental processes (skin/cuticle development, larval cuticle formation, morphogenesis, gonad development) combined with signaling (estradiol, cAMP) and post-translational modifications (O-linked glycosylation, O-GlcNAcylation). The common thread appears to be developmental programs that are modulated by signaling and glycosylation, even though the exact roles may vary across species. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043588","count":2},{"id":"GO:0071320","count":2},{"id":"GO:0008363","count":1},{"id":"GO:0097370","count":1},{"id":"GO:0035269","count":1}]},{"hash":"880147233014559974","title":"Mitosis and Chromosome Segregation","description":"The strongest signal is mitosis-related: mitotic cell cycle, cell division, and CENP-A\u2013containing chromatin assembly, plus microtubule severing, which points to spindle dynamics and chromosome segregation. While some terms touch on transcription and trafficking, the core theme centers on cell division machinery and chromatin assembly. ","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0051013","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0006888","count":5},{"id":"GO:0000278","count":5}]},{"hash":"1234533480238112069","title":"Mitotic spindle and microtubule dynamics","description":"This cluster is enriched for GO terms tied to mitotic spindle assembly, elongation, meiotic spindle orientation, and cytokinesis, highlighting microtubule-driven division processes. Additional terms about minus-end directed microtubule sliding and chromosome recapture support a cohesive theme around spindle function. Some non-mitotic terms (stress granule disassembly, Purkinje cell layer organization, chloroplast movement) reflect broader cytoskeletal roles, but the dominant signal is spindle/microtubule dynamics.","confidence":"High","size":10,"edges":10,"triangles":0,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0090307","count":6},{"id":"GO:0035617","count":5},{"id":"GO:0000743","count":4},{"id":"GO:1990942","count":4},{"id":"GO:0021693","count":4}]},{"hash":"644771916912976975","title":"Neural development and cocaine response","description":"This cluster is driven by brain-related terms: substantia nigra development, neural precursor cell proliferation, and response to cocaine, suggesting a theme around neural development and drug-response signaling. While there are some metabolic and chromatin-related terms present (e.g., thiamine and guanine metabolism, histone modifications), these are less central to the cluster\u2019s core pattern. Overall, a neural-development/drug-response theme best captures the shared functions of these proteins.","confidence":"Medium","size":10,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042220","count":2},{"id":"GO:0021762","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0045793","count":2},{"id":"GO:0009228","count":2}]},{"hash":"1562796761283950039","title":"Transmembrane Transport of Ions and Small Molecules","description":"This cluster is dominated by GO terms for transport across membranes\u2014vitamins, sodium ions, glucose, xenobiotics, and related vesicular neurotransmitter loading\u2014indicating a common role in moving substrates across membranes. Despite a couple of legacy terms, the core pattern points to membrane transport as the unifying function of these proteins.","confidence":"High","size":10,"edges":16,"triangles":7,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":3},{"id":"GO:0042891","count":3},{"id":"GO:0006855","count":3},{"id":"GO:0098700","count":2},{"id":"GO:0042128","count":2}]},{"hash":"817982948034243742","title":"Unknown","description":"The GO terms are scattered across neural processes (neuron apoptotic regulation, synapse organization, ERK signaling) and unrelated areas (xenobiotic metabolism, nitric oxide production, hormone response, and redox), with no strong, coherent shared function across the cluster. The lack of edges and a unifying pathway makes it hard to assign a specific biological theme.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043525","count":2},{"id":"GO:0050808","count":2},{"id":"GO:0006805","count":1},{"id":"GO:0032414","count":1},{"id":"GO:0006809","count":1}]},{"hash":"663761909891285555","title":"Bacterial membrane transporters and secretion proteins","description":"The Top Terms indicate transport of amino acids, vitamins, metals, xenobiotics, and fatty acids, plus a Type I secretion system component, all pointing to membrane transport/secretion roles in bacteria. An outlier DNA replication term is present but does not override the overall transport/secretion theme.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0015803","count":2},{"id":"GO:0030253","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0015689","count":2}]},{"hash":"1131592487286656326","title":"Retroviral Integration and Latent Infection","description":"The dominant GO terms map to the retroviral life cycle: DNA integration, proviral latency, reverse transcription (RNA-templated DNA biosynthesis), entry into host cells and transport to the nucleus, and DNA recombination/ replication; along with viral suppression of RNA silencing. A few terms about symbiont interactions or insulin signaling are peripheral.","confidence":"High","size":10,"edges":10,"triangles":7,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0015074","count":6},{"id":"GO:0075713","count":6},{"id":"GO:0046718","count":6},{"id":"GO:0006278","count":5},{"id":"GO:0006260","count":5}]},{"hash":"47262918977575725","title":"Stress-responsive metabolism and signaling pathways","description":"The cluster includes terms related to metal stress (cadmium), apoptosis regulation, and a variety of metabolic processes (androgen, retinal, retinol, fructose, LPS biosynthesis) plus transcription. This suggests broadly coordinated metabolic activities intertwined with stress and signaling responses rather than a single specific pathway, justifying a label that captures both metabolism and stress signaling.","confidence":"Medium","size":10,"edges":12,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0071276","count":3},{"id":"GO:0043066","count":3},{"id":"GO:0008209","count":3},{"id":"GO:0042574","count":3}]},{"hash":"777603886312509708","title":"Ion and carbohydrate transmembrane transport","description":"The proteins are linked by membrane transport activity across diverse substrates: sodium ions, various sugars (galactose), sialic acid, phosphate, and xenobiotics, with an additional neuron-related example of neurotransmitter loading into synaptic vesicles. This common thread is transmembrane transport of ions and small solutes, so a concise label focusing on Ion and carbohydrate transmembrane transport fits best.","confidence":"High","size":10,"edges":24,"triangles":22,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0008643","count":1},{"id":"GO:0055085","count":1},{"id":"GO:0006814","count":1},{"id":"GO:0042891","count":1},{"id":"GO:0006855","count":1}]},{"hash":"1082642281098310802","title":"Unknown","description":"The GO terms span diverse processes (ER-associated degradation, microtubule organization, autophagy regulation, NK cell signaling, nucleotide-excision repair, GPCR trafficking, and interferon response) with no single cohesive function. Several annotations are marked obsolete, indicating noise and weak linkages, so there isn\u2019t a clear common theme to label this cluster meaningfully.","confidence":"","size":10,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0035278","count":2},{"id":"GO:1903071","count":1},{"id":"GO:0000226","count":1},{"id":"GO:1901097","count":1}]},{"hash":"392029247529391945","title":"Neuronal development and synaptic actin remodeling","description":"This cluster is enriched for brain and neuron projection development terms, plus Wnt signaling, and cytoskeletal remodeling (Arp2/3 actin nucleation, lamellipodium assembly, Rac signaling) and synaptic vesicle exocytosis, plus intracellular transport. Together these indicate a theme of neural development coupled with actin-driven morphogenesis and vesicle trafficking at synapses, supporting a cohesive neuronal function label.","confidence":"High","size":10,"edges":42,"triangles":99,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:0090263","count":2},{"id":"GO:0010796","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0031384","count":2}]},{"hash":"1002816874431867664","title":"Spliceosome-Mediated mRNA Splicing Regulation","description":"The cluster is dominated by GO terms centered on mRNA splicing via the spliceosome, including both positive and negative regulation, cis-splicing, and splice-site recognition, pointing to RNA processing and spliceosome assembly as the shared function. A few terms touch ncRNA-mediated silencing and translation initiation factor assembly, but the core theme remains RNA splicing regulation.","confidence":"High","size":10,"edges":5,"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:1902625","count":3},{"id":"GO:0075525","count":3},{"id":"GO:1905663","count":3}]},{"hash":"2059816747566823769","title":"Proteostasis and Protein Degradation","description":"The GO terms cluster around protein quality control and degradation pathways, notably nuclear protein quality control by the ubiquitin-proteasome system, misfolded protein transport, and ubiquitin-dependent ERAD. These strongly point to roles in protein homeostasis and turnover, with other terms appearing incidental. Thus, the cluster is best described as a proteostasis/degradation module.","confidence":"Medium","size":10,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":1},{"id":"GO:0097428","count":1},{"id":"GO:0032781","count":1},{"id":"GO:0001707","count":1},{"id":"GO:0006469","count":1}]},{"hash":"730865894865428812","title":"Unknown","description":"The GO terms span several unrelated processes (Notch signaling regulation, ER-stress\u2013induced apoptosis, glutathione catabolism, nuclear migration during cellular fusion, T cell lineage commitment, centriole cohesion, retrograde synaptic vesicle transport, deubiquitination, palmitoylation, and necroptosis via the ripoptosome), indicating no single cohesive function ties these proteins together. Thus a coherent cluster label cannot be confidently assigned.","confidence":"","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045746","count":1},{"id":"GO:0070059","count":1},{"id":"GO:0006751","count":1},{"id":"GO:0000743","count":1},{"id":"GO:0043369","count":1}]},{"hash":"824229612065468568","title":"Spliceosome Remodeling Proteins","description":"Based on GO:0000388 (spliceosome conformational change to release U4/U6 and U1/U11), this cluster appears to consist of splicing-related proteins; the other terms (ion response and obsolete methylation term) are weaker associations and do not contradict the spliceosome theme.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000388","count":1},{"id":"GO:0010226","count":1},{"id":"GO:0090116","count":1}]},{"hash":"487286273136150389","title":"Redox and Renin\u2013Angiotensin Hormone Regulation","description":"The cluster combines redox-related terms (oxidation-reduction, redox homeostasis) with renin-angiotensin\u2013axis functions (aldosterone production, blood volume regulation, angiotensin maturation), indicating a theme of oxidative stress responses tied to cardiovascular hormone signaling. Additional xenobiotic response and peptide-related terms support a broader stress-response context but do not override the central link to redox balance and renin-angiotensin pathways.","confidence":"High","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0071375","count":2},{"id":"GO:0002018","count":1}]},{"hash":"235922481563850977","title":"Unknown","description":"The top GO terms span several unrelated themes (virion attachment to host cell, photoreceptor/chromophore linkage and phototransduction, DNA replication, hypoxia sensing, proteasome regulation, ATP response, and kinase signaling). This absence of a cohesive, single function suggests there is no clear common biology uniting the cluster, so a precise label isn\u2019t supported beyond Unknown.","confidence":"","size":10,"edges":7,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0019062","count":1},{"id":"GO:0017006","count":1},{"id":"GO:0070483","count":1},{"id":"GO:0006261","count":1},{"id":"GO:0045793","count":1}]},{"hash":"440134306677338509","title":"Mucosal Immunity and IgA Switching","description":"The top GO terms cluster around immune activation (inflammatory response, T cell\u2013mediated regulation) and IgA isotype switching, plus lacrimal and mammary gland development, pointing to a mucosal/secretory immune function; a few outliers (DNA replication, mitochondrial transcription) are general cellular processes but do not define the main theme. ","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:0006260","count":1},{"id":"GO:0060807","count":1},{"id":"GO:0006391","count":1},{"id":"GO:0006469","count":1}]},{"hash":"2083331102652635619","title":"NO detox and heme-oxygen metabolism in plant-associated microbes","description":"This cluster\u2019s GO terms cluster around nitrosative/oxidative stress handling (nitric oxide catabolic process, detoxification of nitrogen compounds, oxygen transport) and heme biosynthesis/metabolism, with additional signals of plant interaction (plant-type cell wall assembly, defense to host NO). The combination suggests a set of proteins involved in managing host-derived nitrosative stress and heme-dependent processes in a plant-associated microbial context, rather than a single uniform pathway. Therefore, the label reflects a cohesive theme of NO detox and heme-oxygen metabolism in plant-associated microbes.","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006284","count":1},{"id":"GO:0070453","count":1},{"id":"GO:0006783","count":1},{"id":"GO:0071668","count":1},{"id":"GO:1902001","count":1}]},{"hash":"88729952589828294","title":"DNA replication and genome maintenance in development","description":"These proteins cluster around DNA-focused processes: DNA replication and biosynthesis, genome integrity (UV protection, camptothecin response, DNA ligation), and development (multicellular growth, male gonad development). Some terms point to telomere biology or recombination (t-circle formation, gene conversion at mating-type locus), reinforcing a common theme of preserving and duplicating DNA during growth. Overall, the pattern supports a label centered on DNA replication/maintenance during development, with moderate confidence due to some divergent terms. ","confidence":"Medium","size":10,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035264","count":2},{"id":"GO:0090656","count":1},{"id":"GO:0051106","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0072757","count":1}]},{"hash":"1824924082625003085","title":"Mitochondrial Transport and Energy Metabolism","description":"The cluster centers on mitochondrial transport and energy-related processes, including transport of various metabolites (manganese, alpha-ketoglutarate, ornithine, ATP, pyrimidine nucleotides), the malate-aspartate shuttle, and mitochondrial membrane fission, with a nod to energy regulation like adaptive thermogenesis. This suggests proteins functioning in mitochondrial transport and energy homeostasis.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006828","count":2},{"id":"GO:0015742","count":1},{"id":"GO:0000066","count":1},{"id":"GO:1990544","count":1},{"id":"GO:1990519","count":1}]},{"hash":"2174669772253322342","title":"Unknown","description":"The GO terms are highly diverse, spanning innate immune responses (innate immune response, inflammatory response, interferon production) and various developmental/neural processes (bone development, metanephric glomerulus development, regulation of neuron maturation, vestibuloocular reflex), with a few unrelated terms. The cluster also shows no edges or triangles, suggesting little direct functional connectivity. There isn\u2019t a single cohesive theme linking these proteins, so the label Unknown is most appropriate.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0060348","count":2},{"id":"GO:0032968","count":2},{"id":"GO:0070100","count":1},{"id":"GO:0050729","count":1}]},{"hash":"2241784635239786239","title":"Meiosis-linked RNA processing and chromosome dynamics","description":"The top GO terms highlight nuclear RNA processing and spliceosome assembly alongside chromosome condensation and meiosis chromosome segregation, plus a note on DNA repair regulation. This points to a coordinated meiotic program where RNA maturation and chromatin dynamics are linked. Even though there are no edges to define a tighter network, the common theme is meiosis-associated chromatin remodeling and RNA processing, so the name reflects both aspects.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045739","count":1},{"id":"GO:0007060","count":1},{"id":"GO:0030261","count":1},{"id":"GO:0006396","count":1},{"id":"GO:0000387","count":1}]},{"hash":"6233719476961026","title":"Temperature and pain sensing with calcium signaling","description":"This cluster centers on thermoception, cold response, and pain, indicating a shared function in sensing environmental temperature and nociceptive signals, likely involving calcium-dependent signaling (calcium ion import). The presence of terms like response to capsazepine (TRPV1-related) supports a temperature/pain pathway connection. Some terms about vasopressin secretion and endothelial changes suggest additional vascular/endocrine regulatory roles that accompany sensory signaling, but the core theme is temperature- and pain-associated signaling mediated through calcium.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050955","count":2},{"id":"GO:1901594","count":2},{"id":"GO:0098907","count":2},{"id":"GO:1903444","count":2},{"id":"GO:0098703","count":2}]},{"hash":"1245555605262517053","title":"Plant cell wall remodeling under oxidative stress","description":"This cluster centers on lignin catabolic processes and plant-type cell wall organization, alongside oxidative stress responses and hydrogen peroxide catabolism, implying coordinated cell wall modification with reactive oxygen species detoxification; tubulin folding terms suggest cytoskeletal involvement in remodeling.","confidence":"Medium","size":10,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0046274","count":1},{"id":"GO:0009664","count":1},{"id":"GO:0098869","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0006979","count":1}]},{"hash":"2075948916173136014","title":"Mitochondrial respiration and aging","description":"The cluster shows strong signals for mitochondrial electron transport (ubiquinol to cytochrome c), proton transmembrane transport, and aerobic respiration, indicating a core theme of mitochondrial energy metabolism. The presence of adult lifespan determination and broader metabolic processes (hormone catabolism, amyloid-beta metabolism, trehalose regulation) suggests these proteins may coordinate energy production with aging-related metabolic regulation. Overall, the terms align best with mitochondrial energy metabolism linked to aging, hence the label.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071432","count":1},{"id":"GO:0006122","count":1},{"id":"GO:0045861","count":1},{"id":"GO:0008340","count":1},{"id":"GO:0042447","count":1}]},{"hash":"1434244868497646643","title":"Mitochondrial Transport and Energy Metabolism","description":"GO terms indicate transport of metabolites across the mitochondrial membrane (alpha-ketoglutarate, ornithine, nucleotides, magnesium), ATP translocation, the malate-aspartate shuttle, and mitochondrial dynamics (membrane fission) along with links to adaptive thermogenesis and mitochondrial influences on insulin secretion. This points to a cohesive mitochondria-centered module governing metabolite exchange, energy production, and mitochondrial remodeling.","confidence":"High","size":10,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0015742","count":6},{"id":"GO:0000066","count":6},{"id":"GO:1990544","count":6},{"id":"GO:1990519","count":6},{"id":"GO:1990845","count":6}]},{"hash":"702226289088324259","title":"Unknown","description":"The terms span immune regulation, growth factor signaling, and embryonic development with no clear, single shared function tying all proteins together, so a cohesive label cannot be assigned.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071385","count":1},{"id":"GO:0045085","count":1},{"id":"GO:0045647","count":1},{"id":"GO:0060710","count":1},{"id":"GO:0044344","count":1}]},{"hash":"808800363934074440","title":"Autophagy and ROS regulation in immune signaling","description":"The cluster centers on autophagy-related processes (macroautophagy, mitophagy), regulation of reactive oxygen species (hydrogen peroxide metabolism, respiratory burst), and inflammatory modulation (IL-8 and Th2 cytokine production), suggesting a cohesive theme of autophagy- and ROS-mediated immune regulation. Some terms appear incidental (cell polarity, centrosome localization) but do not define the core function.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000769","count":1},{"id":"GO:2000553","count":1},{"id":"GO:1904781","count":1},{"id":"GO:0061635","count":1},{"id":"GO:0007502","count":1}]},{"hash":"1233212311570075643","title":"Ribosome biogenesis and tRNA aminoacylation","description":"The dominant terms are translation and ribosome biogenesis, with several entries for mitochondrial tRNA charging (threonyl, seryl, prolyl) and related translation processes, plus a note on selenocysteine biosynthesis linked to translation. This points to a cluster of proteins involved in ribosome assembly and the charging of tRNAs for translation, including mitochondrial contexts, justifying the label.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0000447","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0070159","count":1},{"id":"GO:0097056","count":1}]},{"hash":"127355354309224743","title":"Glycolysis Regulation and Glucose Metabolism","description":"The top GO terms are dominated by glycolytic processes and their regulation (glycolytic process, carbohydrate phosphorylation, negative regulation of glycolysis, dephosphorylation, and negative regulation of glucose catabolic to lactate via pyruvate), with a few related metabolic terms (gluconeogenesis, serine biosynthesis) and a couple development terms, suggesting a core focus on how glycolysis and glucose metabolism are controlled, with some ancillary metabolic and developmental associations.","confidence":"High","size":10,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006096","count":2},{"id":"GO:0045820","count":1},{"id":"GO:0046835","count":1},{"id":"GO:0016311","count":1}]},{"hash":"181763807778029608","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":42,"triangles":97,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0007219","count":5},{"id":"GO:0097053","count":5},{"id":"GO:0042853","count":5},{"id":"GO:0018283","count":4},{"id":"GO:0044571","count":4}]},{"hash":"1269061411679753806","title":"DNA replication and transcription regulation","description":"The cluster\u2019s top GO terms are centered on nuclear functions: DNA replication and positive regulation of transcription by RNA polymerase II, pointing to genome maintenance and gene expression control. Additional signals touch on RNA localization and stabilization, which may reflect RNA processing roles, but the dominant theme remains DNA metabolism and transcription control. Some terms are obsolete or context-specific, suggesting noisy annotations, but the core connection is nuclear DNA replication and transcription regulation.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0045944","count":1},{"id":"GO:0007317","count":1},{"id":"GO:1904574","count":1},{"id":"GO:1990416","count":1}]},{"hash":"932207216675819293","title":"Unknown","description":"The terms span unrelated themes (ion transport/homeostasis, lipid metabolism and myelin/skin differentiation) and there are no protein\u2013protein connections in the cluster, so there is no coherent single function linking the members. Unknown is therefore appropriate.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071421","count":1},{"id":"GO:0071281","count":1},{"id":"GO:0006880","count":1},{"id":"GO:0030026","count":1},{"id":"GO:0071369","count":1}]},{"hash":"2247714948829627373","title":"Triglyceride catabolism and phospholipid remodeling","description":"This cluster is dominated by GO terms for triglyceride catabolic processes, triglyceride mobilization, and remodeling of lipid acyl chains, along with phospholipid (phosphatidylcholine and phosphatidylethanolamine) catabolism. These points converge on lipid breakdown and membrane lipid remodeling. A few outlier terms (e.g., PKA activity regulation and solvent/antibiotic-related processes) do not override the lipid-centric theme.","confidence":"High","size":10,"edges":14,"triangles":5,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":4},{"id":"GO:0010898","count":2},{"id":"GO:0036153","count":2},{"id":"GO:0006642","count":2},{"id":"GO:0034638","count":2}]},{"hash":"378326462478337589","title":"Membrane Transporters and Vesicle Loading","description":"These proteins show strong representation of transmembrane transport GO terms across substrates (sodium-dependent/independent transport, glucose, vitamins, organic anions, nitrate uptake/assimilation) and neurotransmitter loading into vesicles, suggesting a functional cluster of membrane transport/buffering and vesicle packaging proteins. A minor outlier term about replicative senescence does not override the overall transport theme.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071718","count":2},{"id":"GO:0098700","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0042891","count":2}]},{"hash":"1376996605941772107","title":"Androgen receptor signaling in male development","description":"The strongest GO signals are prostate gland development, male sex differentiation, and steroid hormone receptor complex assembly, which together point to nuclear receptor\u2013mediated steroid signaling\u2014predominantly androgen receptor pathways involved in male reproductive development. Additional signals for glucocorticoid signaling fit the broader steroid-receptor theme, while interferon response and cilium assembly terms appear as less central outliers. Confidence: Medium","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0030850","count":4},{"id":"GO:0046661","count":4},{"id":"GO:0006463","count":4},{"id":"GO:2000324","count":3},{"id":"GO:1903071","count":3}]},{"hash":"1590435383995035054","title":"Unknown","description":"The top GO terms span very disparate processes\u2014from actin cytoskeleton regulation and cell fusion to proliferation, apoptosis, chromatin remodeling, splicing, and hormone response\u2014without a unifying function or pathway that ties all 10 proteins together, so a single coherent label cannot be assigned.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034316","count":2},{"id":"GO:0000747","count":1},{"id":"GO:0050679","count":1},{"id":"GO:1902510","count":1},{"id":"GO:0001845","count":1}]},{"hash":"449268670433974773","title":"Unknown","description":"The only GO terms are one about initiator methionine removal in protein maturation and one about platelet aggregation, which do not suggest a shared function; with zero edges among the proteins, there is no coherent theme to label this cluster.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035551","count":1},{"id":"GO:0070527","count":1}]},{"hash":"1634232462412478739","title":"Chromatin regulation and transcription control","description":"The terms cluster around chromatin dynamics (nucleosome positioning, histone exchange, chromatin remodeling) and transcriptional regulation via RNA Pol II, including epigenetic silencing of transposable elements; these together indicate chromatin-based control of gene expression.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016584","count":1},{"id":"GO:0001198","count":1},{"id":"GO:0000433","count":1},{"id":"GO:0035955","count":1},{"id":"GO:0007070","count":1}]},{"hash":"928053006893084936","title":"Chromatin modification and ubiquitin regulation","description":"The terms point to nuclear chromatin-related functions (DNA-templated transcription, spliceosome assembly, histone methylation) and ubiquitin signaling (K48-, K11-, and linear deubiquitination). Together they suggest a cluster centered on chromatin regulation with ubiquitin-mediated control, even though a couple annotations (e.g., ripoptosome, righting reflex) may be peripheral noise.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":1},{"id":"GO:0000245","count":1},{"id":"GO:0071108","count":1},{"id":"GO:1990108","count":1},{"id":"GO:1903070","count":1}]},{"hash":"1405728149963524492","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016554","count":1},{"id":"GO:0080156","count":1},{"id":"GO:0042793","count":1},{"id":"GO:0031425","count":1},{"id":"GO:1900865","count":1}]},{"hash":"824156802393229593","title":"Detox and Redox Stress Response","description":"This cluster reflects detoxification and redox homeostasis, highlighted by glutathione metabolism, oxidant detoxification, toxin catabolism, and nitric oxide storage; along with metabolic stress signals (starvation response, aromatic amino acid metabolism) and calcium-regulated muscle contraction, pointing to a broader stress-response module rather than a single pathway.","confidence":"Medium","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0060316","count":9},{"id":"GO:0006749","count":9},{"id":"GO:0009407","count":9},{"id":"GO:0042594","count":9},{"id":"GO:0014810","count":9}]},{"hash":"330478284397578368","title":"Translation Machinery and Regulation","description":"The cluster is dominated by GO terms related to both the core process of translation (cytoplasmic translation, translation, translational termination, mitochondrial translation) and its regulation (positive regulation of cytoplasmic translation, translational fidelity, selenocysteine incorporation). A couple of outliers exist (glial cell proliferation, response to antibiotic), but the strongest signal points to translation machinery and its control. This makes a concise, specific label appropriate.","confidence":"Medium","size":9,"edges":33,"triangles":66,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0002184","count":1},{"id":"GO:0006412","count":1},{"id":"GO:2000767","count":1},{"id":"GO:0000288","count":1},{"id":"GO:0070125","count":1}]},{"hash":"310304574096413007","title":"Cerebellar development and axon regeneration","description":"This cluster is driven by cerebellum-focused terms: cerebellar cortex formation and Bergmann glial differentiation, plus regulation of axon regeneration, indicating a cohesive theme of cerebellar neural development and glial maturation. While there are also general signaling pathways (Hippo, insulin receptor) and proliferation regulation terms present, the cerebellar development signals appear to be the strongest thread binding the cluster.","confidence":"High","size":9,"edges":20,"triangles":30,"max_degree":6,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0007118","count":8},{"id":"GO:0035329","count":7},{"id":"GO:0070059","count":7},{"id":"GO:0050852","count":7},{"id":"GO:0060020","count":7}]},{"hash":"1688977227786509866","title":"Cell signaling in development and apoptosis","description":"The top GO terms point to multiple signaling pathways (MAPK cascade, osmosensory signaling, trans-synaptic signaling) and developmental processes (myotube differentiation, optic nerve morphogenesis), with apoptosis also represented. Together, they suggest a cluster of proteins involved in regulating cell fate and development through signaling, though the presence of telomere maintenance and immune-related terms adds heterogeneity. Confidence: Medium.","confidence":"","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006915","count":5},{"id":"GO:0032212","count":5},{"id":"GO:0060044","count":5},{"id":"GO:1904355","count":5},{"id":"GO:0050798","count":4}]},{"hash":"1971806128663573358","title":"Diverse Cell Signaling Pathways","description":"The dominant theme is signaling networks: ERK1/2 and JNK cascades, T cell receptor signaling, ephrin receptor signaling, and mast cell degranulation regulation. A few terms point to neural development and dopamine response, while others relate to general cellular processes, making the cluster best described as Diverse Cell Signaling Pathways.","confidence":"Medium","size":9,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0070374","count":2},{"id":"GO:0050852","count":2},{"id":"GO:0046330","count":2}]},{"hash":"417463069542444204","title":"Cell-cycle and transcriptional regulation with differentiation cues","description":"Based on the top GO terms, the cluster is enriched for DNA replication, DNA-templated transcription, and G1/S transition, which point to cell-cycle progression and gene expression control. Additional terms suggest involvement in development and differentiation (dendrite morphogenesis, cardiac muscle differentiation) and regulation of nuclear export and ion transport, indicating a broader regulatory network that links growth, signaling, and differentiation. The label emphasizes core cell-cycle and transcriptional regulation with differentiation cues as the common theme.","confidence":"Medium","size":9,"edges":17,"triangles":14,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0043552","count":7},{"id":"GO:0048813","count":7},{"id":"GO:0006260","count":7},{"id":"GO:0006813","count":7},{"id":"GO:0046827","count":7}]},{"hash":"390345091293323408","title":"Mitotic cell cycle regulation and transcription control","description":"Proteins in this cluster are enriched for cell cycle and mitosis-related terms (regulation of the mitotic cell cycle; mitotic phase transitions; cell cycle) as well as transcriptional regulation (DNA-templated transcription; RNA polymerase II\u2013mediated transcription). Kinase activation/regulation further ties signaling to cell-cycle progression, supporting a cohesive role in coordinating mitosis with transcriptional control.","confidence":"High","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019358","count":2},{"id":"GO:0045737","count":1},{"id":"GO:0060303","count":1},{"id":"GO:0045893","count":1},{"id":"GO:0007346","count":1}]},{"hash":"2243956915314243290","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":3},{"id":"GO:0006378","count":3},{"id":"GO:0070651","count":2},{"id":"GO:0034475","count":2},{"id":"GO:0000467","count":2}]},{"hash":"2125888564305084706","title":"RNA processing and export regulation","description":"A cluster dominated by RNA maturation and gene regulation steps: mRNA capping, export from the nucleus, splicing regulation, and ncRNA-mediated silencing, indicating a core theme of RNA processing and post-transcriptional control (with some development terms as potential noise).","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":2},{"id":"GO:0048820","count":2},{"id":"GO:0006370","count":2},{"id":"GO:0043547","count":2},{"id":"GO:2001241","count":2}]},{"hash":"896419703699650224","title":"DNA replication, repair, and cell division","description":"The top GO terms cluster around core genome maintenance: DNA replication, DNA strand elongation, and cytokinesis, plus single-strand DNA repair. There are also hints of chromatin regulation via histone acetylation and ubiquitination, which are commonly linked to DNA replication timing and genome integrity during cell division. This combination points to a cohesive theme of genome duplication and proper chromosome segregation, with supporting repair and regulatory processes.","confidence":"Medium","size":9,"edges":16,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0051301","count":2},{"id":"GO:1990966","count":1},{"id":"GO:2000620","count":1},{"id":"GO:0085020","count":1}]},{"hash":"778551282035590313","title":"DNA replication and genome maintenance","description":"The most represented GO terms cluster around DNA replication, its regulation, telomere maintenance via recombination, and DNA damage tolerance (translesion synthesis) and trinucleotide repeat maintenance, suggesting a cohesive theme of genome integrity governance, despite some outlier terms like spermatid/heart development or viral process that may reflect broader or misannotated functions.","confidence":"Medium","size":9,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045740","count":2},{"id":"GO:0007286","count":2},{"id":"GO:0016032","count":2},{"id":"GO:0006260","count":1},{"id":"GO:0042276","count":1}]},{"hash":"1380703358992456700","title":"Ribosome biogenesis and RNA processing","description":"This cluster is dominated by GO terms for rRNA maturation (SSU/5.8S/LSU) and ribosomal large subunit biogenesis, with additional RNA-processing activities like mRNA splicing and transcription. Together these points suggest a nucleolar, ribosome-production focus rather than a signaling or cellular-structure pathway; the neuron projection development term appears incidental. ","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031175","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0000398","count":2}]},{"hash":"1956174362865241442","title":"Neuronal RNA regulation and signaling","description":"This cluster centers on RNA-level control (mRNA binding, splicing, stability, and miRNA-mediated silencing) and also includes neuronal functions (forebrain development, regulation of neuronal action potential), suggesting a theme of RNA processing and gene regulation in neural contexts. Some terms are less cohesive (e.g., carotene biosynthesis or obsolete GO terms), but the core pattern points to neural RNA regulation and signaling.","confidence":"Medium","size":9,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1902416","count":1},{"id":"GO:0010738","count":1},{"id":"GO:0090503","count":1},{"id":"GO:0022013","count":1},{"id":"GO:2000627","count":1}]},{"hash":"403023981907204663","title":"Neural synapse formation and plasticity","description":"The top GO terms cluster around synapse development and plasticity\u2014axon targeting, dendritic spine morphogenesis, synapse organization, and regulation of excitatory signaling\u2014with links to auditory perception and vocalization, suggesting a coherent theme of neural synapse formation and plasticity underlying social/communication behaviors.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000463","count":2},{"id":"GO:0007412","count":2},{"id":"GO:0060997","count":2},{"id":"GO:0007605","count":2},{"id":"GO:0071625","count":2}]},{"hash":"793428479774937844","title":"Mitotic/meiotic spindle regulation and cell cycle control","description":"Top GO terms point to control of cell division, including G1/S transition, meiotic spindle organization and checkpoint signaling, and p53-mediated signaling, with overlapping receptor kinase pathways. While some terms touch autophagy or viral response, the dominant pattern centers on mitotic/meiotic regulation and cell cycle control.","confidence":"Medium","size":9,"edges":30,"triangles":50,"max_degree":8,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0016242","count":9},{"id":"GO:2000727","count":9},{"id":"GO:0010765","count":9},{"id":"GO:0000082","count":9},{"id":"GO:0000212","count":9}]},{"hash":"1445840869073882657","title":"Embryonic mesodermal and organ development","description":"The proteins show strong representation of developmental processes such as mesoderm formation, heart development, myoblast fusion, and angiogenesis, suggesting a theme of embryonic tissue formation and organogenesis. Additional terms like multicellular organism development and Schwann cell development support a broad developmental program, while DNA replication reflects proliferative phases. A plant-specific term may be annotation noise but does not override the overall developmental theme.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0014850","count":3},{"id":"GO:0007520","count":3},{"id":"GO:0001707","count":3},{"id":"GO:0007507","count":3}]},{"hash":"916401704717287283","title":"Growth and Immune Signaling Regulation","description":"The cluster shows enrichment for regulatory processes that dampen growth (negative regulation of fibroblast proliferation, overall growth regulation) and modulate immune/inflammatory signaling (negative regulation of TNF-mediated signaling, negative regulation of IL-1 beta production), along with hormone-related responses (auxin-activated signaling, glucocorticoid response). Additional terms on detoxification and CNS development suggest a broader stress-response context, but the core theme centers on coordinated growth and immune/hormonal signaling regulation.","confidence":"Medium","size":9,"edges":22,"triangles":22,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0048147","count":5},{"id":"GO:0098869","count":5},{"id":"GO:0009734","count":4},{"id":"GO:0071385","count":4},{"id":"GO:0040008","count":4}]},{"hash":"1149793825347722947","title":"Cell Cycle and Division","description":"Based on the top GO terms, the most represented function is related to the cell cycle, cell division, and mitotic progression (cell cycle, cell division, positive regulation of mitotic metaphase/anaphase transition). Other terms such as transcription regulation, interferon response, and photoreceptor localization appear but are less cohesive with the dominant signal. Still, the core theme centers on cell cycle control.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045892","count":2},{"id":"GO:0019363","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0071357","count":2}]},{"hash":"2034765700684041832","title":"Unknown","description":"The GO terms listed are scattered across multiple distinct biological areas (telomere maintenance, pinocytosis, NOD1 signaling, thermoception/heat-stress response, transcription regulation, cell cycle, synaptic plasticity, telomeric chromosome localization, and calcium signaling) with no clear, shared function or pathway connecting the proteins. This lack of a cohesive theme makes a specific, representative label inappropriate.","confidence":"","size":9,"edges":10,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":1},{"id":"GO:0048549","count":1},{"id":"GO:0070427","count":1},{"id":"GO:0050955","count":1},{"id":"GO:1901594","count":1}]},{"hash":"142601877025702400","title":"Protein quality control and ubiquitin-proteasome regulation","description":"Based on GO terms like nuclear protein quality control by the ubiquitin-proteasome system, ubiquitin-dependent ERAD pathway, and misfolded protein transport, the cluster appears enriched for protein quality control and ubiquitin-proteasome\u2013mediated degradation processes. Occasional terms related to DNA replication and developmental signaling are likely background noise or multi-function proteins, but the dominant theme is handling of misfolded or damaged proteins via ubiquitin/proteasome pathways.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":1},{"id":"GO:0097428","count":1},{"id":"GO:0032781","count":1},{"id":"GO:0001707","count":1},{"id":"GO:0006469","count":1}]},{"hash":"1808362108872029907","title":"Multi-Substrate Membrane Transporters","description":"The top GO terms point to transmembrane transport across a wide range of substrates (nitrate, arabinose, fucose, 4-hydroxyphenylacetate, xenobiotics, sodium ions, vitamins) and a vesicular neurotransmitter loading process. This pattern suggests a cluster of proteins associated with membrane transport rather than a single substrate or pathway, best described as multi-substrate membrane transporters.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098700","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0042891","count":2},{"id":"GO:0035725","count":2}]},{"hash":"106039501838415195","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042245","count":1},{"id":"GO:0006378","count":1},{"id":"GO:0051607","count":1},{"id":"GO:0071037","count":1},{"id":"GO:0006808","count":1}]},{"hash":"940530333755776910","title":"Mitochondrial function and lipid signaling","description":"Most GO terms point to mitochondrial processes (protein import into mitochondrial matrix, regulation of mitochondrial membrane permeability) and lipid-related signaling/metabolism (phosphatidylinositol signaling, triglyceride biosynthesis, phosphatidate phosphatase activity). A calcium-detection term further supports a signaling role linked to mitochondria. A few terms (xenobiotic response, cell cycle regulation, kidney development) appear ancillary or noise. Overall, the cluster centers on mitochondria-associated metabolism and signaling.","confidence":"Medium","size":9,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":2},{"id":"GO:2000134","count":1},{"id":"GO:0070940","count":1},{"id":"GO:0046902","count":1},{"id":"GO:0010867","count":1}]},{"hash":"1004366978754449935","title":"Proteostasis and TOR-regulated translation","description":"This cluster is dominated by ubiquitin-proteasome\u2013mediated proteolysis and ribosome-associated degradation, linked to TOR signaling and amino-acid sensing, suggesting a proteostasis-translation theme. RNA-related terms (splicing, RISC) hint at broader RNA regulation, but the core pattern is protein turnover tied to growth control; some terms appear as noise.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0071629","count":1},{"id":"GO:0001967","count":1},{"id":"GO:0071596","count":1},{"id":"GO:1990116","count":1}]},{"hash":"1633272231997935648","title":"Renin-angiotensin signaling and proteolysis in kidney","description":"Most of the GO terms converge on the renal renin-angiotensin system (aldosterone production, blood volume regulation, angiotensin maturation) along with proteolytic processes (proteolysis, membrane proteolysis, autoprocessing). While there is some overlap with antigen processing and development terms, the dominant theme is renin-angiotensin\u2013driven proteolytic regulation in kidney/mesonephros context, justifying a kidney-centric proteolysis label.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002018","count":2},{"id":"GO:0002803","count":2},{"id":"GO:0002003","count":2},{"id":"GO:0033619","count":2},{"id":"GO:0042985","count":2}]},{"hash":"1196778634320526232","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090116","count":1},{"id":"GO:0016554","count":1},{"id":"GO:0070129","count":1},{"id":"GO:0080156","count":1},{"id":"GO:0042793","count":1}]},{"hash":"215203906685330299","title":"Ubiquitination and Proteasomal Degradation","description":"This cluster is dominated by GO terms for ubiquitin-dependent protein catabolic processes, including autoubiquitination and K48- and K6-linked ubiquitination, pointing to a shared role in tagging and removing proteins via the ubiquitin-proteasome system. Peripheral terms touch on related catabolic or regulatory processes but do not override the central ubiquitination theme.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0051865","count":4},{"id":"GO:0070936","count":3},{"id":"GO:0085020","count":2},{"id":"GO:1903265","count":2}]},{"hash":"579274821388528490","title":"Unknown","description":"The GO terms span disparate biological themes (circadian rhythm regulation, renal tubule development/morphogenesis, skeletal muscle differentiation, germinal center formation, viral latency release, plant brassinosteroid signaling) and some general processes, with no dominant shared function or connectivity. This lack of a cohesive theme makes a specific, concise label inappropriate.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042752","count":1},{"id":"GO:0070294","count":1},{"id":"GO:0072156","count":1},{"id":"GO:0031397","count":1},{"id":"GO:0048741","count":1}]},{"hash":"2239172572054965537","title":"Ubiquitin-Dependent Degradation","description":"The cluster is dominated by GO terms for ubiquitin-mediated protein turnover, including ubiquitin-dependent protein catabolic process, K48-linked ubiquitination, and autoubiquitination, suggesting a cohesive role in tagging proteins for proteasomal/ERAD degradation; ancillary terms like peroxisome import and growth regulation are likely secondary connections.","confidence":"High","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:1900095","count":3},{"id":"GO:0070936","count":3},{"id":"GO:0016558","count":3},{"id":"GO:0038018","count":3}]},{"hash":"1034239305793577016","title":"Unknown","description":"The GO terms show a highly diverse mix, including plant defense responses, root development, stress responses, telomerase assembly, and centrosomal localization, with no dominant function or shared pathway among all 9 proteins. Because there is no cohesive theme connecting all terms and no edges to suggest a common process, I cannot assign a specific, representative label.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009626","count":1},{"id":"GO:0009817","count":1},{"id":"GO:0010449","count":1},{"id":"GO:1900037","count":1},{"id":"GO:0043947","count":1}]},{"hash":"1088204652480769260","title":"Unknown","description":"The top terms are scattered across DNA replication, muscle attachment, chromatin regulation, post-translational modification, host-virus interactions, platelet biology, and development, with no shared pathway or substantial connectivity (Edges: 0, Triangles: 0, Max Degree: 0). There isn\u2019t a cohesive function tying these proteins together, so a single descriptive name isn\u2019t justifiable. ","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0016203","count":1},{"id":"GO:0061635","count":1},{"id":"GO:1902083","count":1},{"id":"GO:0043923","count":1}]},{"hash":"1558626524125737995","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016554","count":2},{"id":"GO:0080156","count":2},{"id":"GO:0042793","count":2},{"id":"GO:0031425","count":2},{"id":"GO:0090617","count":2}]},{"hash":"1208322687821843424","title":"Oxidative Stress Response and Angiogenesis","description":"The cluster shows a convergence on redox biology and vascular remodeling. Terms like response to hydroperoxide, protein oxidation, cellular oxidant detoxification, and negative regulation of oxidative stress-induced intrinsic apoptotic signaling indicate oxidative stress management. Concurrently, endothelial cell migration and angiogenesis involved in wound healing point to vascular remodeling as a functional theme. A few terms (sensory perception of sound, UV protection, triglyceride metabolic process, fat cell differentiation) are less clearly connected and may reflect annotation noise or broad functional associations, but the dominant signal is redox homeostasis coupled to angiogenic processes.","confidence":"Medium","size":9,"edges":8,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007605","count":2},{"id":"GO:0009650","count":1},{"id":"GO:0006641","count":1},{"id":"GO:0043534","count":1},{"id":"GO:0033194","count":1}]},{"hash":"2122163504345816346","title":"Unknown","description":"The top GO terms span diverse functions from cellular targeting to signaling, calcium detection, kidney development, and broad physiological responses, with no clear shared function tying the proteins together. This heterogeneity makes a concise, representative label unlikely.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006613","count":1},{"id":"GO:0048015","count":1},{"id":"GO:0005513","count":1},{"id":"GO:0072221","count":1},{"id":"GO:0060316","count":1}]},{"hash":"1415252610274763132","title":"Ciliary function and interferon signaling","description":"The top GO terms cluster around ciliary biology (regulation of cilium beat frequency; non-motile cilium assembly) and innate immune signaling (cellular response to type I interferon), suggesting a shared theme of ciliary dynamics linked to interferon responsiveness. While other terms touch on hormone signaling and tissue development, these are less central to the cluster, making the cilia/interferon axis the most representative label.","confidence":"Medium","size":9,"edges":18,"triangles":23,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000105","count":2},{"id":"GO:0003085","count":2},{"id":"GO:1903071","count":2},{"id":"GO:0060296","count":2},{"id":"GO:2000324","count":2}]},{"hash":"514822813269415567","title":"Actin cytoskeleton remodeling and cell cycle signaling","description":"The top terms highlight actin dynamics (positive regulation of Arp2/3-mediated actin nucleation), GTPase regulation, and microtubule severing, along with mitotic cell cycle and kinase signaling, suggesting a cluster focused on cytoskeletal remodeling linked to cell cycle control. Some vesicle transport and broader stress/development terms are present, but the core theme is actin/microtubule regulation and associated signaling.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0051013","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0007275","count":5},{"id":"GO:2000601","count":5}]},{"hash":"2102601496250288264","title":"ER and nuclear protein quality control via ubiquitin-proteasome","description":"The top terms cluster around ER-associated processes (protein folding in the ER, ERAD) and nuclear protein quality control by the ubiquitin-proteasome system, indicating a group of proteins involved in folding and targeted degradation to maintain proteostasis in both ER and nucleus.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0071630","count":5},{"id":"GO:0051259","count":5},{"id":"GO:0070389","count":5}]},{"hash":"2050639690446053842","title":"Mitochondrial dynamics and inheritance","description":"This cluster centers on mitochondrial distribution, fission, and membrane organization, including mitochondrion inheritance, which together describe mitochondrial dynamics and partitioning during cell division. While a few terms touch on other trafficking or stress responses (e.g., amino acid starvation, endocytic recycling, GABAergic signaling), the dominant GO signals point to mitochondria-centric processes guiding organelle maintenance and inheritance.","confidence":"Medium","size":9,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0048312","count":3},{"id":"GO:0000266","count":2},{"id":"GO:0051932","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0007006","count":2}]},{"hash":"1365640131067687139","title":"Ubiquitin-Driven Cell Cycle and Chromatin Regulation","description":"This cluster centers on ubiquitination signals (K29- and K48-linked) and mitosis-related terms (exit from mitosis, spindle elongation) alongside chromatin processes (chromatin organization, subtelomeric heterochromatin formation). The presence of peroxisome import and C-type lectin signaling terms suggests broader regulatory roles, but the dominant pattern points to ubiquitin-mediated control of the cell cycle and chromatin state.","confidence":"Medium","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0035519","count":9},{"id":"GO:0010458","count":9},{"id":"GO:0070936","count":9},{"id":"GO:0000022","count":9},{"id":"GO:0002223","count":9}]},{"hash":"841336564040829596","title":"Selenocysteine incorporation during translation","description":"The dominant GO terms point to translation and the specialized process of incorporating selenocysteine into proteins (selenocysteine incorporation, selenocysteinyl-tRNA biosynthesis). Although several listed terms are obsolete (e.g., certain lysine metabolism and redox processes), the non-obsolete terms strongly indicate a cluster centered on the machinery for selenocysteine insertion during translation. This makes the label specific and representative for the cluster\u2019s function.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0097056","count":1},{"id":"GO:0001514","count":1},{"id":"GO:0071952","count":1},{"id":"GO:0016259","count":1}]},{"hash":"2048445405210912377","title":"Unknown","description":"The GO terms are scattered across diverse, largely unrelated processes (antibiotic and tetracenomycin biosynthesis, GPI anchor biosynthesis, GPI attachment, C-terminal methylation, wybutosine biosynthesis, JAK-STAT regulation, glucose metabolism, and mitotic spindle checkpoint), with no single cohesive function tying the cluster together. Therefore a coherent, specific label isn\u2019t evident.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":2},{"id":"GO:0050976","count":1},{"id":"GO:0006506","count":1},{"id":"GO:0046425","count":1},{"id":"GO:0016255","count":1}]},{"hash":"2191574084631303052","title":"Golgi\u2013endosome vesicle trafficking and recycling","description":"This cluster is dominated by GO terms related to intracellular transport within the Golgi\u2013endosome\u2013vacuole system, including Golgi to vacuole transport, retrograde transport from endosome to Golgi, general protein transport, and endocytic recycling. These collectively point to a cohesive function in vesicle trafficking and recycling within the endomembrane network, with a few outlier terms (lipid A biosynthesis, xenobiotic response) likely incidental. ","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009245","count":2},{"id":"GO:0070940","count":2},{"id":"GO:0061587","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0071375","count":2}]},{"hash":"1126725682533077650","title":"Unknown","description":"The top GO terms cover a wide and disparate set of processes\u2014from DNA recombination and demethylation to stress responses, hormone signaling, and post-transcriptional RNA regulation\u2014with several entries being obsolete. There is no single cohesive biological theme or pathway that links these functions, and the network shows no interactions to reinforce a shared function. Therefore no intuitive, specific label can be assigned beyond Unknown.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":5},{"id":"GO:0080111","count":4},{"id":"GO:0090502","count":4},{"id":"GO:0014912","count":4},{"id":"GO:0042493","count":4}]},{"hash":"1418273241193066623","title":"Heat-stress response signaling","description":"This cluster is dominated by terms related to temperature sensing and heat-stress responses, including thermoception, transcriptional responses to heat stress, and responses to capsazepine. While other terms in the set (telomere maintenance, telomeric chromosome localization, calcium release, etc.) are more divergent, the clearest cross-cutting theme among the top terms is cellular response to heat and temperature stress, suggesting a heat-stress signaling cluster. Confidence: Medium","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":3},{"id":"GO:0048549","count":3},{"id":"GO:0070427","count":3},{"id":"GO:0050955","count":3},{"id":"GO:1901594","count":3}]},{"hash":"2121877837655864360","title":"Cellular stress signaling and calcium dynamics","description":"These terms span heat/stress responses (thermoception, heat-stress transcriptional regulation, response to capsazepine), immune/signal transduction (NOD1 signaling), neuronal signaling (synaptic plasticity regulation), telomere regulation/localization, pinocytosis, cell cycle, and calcium release. The common thread appears to be broad regulatory signaling events modulated by stress and calcium as a downstream signal, rather than a single cohesive pathway, so a label emphasizing stress-related signaling with calcium dynamics is most representative.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":6},{"id":"GO:0048549","count":6},{"id":"GO:0070427","count":6},{"id":"GO:0050955","count":6},{"id":"GO:1901594","count":6}]},{"hash":"1274542187516608604","title":"Transposon and Proviral DNA Integration","description":"The dominant GO terms point to DNA integration and transposition (including proviral latency) and, secondarily, cell cycle and chromosome segregation, suggesting a cluster of proteins involved in mobile element insertion within host genomes and the related cell-cycle context. The \"symbiont entry into host cell\" term is peripheral but could reflect related entry processes; overall, the theme is integration of mobile genetic elements and associated cellular processes.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":1},{"id":"GO:0006313","count":1},{"id":"GO:0007049","count":1},{"id":"GO:0007059","count":1},{"id":"GO:0075713","count":1}]},{"hash":"1754998831353011897","title":"Acetylation and chromatin modification","description":"GO terms are dominated by acetylation-related processes (histone H4 acetylation, N-terminal acetylation, N-terminal propionylation, putrescine acetylation, N-acetylglucosamine metabolism) and chromatin-related activities (subtelomeric heterochromatin formation). The melatonin biosynthetic process also involves acetylation steps, reinforcing a central theme of acetyl group transfer and regulation. Although some terms pertain to plant-specific growth processes (leaf formation, angiogenesis), the shared thread is acetylation/modification and chromatin regulation, suggesting this cluster centers on acetylation-linked modification and metabolism pathways.","confidence":"Medium","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0030187","count":9},{"id":"GO:0043967","count":9},{"id":"GO:0017198","count":9},{"id":"GO:0001525","count":9},{"id":"GO:0006348","count":9}]},{"hash":"1728460916869042349","title":"Vacuolar amino acid transport","description":"This cluster shows multiple GO terms for transmembrane import of various amino acids (lysine, arginine, serine, tyrosine, histidine, glutamate) into the vacuole, along with related transport regulation and cellular responses to nitrogen starvation. The pattern suggests a cohesive set of vacuolar amino acid transporters active under nutrient stress, making \"Vacuolar amino acid transport\" a concise and representative label.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901482","count":2},{"id":"GO:0090518","count":2},{"id":"GO:0090516","count":2},{"id":"GO:2000487","count":2},{"id":"GO:0090514","count":2}]},{"hash":"238581658698982742","title":"Dopamine Metabolism and Neural Proliferation","description":"This cluster centers on dopamine catabolic/metabolic processes and on positive regulation of neural precursor cell proliferation, suggesting a dopaminergic signaling and neural development role. Additional signals for xenobiotic and lipopolysaccharide responses imply stress/inflammation context, but the strongest shared function among proteins appears to be modulation of dopamine metabolism and neural progenitor proliferation.","confidence":"Medium","size":9,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042420","count":2},{"id":"GO:0042135","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0045793","count":2},{"id":"GO:0032496","count":2}]},{"hash":"2126827301475258122","title":"Zinc ion transport and homeostasis","description":"The cluster is centered on zinc-related processes: cellular response to zinc ion starvation, detoxification of zinc ion, intracellular zinc ion homeostasis, and zinc ion import across the plasma membrane, which together indicate a cohesive zinc handling and transport function. The cadmium ion transmembrane transport term further supports metal ion transport. A couple of outlier terms (limb development, mRNA splicing via spliceosome) may reflect multi-functionality of some proteins or annotation noise, but the dominant zinc-related terms define the main theme.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034224","count":1},{"id":"GO:0010312","count":1},{"id":"GO:0006882","count":1},{"id":"GO:0070574","count":1},{"id":"GO:1903615","count":1}]},{"hash":"379458367242849013","title":"Golgi\u2013endosome vesicle trafficking","description":"This cluster\u2019s terms converge on intracellular transport involving Golgi and endosomal compartments (recycling endosome to Golgi, late endosome to Golgi, COPII cargo loading), indicating a vesicle-trafficking module. Some terms touch on unrelated processes such as spindle regulation or lens development, likely reflecting multifunctional proteins present in the set.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051534","count":1},{"id":"GO:0031578","count":1},{"id":"GO:1902018","count":1},{"id":"GO:0070309","count":1},{"id":"GO:1902543","count":1}]},{"hash":"1733343736250730152","title":"Vesicle trafficking and vitamin/lipid metabolism","description":"The top GO terms cluster around intracellular transport and lipid/vitamin handling: lysosome organization and Golgi to plasma membrane transport point to vesicular trafficking; vitamin E metabolic process and vitamin transport indicate vitamin/lipid metabolism; phosphatidylcholine and phosphatidylglycerol biosynthesis regulation reflect lipid metabolism; nutrient and toxic substance responses suggest a broader metabolic context. While some terms are diffuse (e.g., placental development), the strongest common thread is vesicle trafficking coupled with lipid and vitamin metabolism, supporting this label.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007584","count":2},{"id":"GO:0051452","count":1},{"id":"GO:0042360","count":1},{"id":"GO:0001892","count":1},{"id":"GO:0007040","count":1}]},{"hash":"418546427944499163","title":"ER protein trafficking and unfolded protein response","description":"This cluster centers on functions related to the endoplasmic reticulum, including localization to the ER, COPII-coated vesicle budding, and general protein transport, as well as the ER unfolded protein response and calcium homeostasis. While a few terms refer to host\u2013virus interactions, the dominant signal is ER-associated trafficking and stress response pathways, suggesting these proteins work together in ER-to-Golgi transport and UPR signaling.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070972","count":1},{"id":"GO:0044791","count":1},{"id":"GO:0060304","count":1},{"id":"GO:0044828","count":1},{"id":"GO:0006874","count":1}]},{"hash":"827321236168502360","title":"ERAD Ubiquitination and Deubiquitination","description":"The top GO terms cluster around ubiquitin-related processes: protein ubiquitination and deubiquitination with emphasis on K6- and K29-linked edits, plus ER-associated degradation (ERAD) pathways. This suggests the proteins function together in ubiquitin-mediated quality control of ER proteins rather than forming a connected interaction network. Some miscellaneous terms appear, but the dominant theme is ubiquitin modification and ERAD-driven proteostasis.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0044313","count":2},{"id":"GO:0035523","count":2},{"id":"GO:1904378","count":2},{"id":"GO:1903071","count":1}]},{"hash":"2245817713639112057","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002377","count":1},{"id":"GO:0015693","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0042274","count":1},{"id":"GO:0000472","count":1}]},{"hash":"281543166520563659","title":"Unknown","description":"There are no top GO terms and no interactions (Edges/Triangles = 0; Top Terms empty), so no shared function can be inferred to name this cluster. ","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1454846548394493513","title":"Blue-light GPCR signaling and potassium transport","description":"The cluster's prominent GO terms cluster around blue light signaling, GPCR signaling pathways (adenylate cyclase-activating adrenergic receptor signaling and adenosine receptor signaling), and cGMP biosynthesis, all characteristic of phototransduction cascades mediated by GPCRs and subsequent ion-channel regulation, including potassium flux. While a few terms like viral genome replication and cell division seem less related, the dominant theme points to photoreceptive GPCR signaling with ion transport. ","confidence":"Medium","size":8,"edges":6,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0019079","count":2},{"id":"GO:0051301","count":2},{"id":"GO:1990573","count":2},{"id":"GO:0097623","count":2}]},{"hash":"1765552807287409178","title":"Glandular and reproductive tissue development with lipid metabolism","description":"This cluster features GO terms tied to development of various tissues (digestive tract, mammary gland, female gonad, tongue muscle) alongside lipid metabolism and prostaglandin-related processes. The common thread appears to be developmental programs in glandular/reproductive tissues that are modulated by lipid signaling and metabolism, hence the label.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0048565","count":3},{"id":"GO:0035902","count":3},{"id":"GO:0010430","count":3},{"id":"GO:0008585","count":3},{"id":"GO:0001516","count":3}]},{"hash":"157375110110123344","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0071035","count":3},{"id":"GO:0071042","count":3},{"id":"GO:0071049","count":3}]},{"hash":"1591384212700225953","title":"Immune and Hormone Stimulus Response","description":"This cluster centers on proteins involved in cellular signaling in response to a variety of stimuli, including cytokine/growth factor cues (e.g., TGF-beta), hormones and amines (epinephrine, serotonin), and immune-related signals (neutrophil chemotaxis, macrophage colony-stimulating factor). The mix of stimulus-response GO terms suggests a shared role in transducing diverse external signals into coordinated cellular responses, rather than a single, cohesive pathway. Confidence: Medium.","confidence":"","size":8,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071560","count":4},{"id":"GO:0019933","count":3},{"id":"GO:0030593","count":3},{"id":"GO:1903206","count":3},{"id":"GO:0071872","count":3}]},{"hash":"777856561296581205","title":"GPCR-driven cyclic nucleotide signaling","description":"This cluster is dominated by GO terms for G protein-coupled receptor signaling (e.g., receptor guanylyl cyclase, adenosine receptor, adrenergic receptor pathways) and for the production of second messengers like cAMP and cGMP, plus related signaling such as blue light pathways. Together these suggest proteins functioning in GPCR-mediated signaling cascades that regulate transcription and cellular responses via cyclic nucleotides. Unknown terms like budding growth or hypoxia detection appear ancillary.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007118","count":3},{"id":"GO:0071880","count":2},{"id":"GO:0070483","count":2},{"id":"GO:0006182","count":2},{"id":"GO:0009785","count":2}]},{"hash":"1133374252845132472","title":"Amino acid and cofactor biosynthesis","description":"The top GO terms are dominated by biosynthetic processes for several amino acids (lysine, histidine, tyrosine, phenylalanine) and cofactors (biotin, protoporphyrinogen IX), suggesting the proteins in this cluster mainly participate in biosynthesis pathways. There are a few outliers (DNA-templated transcription, Notch signaling) that are less representative but don\u2019t override the overall biosynthetic theme. Therefore, a label focused on amino acid and cofactor biosynthesis is appropriate, with moderate confidence due to the presence of some non-biosynthetic terms.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019878","count":5},{"id":"GO:0006782","count":5},{"id":"GO:0009102","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0042218","count":4}]},{"hash":"1992181909020795277","title":"Autophagy and Cvt pathway proteins","description":"The top GO terms are dominated by autophagic processes: macroautophagy and the cytoplasm-to-vacuole targeting (Cvt) pathway, with mentions of nucleophagy, which together point to proteins involved in autophagy and vacuolar delivery. This provides a coherent functional label, despite a few outlier terms (tRNA thiolation, thiamine biosynthesis, transcription regulation, sumoylation, lipidation) that may reflect ancillary roles or annotation noise.","confidence":"High","size":8,"edges":17,"triangles":14,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0044805","count":5},{"id":"GO:0032258","count":5},{"id":"GO:0002143","count":5},{"id":"GO:0009229","count":5},{"id":"GO:0009228","count":5}]},{"hash":"1999347523178936014","title":"Unknown","description":"There are no GO terms listed for this cluster, and the small, sparsely connected network (8 proteins, 2 edges, no triangles) provides no obvious common function or pathway to unify the proteins. Therefore, the cluster is best labeled Unknown with confidence None.","confidence":"","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[]},{"hash":"1010973032834087611","title":"Neuronal transcriptional regulation and RNA processing","description":"The top terms converge on regulation of transcription (RNA Pol II) and RNA fate (nonsense-mediated decay, RNA-protein interactions, RNA processing), with hints of DNA topology context. The presence of neural-related terms (BDNF response, associative learning) suggests this cluster centers on gene-expression control in neuronal settings. Confidence: Medium","confidence":"","size":8,"edges":19,"triangles":22,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0045944","count":3},{"id":"GO:1904574","count":3},{"id":"GO:0000184","count":3},{"id":"GO:1990416","count":3}]},{"hash":"2065490173309004207","title":"Ciliary transport and brain development signaling","description":"This cluster features intraciliary transport in cilium assembly and mushroom body development, pointing to a module involved in neuronal development. The presence of TOR signaling regulation and GTPase activity regulation suggests linked growth and signaling processes that can influence brain development. Although other terms are broad or obsolete, the combination of cilium-related transport and brain development points to a cohesive theme of ciliary-associated signaling in neural development.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071230","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0000186","count":1},{"id":"GO:0035735","count":1},{"id":"GO:0032008","count":1}]},{"hash":"518377358988620394","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":12,"triangles":6,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0016584","count":4},{"id":"GO:0000480","count":4},{"id":"GO:0000472","count":4},{"id":"GO:0042766","count":4}]},{"hash":"1439641287099685267","title":"Chromatin Regulation & RNA Processing","description":"The top GO terms converge on nuclear processes: chromatin organization and histone modification (including historical histone acetylation), plus RNA processing/modification steps (RNA guanine-N7 methylation and mRNA branch site recognition). This suggests a cluster centered on chromatin-level control of gene expression and RNA maturation. A few terms (e.g., TORC1 signaling, phagolysosome assembly, epithelial proliferation) are less directly related and may reflect broader cellular processes or annotation noise, but do not dominate the theme. Confidence: Medium","confidence":"","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1904263","count":3},{"id":"GO:0036265","count":3},{"id":"GO:0000747","count":2},{"id":"GO:0050679","count":2},{"id":"GO:1902510","count":2}]},{"hash":"19850743670618148","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":10,"triangles":4,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0031167","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0008033","count":1},{"id":"GO:0048254","count":1},{"id":"GO:0000494","count":1}]},{"hash":"2221670476705994669","title":"Viral entry, replication, and virion assembly","description":"The top GO terms cluster around viral processes: fusion of viral membranes with host membranes, viral life cycle, virion assembly, and RNA-templated DNA biosynthesis, which together point to viral infection and production of viral particles. Additional terms like leukocyte migration reflect host response to infection, while protein folding and secretion regulation may relate to host machinery engaged during viral replication. Overall, this set centers on virus-host interaction and the viral life cycle.","confidence":"High","size":8,"edges":7,"triangles":3,"max_degree":4,"top_function":"protein folding","top_go_terms":[{"id":"GO:0010849","count":4},{"id":"GO:2000276","count":4},{"id":"GO:0019064","count":4},{"id":"GO:0050900","count":4},{"id":"GO:0019058","count":4}]},{"hash":"1411689865562278292","title":"Ribosome biogenesis and rRNA maturation","description":"The top terms are dominated by ribosome-related processes: ribosome biogenesis, LSU-rRNA maturation, snoRNP assembly, and translation. These indicate the cluster mainly centers on ribosome assembly and RNA processing, with occasional unrelated terms (developmental signaling) that are less representative. Therefore the label reflects the core function of the cluster.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0007338","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0000278","count":2}]},{"hash":"2148587020103213498","title":"DNA Replication and Chromosome Maintenance","description":"The dominant signals are DNA replication and related processes (DNA replication, premeiotic DNA replication, DNA strand elongation, DNA unwinding) plus a repair angle (double-strand break repair via break-induced replication) and subtelomeric heterochromatin formation, which together point to genome duplication and maintenance. A few terms appear tangential (gas vesicle organization, cochlea development, cilium movement, dense core vesicle transport), likely annotation noise, but do not override the core replication/maintenance theme.","confidence":"High","size":8,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":1},{"id":"GO:0031412","count":1},{"id":"GO:0090102","count":1},{"id":"GO:0006279","count":1},{"id":"GO:0006271","count":1}]},{"hash":"2166760795534344713","title":"Bacterial DNA Repair and Cell Wall Biosynthesis","description":"This cluster centers on nucleotide-excision repair and cell wall-related processes (peptidoglycan biosynthesis and cell wall organization), suggesting proteins involved in genome maintenance alongside envelope biogenesis in bacteria. Additional terms for detoxification and aromatic amino acid metabolism imply a broader stress-response context rather than a single pathway.","confidence":"Medium","size":8,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006289","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0008360","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0009252","count":2}]},{"hash":"1163617808053572559","title":"Lipid Signaling and Inflammation","description":"The dominant terms point to lipid-mediated signaling pathways (diacylglycerol metabolism, sphingoid catabolic process, lipid phosphorylation) and the inflammatory response, suggesting a cohesive theme around lipid signaling in inflammation. A few other terms (blood vessel development, leaf development, progesterone regulation) appear infrequently and may reflect annotation noise or broader cross-terms, but the main cluster is lipid signaling linked to inflammation. Confidence: Medium","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046521","count":1},{"id":"GO:0019933","count":1},{"id":"GO:0001568","count":1},{"id":"GO:0048366","count":1},{"id":"GO:0010801","count":1}]},{"hash":"2254734206728292201","title":"Calcium signaling and kinase regulation","description":"Most GO terms point to calcium signaling (detection of Ca2+, ryanodine-sensitive calcium release, Ca2+ import regulation) and phosphorylation/kinase pathways (peptidyl-threonine phosphorylation, protein kinase activity, calcineurin-NFAT signaling). A few terms are tangential (developmental, structural/bioluminescence), suggesting partial annotation noise. Overall, a calcium- and kinase-signaling theme fits best, but the coherence is not perfect.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060316","count":2},{"id":"GO:0048015","count":1},{"id":"GO:0005513","count":1},{"id":"GO:0072221","count":1},{"id":"GO:0008218","count":1}]},{"hash":"910599810377182003","title":"RNA processing and splicing regulation","description":"The top terms cluster around tRNA processing, mRNA splicing via the spliceosome, regulation of mRNA stability, and ncRNA-mediated gene silencing/miRNA regulation, indicating a shared focus on post-transcriptional RNA maturation and regulation. Minor terms related to RNA regulation reinforce this theme, while unrelated metabolic terms are incidental. Confidence: High","confidence":"","size":8,"edges":20,"triangles":22,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":3},{"id":"GO:0045292","count":3},{"id":"GO:1901407","count":3},{"id":"GO:0010610","count":3},{"id":"GO:2000627","count":2}]},{"hash":"254981339061275999","title":"Calcium signaling and calcineurin-NFAT pathway","description":"The cluster is dominated by GO terms for calcium ion detection/response, PI-mediated signaling, and calcineurin-NFAT regulation, suggesting a calcium-dependent signaling module influencing muscle activity, vascular tone, and kidney development; a few outliers (digestion, bioluminescence) do not negate the central theme.","confidence":"Medium","size":8,"edges":23,"triangles":36,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007586","count":8},{"id":"GO:0071277","count":8},{"id":"GO:0048015","count":7},{"id":"GO:0005513","count":7},{"id":"GO:0003073","count":7}]},{"hash":"1119107490076101459","title":"Mitotic spindle assembly and chromosome segregation","description":"This cluster is dominated by GO terms tied to spindle formation and microtubule dynamics during cell division: mitotic spindle assembly, spindle elongation and orientation, kinetochore-microtubule attachment, minus-end directed sliding, and cytokinesis-related processes. While a couple terms reference chloroplast movement or neuronal structure, the prevailing signal is mitotic spindle function and chromosome movement, suggesting proteins that coordinate spindle assembly and chromosome segregation.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000743","count":6},{"id":"GO:1990942","count":6},{"id":"GO:0021693","count":6},{"id":"GO:0000022","count":6},{"id":"GO:0051296","count":6}]},{"hash":"1004401574183921358","title":"Nuclear Transcription, RNA Processing, and DNA Repair","description":"Its top GO terms cluster around nuclear gene expression (DNA-templated transcription, mRNA splicing, regulation of transcription, ribosomal subunit export) and DNA damage response (nucleotide-excision repair, SOS). This combination suggests a coherent theme of nuclear transcription/RNA processing alongside DNA repair mechanisms, rather than a single enzymatic function. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0030420","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0006289","count":1}]},{"hash":"777059356170280103","title":"RNA Processing and Transcription Regulation","description":"The cluster is dominated by GO terms for RNA processing and gene expression control, including positive regulation of mRNA splicing via spliceosome, ncRNA-mediated gene silencing, and positive regulation of transcription by RNA polymerase II, with supporting signals from RNA decay and RNA structure-related terms. Some terms about DNA replication or neuronal learning are less central but do not contradict the main RNA-centric theme.","confidence":"High","size":8,"edges":25,"triangles":41,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":6},{"id":"GO:0031047","count":6},{"id":"GO:0045944","count":4},{"id":"GO:0006260","count":4},{"id":"GO:1904574","count":4}]},{"hash":"2287123654107960200","title":"Unknown","description":"The GO terms span diverse processes including apoptosis regulation, calcium import, DNA replication, transcription from RNAP II, cholesterol biosynthesis, carbohydrate phosphorylation, lactation, autophagy regulation, and differentiation in heart tissue, with no single unifying function. Therefore, there isn\u2019t a coherent, specific cluster label beyond Unknown.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043065","count":2},{"id":"GO:0070509","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0000435","count":2},{"id":"GO:0006695","count":2}]},{"hash":"153536197788388657","title":"Unknown","description":"The eight proteins are annotated with a highly heterogeneous set of GO terms, including glucocorticoid signaling, ER-associated ubiquitin-protein catabolic processes, DNA replication, interferon response, hematopoietic stem cell differentiation, prostate and male sex development, hydrogen peroxide response, and morphine response, with no single dominant theme evident.","confidence":"","size":8,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2000324","count":1},{"id":"GO:1903071","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0071357","count":1},{"id":"GO:1902037","count":1}]},{"hash":"1370364508423913598","title":"Regulated kinase signaling and growth processes","description":"The cluster shows representation of protein kinase activation and inhibition, ribosome biogenesis, and DNA replication, pointing to coordination of signaling with core growth and biosynthetic processes. Some terms reflect development and stress-related pathways, with a few obsolete entries adding noise. Overall, the common theme centers on regulation of kinase signaling in growth-related cellular functions.","confidence":"Medium","size":8,"edges":9,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0032147","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0006260","count":2},{"id":"GO:1905259","count":2},{"id":"GO:0097428","count":2}]},{"hash":"1130920238869646385","title":"Vesicle trafficking and membrane remodeling","description":"The cluster is dominated by GO terms related to endomembrane dynamics and membrane remodeling, including vesicle budding, endosome to plasma membrane transport, lysosomal membrane organization, and membrane tubulation, indicating a shared function in vesicle trafficking and membrane dynamics. Some cell-cycle related terms appear but are less representative of the core theme.","confidence":"Medium","size":8,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0060325","count":1},{"id":"GO:0030037","count":1},{"id":"GO:0097212","count":1},{"id":"GO:0070142","count":1},{"id":"GO:1903527","count":1}]},{"hash":"154030063772795812","title":"Unknown","description":"The top GO terms are highly diverse (development, biofilm regulation, glucose signaling, sugar and alcohol metabolism, histone modification, viral transcription activation, and amino acid starvation responses) and several entries are obsolete. There is no clear, single biological function or pathway that binds these eight proteins, so a concise, accurate label cannot be confidently assigned.","confidence":"","size":8,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1903709","count":1},{"id":"GO:1900189","count":1},{"id":"GO:1902661","count":1},{"id":"GO:0044109","count":1},{"id":"GO:0001207","count":1}]},{"hash":"632472243779652711","title":"Developmental regulation and cell cycle control","description":"This cluster centers on development-related processes (mesoderm formation, cell morphogenesis, neural tube patterning) together with core cell cycle activities (DNA replication, mitotic cell cycle), plus regulatory signaling terms (kinase activity, Smoothened pathway) and hormone response. The mix implies a set of proteins coordinating developmental signaling with proliferation and morphogenesis, hence a label focused on developmental regulation linked to cell cycle control.","confidence":"Medium","size":8,"edges":14,"triangles":11,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0001707","count":2},{"id":"GO:1901621","count":2},{"id":"GO:0071374","count":2},{"id":"GO:0000278","count":2}]},{"hash":"461027707215546319","title":"Endosome-Lysosome Trafficking and Fusion","description":"The GO terms cluster around intracellular transport within the endomembrane system, especially endosome-to-Golgi and endosome-to-lysosome routes, phagosome-lysosome fusion, and the Cvt pathway to the vacuole, pointing to vesicle trafficking and lysosomal/degradative fusion. Additional terms about cleavage furrow formation and cell polarity likely reflect broader roles of trafficking in cytoskeletal organization and cell shape, but the dominant theme is endocytic/lysosomal transport.","confidence":"Medium","size":8,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0032973","count":1},{"id":"GO:1990034","count":1},{"id":"GO:0036089","count":1},{"id":"GO:0048015","count":1},{"id":"GO:2000769","count":1}]},{"hash":"1674387422269462557","title":"Hormone signaling and vascular remodeling","description":"The terms cluster around regulation of signaling pathways (activin receptor signaling, adiponectin signaling, testosterone response, regulation of protein kinase activity, phosphorylation) and endothelial development (endothelial tube morphogenesis, negative regulation of endothelial cell migration), with an additional note of liver regeneration. This suggests a theme of signaling control in hormone-responsive and vascular contexts, rather than a single specific function.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097421","count":1},{"id":"GO:0032927","count":1},{"id":"GO:0061154","count":1},{"id":"GO:0006656","count":1},{"id":"GO:0045859","count":1}]},{"hash":"654985242486676904","title":"Diverse solute membrane transporters","description":"The top GO terms point to transmembrane transport of a variety of substrates (sodium ions, glucose, vitamins, nitrate, organic anions, selenite) and neurotransmitter loading into vesicles, suggesting a common role as membrane transport proteins handling diverse solutes. While a few terms are obsolete or outliers, the dominant theme is membrane transport across biological membranes.","confidence":"High","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0098700","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0042891","count":2},{"id":"GO:0035725","count":2}]},{"hash":"1245393392674178121","title":"Ribosome Biogenesis and RNA Modification","description":"This cluster is dominated by GO terms tied to ribosome production and RNA processing, including ribosomal small subunit export from the nucleus, rRNA modification, and tRNA wobble uridine modification, suggesting a core function in ribosome biogenesis and RNA modification. The additional stress-related responses appear secondary signals rather than defining features of the group.","confidence":"High","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":3},{"id":"GO:0002098","count":2},{"id":"GO:0000056","count":2},{"id":"GO:0006972","count":2},{"id":"GO:0042220","count":2}]},{"hash":"1999131717636105582","title":"Unknown","description":"There are no GO terms provided for this cluster, so there is no clear common function to tie the eight proteins together. With top terms missing, the available signals (a small network of 6 edges, no triangles) do not indicate a coherent biological role.","confidence":"","size":8,"edges":6,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[]},{"hash":"995344445951856012","title":"Unknown","description":"This cluster lacks any top GO terms (Top Terms list is empty) and has only a single edge with max degree 1, indicating no clear functional connectivity. Without a shared function or theme, there is no basis for a specific label beyond Unknown.","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[]},{"hash":"119427956067333305","title":"Ammonium transport and nitrogen utilization","description":"The Top GO terms cluster around ammonium and nitrogen transport and utilization (ammonium transmembrane transport, methylammonium transport, transepithelial ammonium transport, regulation of nitrogen utilization, nitrogen utilization). While there are related terms about nutrient-limited growth and other metabolic processes (pseudohyphal and invasive growth in response to glucose limitation, CO2 transport, iron homeostasis), the recurring theme is nitrogen metabolism and ammonium transport/uptake. Thus the label highlights the core function of this cluster.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006808","count":1},{"id":"GO:0007124","count":1},{"id":"GO:0060586","count":1},{"id":"GO:0015843","count":1},{"id":"GO:0015670","count":1}]},{"hash":"947279413796737143","title":"Virus entry and replication","description":"The top terms point to stages of viral infection: fusion of the viral membrane with host cells, virion assembly, and the viral life cycle, plus RNA-templated DNA biosynthesis. Also present are host-pathogen interaction aspects (symbiont entry, leukocyte migration) and cellular processes (protein folding, secretion) commonly co-opted during infection. This suggests a cohesive theme of virus-host interaction covering entry, replication, and assembly.","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010849","count":1},{"id":"GO:2000276","count":1},{"id":"GO:0019064","count":1},{"id":"GO:0050900","count":1},{"id":"GO:0019058","count":1}]},{"hash":"2257749636720111063","title":"RNA Splicing Regulation and Translation Initiation","description":"The top GO terms are dominated by mRNA splicing via the spliceosome (positive and negative regulation, cis splicing) and general RNA processing, plus a term for eIF4F complex assembly, indicating involvement in translation initiation. This suggests a cluster of proteins linked to RNA maturation and control of translation, with an additional note of ncRNA-mediated gene silencing supporting broad RNA-level regulatory roles.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901407","count":3},{"id":"GO:0031047","count":2},{"id":"GO:0048026","count":2},{"id":"GO:1902625","count":2},{"id":"GO:0075525","count":2}]},{"hash":"1516558853604894463","title":"Cellular stress response and apoptosis","description":"Based on the top GO terms, the proteins appear linked to cellular responses to various stresses (peptide hormone stimulus, hydrogen peroxide, xenobiotic stimuli) and to apoptosis, with additional signals for gene regulation (mRNA stability) and metabolism (glycogen synthase regulation). Although some terms are obsolete, the common theme is stress-induced signaling and cell fate decisions, which justifies a Cellular stress response and apoptosis label.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071375","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0080111","count":1},{"id":"GO:0090502","count":1},{"id":"GO:0014912","count":1}]},{"hash":"867875668513731082","title":"Unknown","description":"The eight proteins show a wide spread of GO terms\u2014from transcription regulation and ribosome biogenesis to heart development, vacuole fusion, and signaling\u2014with no shared dominant function. There are no edges among members, so there isn\u2019t a single cohesive biological process tying them together. Therefore there isn\u2019t a clear functional theme to label; mark as Unknown.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045944","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0042144","count":2},{"id":"GO:0042254","count":1}]},{"hash":"155939887470133576","title":"Unknown","description":"The top terms cover telomere maintenance, pinocytosis, innate immune signaling (NOD1), temperature sensation, heat-stress transcription response, cell cycle, synaptic plasticity, chromosome telomere localization, and calcium release. This broad and heterogeneous mix lacks a single cohesive function or pathway that ties all proteins together, making a concise, specific cluster name unreliable. Confidence: None","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":4},{"id":"GO:0048549","count":4},{"id":"GO:0070427","count":4},{"id":"GO:0050955","count":4},{"id":"GO:1901594","count":4}]},{"hash":"2103027930303342526","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016239","count":1},{"id":"GO:2000884","count":1},{"id":"GO:0045493","count":1},{"id":"GO:0007283","count":1},{"id":"GO:0052889","count":1}]},{"hash":"1817843219938709544","title":"Cardiac conduction and heart morphogenesis","description":"The top GO terms cluster around regulation of heart electrical activity (SA node and atrial action potentials) and development of cardiac structures (outflow tract, left ventricle). Calcium signaling and calcium transporter activity further support a role in cardiac excitation-contraction coupling. Taken together, these terms point to proteins involved in cardiac function and heart development.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098907","count":4},{"id":"GO:0007205","count":3},{"id":"GO:0005513","count":2},{"id":"GO:1901896","count":2},{"id":"GO:0007275","count":2}]},{"hash":"1973974639164038629","title":"Unknown","description":"The GO terms are scattered across redox balance, capsule biosynthesis, metabolism, methylation, and chromatin-related processes, with no clear unifying function or interactions (no edges). This diversity makes a cohesive label untenable.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0098869","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0045227","count":2},{"id":"GO:0015945","count":2}]},{"hash":"2119241313486825617","title":"RNA Processing and Translation Regulation","description":"The proteins show enrichment for mRNA stability regulation, splicing, and polyadenylation, along with ncRNA-mediated gene silencing and assembly of the translation initiation complex, indicating a cohesive role in RNA maturation and control of translation.","confidence":"High","size":8,"edges":26,"triangles":45,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":6},{"id":"GO:0006378","count":5},{"id":"GO:0031047","count":4},{"id":"GO:0048026","count":4},{"id":"GO:1902625","count":4}]},{"hash":"2273572777083660555","title":"ER-Associated Protein Quality Control (ERAD)","description":"Based on the GO terms, the cluster centers on handling misfolded proteins and their degradation, especially in the endoplasmic reticulum. Key terms include cellular response to misfolded protein, ER-associated misfolded protein catabolic process, and ubiquitin-related proteolysis, indicating ER quality control and proteasome-mediated degradation. ATP-related terms reflect energy dependence of proteostasis. A few terms (DNA replication, peroxisome import) are less aligned but do not override the dominant ERAD/proteostasis theme.","confidence":"High","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071218","count":2},{"id":"GO:0061166","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0046034","count":2},{"id":"GO:0070407","count":2}]},{"hash":"585481933336772640","title":"DNA transposition and proviral integration","description":"The top GO terms cluster around DNA integration, transposition, and proviral latency, with supporting signals from RNA-templated DNA synthesis, DNA replication, and cell-cycle processes. This suggests the proteins are involved in mobile genetic element activity (transposons/retroviruses) and related genome maintenance steps, rather than a single canonical pathway. Therefore this label captures the dominant theme without overgeneralization.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0015074","count":5},{"id":"GO:0075713","count":5},{"id":"GO:0046718","count":5},{"id":"GO:0006313","count":3},{"id":"GO:0007049","count":3}]},{"hash":"1091750355402199259","title":"Ubiquitination and Endolysosomal Trafficking","description":"These GO terms cluster mainly around intracellular vesicle trafficking and protein turnover: ubiquitination, Rab-mediated signal transduction, endosome transport, lysosomal membrane organization, and Cvt pathway delivery to the vacuole. These suggest a core theme of proteostasis and endolysosomal trafficking, with some neuronal and osteoclast-related terms reflecting broader regulatory roles in cell signaling and differentiation. ","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0016567","count":5},{"id":"GO:0032482","count":5},{"id":"GO:0050771","count":5},{"id":"GO:0031584","count":4},{"id":"GO:0097212","count":4}]},{"hash":"904476747545513787","title":"DNA metabolism and host-virus interactions","description":"This cluster shows strong representation of DNA-centric processes\u2014DNA replication, transcription, DNA integration, and recombination\u2014suggesting a group of proteins involved in genome maintenance and manipulation. The presence of symbiont/virus-related terms (proviral latency, symbiont entry, apoptosis activation) and modulation of RNA silencing further implies a link to host-virus or host-symbiont interactions. Together, these signals point to a theme of DNA metabolism with associated host\u2013pathogen interfaces.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042273","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006278","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0039651","count":2}]},{"hash":"197380866733720179","title":"Retroviral DNA integration and proviral latency","description":"The terms cluster around retroviral replication steps: RNA-templated DNA biosynthesis (reverse transcription), DNA integration, establishment of integrated proviral latency, viral entry/penetration into the host nucleus, and DNA replication/recombination. This combination points to a retrovirus life cycle and provirus maintenance as the shared function of the proteins. Confidence: High","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006278","count":3},{"id":"GO:0039651","count":3},{"id":"GO:0015074","count":3},{"id":"GO:0075713","count":3},{"id":"GO:0006310","count":3}]},{"hash":"26104569310083503","title":"Cellular stress responses and regulatory signaling","description":"This cluster centers on GO terms related to cellular responses to various stimuli (xenobiotic, hydrogen peroxide, peptide hormones) and regulatory processes (mRNA stability, glycogen synthase regulation), with related signaling activity (phosphatidylinositol dephosphorylation). Although several terms are obsolete or touch on DNA processing, the prevailing theme is stress/stimulus response coupled with regulation of signaling and gene expression, supporting this label.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0090502","count":4},{"id":"GO:0046856","count":4},{"id":"GO:0006310","count":4},{"id":"GO:0080111","count":3},{"id":"GO:0014912","count":3}]},{"hash":"1419795191421025638","title":"Guard cell morphogenesis and cell wall remodeling","description":"This cluster features plant-specific function hints, notably guard cell morphogenesis (GO:0010442) and cell wall organization (GO:0071555), plus prolyl hydroxylation involved in cell wall protein modification. The combination suggests a theme around guard cell development and plant cell wall remodeling, with additional supporting hints from lipid/phospholipid metabolism and cellular homeostasis terms that are common in plant cells.","confidence":"Medium","size":8,"edges":7,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000272","count":1},{"id":"GO:0071555","count":1},{"id":"GO:0018401","count":1},{"id":"GO:1901874","count":1},{"id":"GO:0055114","count":1}]},{"hash":"1985304715954411357","title":"Retroviral DNA integration and latency","description":"The Top Terms point to retroviral processes: reverse transcription (RNA-templated DNA biosynthetic process), DNA replication and DNA integration, proviral latency establishment, and viral entry/penetration into the host nucleus, with occasional recombination and host apoptotic interactions. This combination strongly supports a theme centered on the retroviral life cycle, including proviral integration and latency.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006278","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0039651","count":1},{"id":"GO:0015074","count":1},{"id":"GO:0075713","count":1}]},{"hash":"1271100360377686982","title":"Ethylene-regulated iron and manganese homeostasis in plants","description":"The top GO terms point to iron and manganese ion transport and homeostasis, with responses to iron and manganese ions and to ethylene signaling, plus a relation to leaf senescence. This pattern suggests a plant-specific module where metal ion management intersects with ethylene-driven senescence processes, even though only a few terms are represented. Overall, the label captures the most coherent common function across the terms.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900056","count":1},{"id":"GO:0071421","count":1},{"id":"GO:0071281","count":1},{"id":"GO:0006880","count":1},{"id":"GO:0030026","count":1}]},{"hash":"85799492870082290","title":"RNA Polymerase III Transcription Machinery","description":"Most GO terms in this cluster relate to RNA polymerase III\u2013driven transcription, including preinitiation complex assembly, transcription by RNA Pol III, and 5S rRNA transcription, with a note of regulation of Pol III as well. A few terms reference oogenesis-related processes, which appear to be incidental annotations rather than defining the cluster.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000999","count":1},{"id":"GO:0001041","count":1},{"id":"GO:0006359","count":1},{"id":"GO:0042791","count":1},{"id":"GO:0001021","count":1}]},{"hash":"1586868344117661371","title":"Plant glycolysis and stress signaling","description":"The cluster centers on glycolytic processes (glycolysis, pyruvate biosynthesis) indicating energy metabolism, while also featuring multiple stress- and signaling-related responses (heat, hypoxia, cAMP, epinephrine, lithium) and seed maturation, suggesting a plant-specific module that links metabolism with stress signaling during development.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"programmed cell death","top_go_terms":[{"id":"GO:0042866","count":5},{"id":"GO:0010226","count":3},{"id":"GO:0061621","count":3},{"id":"GO:0009408","count":3},{"id":"GO:0051591","count":3}]},{"hash":"1675621628543565215","title":"Negative Regulation of TGF-beta/BMP Signaling","description":"The top GO terms are dominated by negative regulation of TGF-beta receptor signaling, BMP signaling, SMAD complex assembly, and non-canonical NF-kappaB pathways, with peptidyl-threonine dephosphorylation supporting signaling shut-off. While some terms touch plant-specific processes (meristem identity, photosystem adjustments), the common thread is modulation and inhibition of growth factor\u2013related signaling pathways, making this a plausible, cohesive cluster label.","confidence":"Medium","size":7,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":5},{"id":"GO:0071560","count":4},{"id":"GO:0035970","count":4},{"id":"GO:0010991","count":4},{"id":"GO:0030512","count":4}]},{"hash":"1914749317050863626","title":"Neddylation-ubiquitin regulation of the cell cycle","description":"The GO terms cluster around protein neddylation and its regulation, ubiquitin-related transferase activity, and cell cycle/division processes, suggesting a coherent role in post-translational modification controlling cell cycle progression and proteolysis, with some related stress response signals (DNA damage from gamma radiation/UV-C).","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035335","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0051301","count":2},{"id":"GO:2000436","count":1},{"id":"GO:0010332","count":1}]},{"hash":"1309325775413823841","title":"GPCR-Mediated Cyclic Nucleotide Signaling","description":"These proteins are enriched for GPCR signaling pathways and the production of cyclic nucleotides (cAMP and cGMP), including adenosine/adrenergic receptor signaling, receptor guanylyl cyclase signaling, and cAMP/cGMP biosynthesis. The presence of blue light signaling and regulation of oocyte maturation further supports roles for cAMP/cGMP as shared mediators in diverse contexts, making GPCR-driven cyclic nucleotide signaling a coherent, representative label.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0071880","count":6},{"id":"GO:0070483","count":6},{"id":"GO:0006182","count":6},{"id":"GO:0009785","count":6},{"id":"GO:0001973","count":6}]},{"hash":"1659751226563015073","title":"Plant jasmonate/oxylipin signaling","description":"The GO terms cluster around jasmonic acid biosynthesis, oxylipin biosynthesis, and related lipid metabolism (fatty acid beta-oxidation) with plant-specific roles in stress responses (oxidative stress, ozone) and development (stamen development). This combination points to a cohesive theme of lipid-derived signaling and defense in plants, anchored by jasmonate/oxylipin pathways, with some secondary carbohydrate catabolism terms as less central context. ","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033543","count":1},{"id":"GO:0031408","count":1},{"id":"GO:0048443","count":1},{"id":"GO:0009636","count":1},{"id":"GO:0010193","count":1}]},{"hash":"1328090204111894355","title":"Mitotic spindle and cell cycle regulation","description":"The terms cluster around mitosis and spindle assembly (mitotic spindle orientation checkpoint signaling, mitotic cell cycle, mitotic spindle assembly) and cytoskeleton/polarity control (cell shape maintenance). A few terms refer to stress responses, but the dominant theme is cell division machinery and spindle/cytoskeleton regulation.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031578","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0071963","count":2},{"id":"GO:0031532","count":2},{"id":"GO:0090307","count":2}]},{"hash":"517913199020563452","title":"Viral entry, replication, and virion assembly","description":"Top GO terms cluster around steps of viral infection: fusion of viral membrane with host, viral life cycle, virion assembly, and entry into host, with associated host immune cell migration and protein secretion; these collectively point to viral infection-related processes.","confidence":"Medium","size":7,"edges":16,"triangles":17,"max_degree":6,"top_function":"protein folding","top_go_terms":[{"id":"GO:0010849","count":6},{"id":"GO:2000276","count":6},{"id":"GO:0019064","count":6},{"id":"GO:0050900","count":6},{"id":"GO:0019058","count":6}]},{"hash":"501143611701389012","title":"Ribosome Biogenesis and RNA Processing","description":"This cluster is dominated by processes related to ribosome biogenesis, rRNA maturation, and RNA modification (e.g., LSU-rRNA maturation, snoRNP assembly, rRNA and snRNA pseudouridine synthesis) as well as translation. The recurring theme is RNA-based ribosome assembly and the translation machinery, with only incidental signaling terms.","confidence":"High","size":7,"edges":8,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0046330","count":1},{"id":"GO:1904571","count":1},{"id":"GO:0000492","count":1},{"id":"GO:0000470","count":1}]},{"hash":"1252687369175711045","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":10,"triangles":10,"max_degree":4,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":7},{"id":"GO:0045944","count":6},{"id":"GO:0006260","count":6},{"id":"GO:0034475","count":6},{"id":"GO:0031047","count":6}]},{"hash":"811817669629832349","title":"Innate Immune Response and Ubiquitin-Proteasome Regulation","description":"The prominent GO terms point to innate immune defense and antiviral responses, with additional emphasis on ubiquitin-mediated protein turnover (SCF-dependent degradation and K48-linked ubiquitination), suggesting a link between immune signaling and proteostasis. Some terms are less directly related (peroxisome import, histone catabolic, bud neck localization), but they do not override the core immune-proteostasis theme.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097271","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0046007","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0031146","count":2}]},{"hash":"2215125939178664231","title":"Unknown","description":"There is no functional theme visible because no GO terms are provided in the Top Terms for this cluster. Without GO annotations, I cannot assign a meaningful, specific label. If you share the GO terms and their frequencies, I can propose an accurate name with a confidence rating.","confidence":"","size":7,"edges":18,"triangles":23,"max_degree":6,"top_function":null,"top_go_terms":[]},{"hash":"315960857593451995","title":"Ribosome biogenesis and rRNA processing regulators","description":"These proteins show a clear pattern around nuclear RNA metabolism and ribosome assembly: positive regulation of rRNA processing, positive regulation of ribosomal small subunit export from the nucleus, maturation of SSU-rRNA, and RNA import into the nucleus, along with associated phosphorylation events. While a couple terms are broader or obsolete or less central (glial proliferation, antibiotic response, methionine salvage), the dominant GO signals cluster around ribosome biogenesis and RNA processing, suggesting regulators of ribosome assembly. ","confidence":"Medium","size":7,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1901407","count":2},{"id":"GO:0060252","count":1},{"id":"GO:0046830","count":1},{"id":"GO:0019509","count":1},{"id":"GO:0046677","count":1}]},{"hash":"524721474823904119","title":"DNA replication, repair, and cell-cycle control","description":"The cluster's top GO terms heavily emphasize DNA replication (GO:0006260), double-strand break repair via nonhomologous end joining (GO:2001034), and G1/S transition of the mitotic cell cycle (GO:0000082), plus maintenance of DNA trinucleotide repeats (GO:0035753). These indicate a module focused on genome integrity and progression through the cell cycle. Other terms involve signaling (NFAT/calcium-related), which may reflect regulatory cross-talk but are not central to the main theme.","confidence":"Medium","size":7,"edges":9,"triangles":5,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070940","count":4},{"id":"GO:2000324","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0005513","count":3},{"id":"GO:0001915","count":3}]},{"hash":"2119258912984732434","title":"mRNA Splicing and Spliceosome Regulation","description":"The cluster centers on mRNA processing via the spliceosome, with multiple terms for cis splicing, spliceosome-mediated splicing regulation, and splice site recognition. While there is a single term related to translation initiation factor assembly, the dominant theme is splicing and its regulation, suggesting a cohesive role in RNA processing. The label captures this primary function without overextending to unrelated processes.","confidence":"High","size":7,"edges":14,"triangles":11,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":2},{"id":"GO:0031047","count":1},{"id":"GO:0048026","count":1},{"id":"GO:1902625","count":1},{"id":"GO:0075525","count":1}]},{"hash":"849057701854122842","title":"Vesicle trafficking and epithelial polarity","description":"The top terms cluster around vesicle transport and organelle localization (cytoplasm to vacuole targeting, endosome to melanosome transport, lysosomal membrane organization), apical protein localization, and establishment of epithelial polarity, plus regulation of the secretory pathway, pointing to coordinated trafficking and polarized secretion rather than a single enzymatic activity. Bone resorption and manganese response can relate to trafficking and stress responses in these pathways, but the dominant signal is vesicle trafficking and polarity.","confidence":"High","size":7,"edges":4,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031584","count":7},{"id":"GO:0097212","count":7},{"id":"GO:0045453","count":7},{"id":"GO:0032258","count":7},{"id":"GO:0035646","count":7}]},{"hash":"198893026129381003","title":"Chromophore-binding light signaling proteins","description":"The cluster's strongest signals are chromophore-related: protein-tetrapyrrole linkage and chromophore linkage, plus red, far-red light phototransduction, suggesting proteins that bind tetrapyrrole chromophores and participate in light sensing/signaling. Other terms like DNA replication and meiosis appear incidental to this theme, so the core association is chromophore binding and light signaling.","confidence":"Medium","size":7,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045151","count":1},{"id":"GO:0017006","count":1},{"id":"GO:0070483","count":1},{"id":"GO:0006261","count":1},{"id":"GO:0045793","count":1}]},{"hash":"113701345716258573","title":"RNA processing and transcription regulation","description":"These proteins cluster around RNA metabolism and transcriptional control, with repeated GO terms for pre-miRNA processing, miRNA catabolism, DNA-templated transcription, transcription antitermination, and CRD-mediated mRNA stabilization, indicating a cohesive theme of RNA processing and transcription regulation, with ancillary links to stress response and kidney development pathways.","confidence":"Medium","size":7,"edges":7,"triangles":2,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0031054","count":3},{"id":"GO:0006351","count":3},{"id":"GO:1902219","count":3},{"id":"GO:0060567","count":3},{"id":"GO:1901724","count":3}]},{"hash":"1165754458857268764","title":"Secreted hormone processing and LDL receptor turnover","description":"The GO terms point to secretory and processing roles for hormones/peptides (nerve growth factor production, renin and insulin processing, pheromone maturation) together with LDL receptor catabolic regulation, implying a cluster of secretory signaling coupled to lipid receptor turnover.","confidence":"Medium","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032902","count":3},{"id":"GO:0002001","count":3},{"id":"GO:0032804","count":3},{"id":"GO:0045453","count":3},{"id":"GO:0032802","count":3}]},{"hash":"1029583369442728258","title":"RNA Pol II Transcription Regulation","description":"The cluster is characterized by strong enrichment for GO terms related to RNA polymerase II\u2013mediated transcription, including DNA-templated transcription and both negative and positive regulation of transcription by RNAP II. While a few proteins touch on auxiliary processes like protein repair or oxidative stress response, the dominant theme remains transcriptional control by RNAP II, making this label representative of the cluster\u2019s function.","confidence":"High","size":7,"edges":16,"triangles":16,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0042766","count":2},{"id":"GO:0006357","count":2},{"id":"GO:0030091","count":1}]},{"hash":"1097742627271672577","title":"Ribosome biogenesis and mitotic regulation","description":"Dominant terms are ribosomal large subunit biogenesis/assembly and translation, pointing to a core ribosome-related protein cluster. The inclusion of mitosis exit and mitotic checkpoint signaling suggests additional cell-cycle regulatory roles. Retina development terms appear sporadically and do not redefine the main theme. ","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042273","count":2},{"id":"GO:0010458","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0032781","count":1},{"id":"GO:0031290","count":1}]},{"hash":"1322273994856076803","title":"Proteasome- and ubiquitin-mediated protein turnover","description":"The cluster\u2019s GO terms cluster around proteasome core complex assembly, APC/C-dependent catabolic processes, and regulation of ubiquitin ligase activity, all pointing to regulated protein degradation. The MHC class I antigen processing term also ties to proteasomal peptide generation. Although other signaling terms (TNF, Wnt) appear, they likely reflect broader regulatory networks linked to proteostasis. Thus the dominant theme is ubiquitin-proteasome\u2013driven protein turnover and cell-cycle control.","confidence":"High","size":7,"edges":12,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051436","count":3},{"id":"GO:0002223","count":3},{"id":"GO:0061418","count":3},{"id":"GO:0002479","count":3},{"id":"GO:0090263","count":3}]},{"hash":"528511042165136201","title":"Retroviral replication and proviral integration","description":"This cluster is dominated by retroviral life-cycle terms: RNA-templated DNA biosynthesis (reverse transcription), DNA replication, DNA integration and recombination, establishment of integrated proviral latency, and viral entry/nuclear penetration. Together they suggest a group of proteins involved in the retroviral replication cycle and integration into the host genome, with additional terms hinting at host-cell responses (misfolded protein response, siRNA processing) during infection.","confidence":"High","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0006278","count":2},{"id":"GO:0039651","count":2},{"id":"GO:0015074","count":2},{"id":"GO:0075713","count":2}]},{"hash":"945801064073666440","title":"Unknown","description":"The top GO terms cover a broad mix of functions (cardiac action potential regulation, GPCR signaling, antibiotic response, telomere maintenance, pinocytosis, NOD1 signaling, thermoception, capsazepine response, heat-stress transcription, and cell cycle) with no evident shared biological theme or direct functional link among the proteins, suggesting the cluster is functionally diverse or unrelated. ","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098907","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0032212","count":1},{"id":"GO:0048549","count":1}]},{"hash":"1670328708903067221","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902187","count":2},{"id":"GO:0070534","count":2},{"id":"GO:0030433","count":2},{"id":"GO:1903265","count":2},{"id":"GO:0000447","count":1}]},{"hash":"1594474700914302518","title":"Unknown","description":"The GO terms include vasoconstriction, hypoxia response, CO2 detection, startle response, thermoception, response to capsazepine, flagellated sperm motility, jasmonic acid regulation, circadian sleep/wake regulation, and synaptic depression. This mix spans multiple kingdoms and themes with no single unifying function, and there are no connecting edges, so no coherent label can be assigned.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042310","count":1},{"id":"GO:0001666","count":1},{"id":"GO:0003031","count":1},{"id":"GO:0001964","count":1},{"id":"GO:0050955","count":1}]},{"hash":"212828260656860353","title":"Aromatic xenobiotic degradation and photosynthesis","description":"The cluster includes catabolic processes for toluene and carbazole (aromatic xenobiotics) and CMP-N-acetylneuraminate metabolism, alongside nitrate assimilation, proton transport, and photosynthesis/nonphotochemical quenching. This mix suggests a set of proteins involved in aromatic compound degradation and energy-related metabolism, including photosynthetic energy handling. Therefore, a label highlighting both xenobiotic degradation and photosynthetic metabolism fits best.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042203","count":1},{"id":"GO:1902600","count":1},{"id":"GO:0046381","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0046232","count":1}]},{"hash":"225975036422938682","title":"RNA processing and transcription regulation","description":"The protein set shows GO terms spanning transcription elongation regulation by RNA Pol II and multiple post-transcriptional RNA processing processes (ncRNA-mediated gene silencing, mRNA splicing, mRNA decay, and polyadenylation-related steps). This points to a cohesive theme of RNA biogenesis and regulation of gene expression at transcriptional and post-transcriptional levels, with a possible noise term about germline cyst formation.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032968","count":1},{"id":"GO:0034244","count":1},{"id":"GO:0031047","count":1},{"id":"GO:0048026","count":1},{"id":"GO:1905612","count":1}]},{"hash":"1533835199659893270","title":"Multi-tissue Developmental Patterning","description":"GO terms point to development and differentiation events across multiple tissues (inner ear, endothelium, somitogenesis, distal tubule, hair, R8 photoreceptor). There's no single pathway or process dominating; while Notch signaling and vascular morphogenesis appear, they don't coalesce around one specific function. The label reflects a broad theme of developmental patterning across diverse tissues.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042491","count":1},{"id":"GO:0097102","count":1},{"id":"GO:0060853","count":1},{"id":"GO:0014807","count":1},{"id":"GO:0070100","count":1}]},{"hash":"340994852602359137","title":"Diverse Metabolite Biosynthesis","description":"The GO terms span biosynthesis of several distinct metabolite classes (mycolic acid, antibiotics, melanin, poly-hydroxybutyrate, steroids like androgens and estrogens, tetrahydrobiopterin), suggesting the cluster groups proteins involved in general biosynthetic processes across diverse lipids, pigments, and steroid-related compounds rather than a single unified pathway. This makes the label representative but broad, hence a Medium confidence.","confidence":"Medium","size":7,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071768","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0017000","count":1},{"id":"GO:0006706","count":1},{"id":"GO:0042438","count":1}]},{"hash":"890406735783466706","title":"Unknown","description":"The GO terms span neuronal differentiation, gonad development, plant phloem development, and basic cellular processes like actin organization and integrin signaling, with no single cohesive function across the set. Therefore a specific, representative label cannot be confidently assigned.","confidence":"","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2000324","count":1},{"id":"GO:0021702","count":1},{"id":"GO:0010088","count":1},{"id":"GO:1904948","count":1},{"id":"GO:2000346","count":1}]},{"hash":"782013334972245954","title":"Transcription, translation, and ribosome biogenesis","description":"This cluster includes GO terms spanning transcription by RNA polymerases I/II/III, RNA-templated transcription, transcription elongation/termination by RNAP III, ribosome biogenesis, translation, tRNA aminoacylation, and RNA processing. Together these reflect core gene-expression machinery from transcription through translation, including RNA processing steps, so the label captures the shared function of these proteins.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042797","count":1},{"id":"GO:0006360","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0006385","count":1},{"id":"GO:0001172","count":1}]},{"hash":"1130003544270143301","title":"Unknown","description":"The terms include chromatin modification and binding (histone demethylation, chromatin binding) alongside metabolic biosynthesis (thiamine diphosphate, thiazole) and stress/immune responses (lipopolysaccharide, xenobiotic), plus neural regulation signals (neural precursor proliferation, serotonin secretion) and cytolysis. This spread suggests no single cohesive biological theme for the cluster, and with no edges observed, it is not possible to assign a clear, representative function label.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034720","count":2},{"id":"GO:0042135","count":1},{"id":"GO:0009229","count":1},{"id":"GO:0032496","count":1},{"id":"GO:0042493","count":1}]},{"hash":"2157084310044319006","title":"Unknown","description":"The proteins show a highly diverse set of GO terms spanning redox/homeostasis, ER protein folding, glycan processing, basic metabolism, mitochondrial electron transport, and several muscle-related processes (heart morphogenesis, neuromuscular/posture control, diaphragm contraction). With only one edge and no clear common functional theme, there isn\u2019t a cohesive function to name a specific cluster\u2014thus Unknown.","confidence":"","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":3},{"id":"GO:0034975","count":2},{"id":"GO:0043181","count":1},{"id":"GO:0006491","count":1},{"id":"GO:0003007","count":1}]},{"hash":"1646145844255125430","title":"Unknown","description":"The GO terms are scattered across several biological areas (mRNA stability regulation, chromatin organization, histone acetylation, cell proliferation, phagolysosome assembly, apoptotic DNA fragmentation, chromosome segregation, and viral translation). With no clear dominant process and some terms being obsolete, there isn\u2019t a cohesive theme linking these proteins. Therefore a precise functional label cannot be assigned.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":2},{"id":"GO:0043488","count":2},{"id":"GO:0000747","count":1},{"id":"GO:0050679","count":1},{"id":"GO:1902510","count":1}]},{"hash":"1337980828033434550","title":"Unknown","description":"The GO terms are highly diverse (redox, serine and thiamine biosynthesis, tRNA wobble modification, neurotransmitter and capsule biosynthesis, and cold/LPS stress responses) with no single dominant theme. The presence of obsolete terms and a small, sparsely connected network suggests annotation noise or functionally heterogeneous proteins, rather than a cohesive pathway. Therefore this cluster is best labeled Unknown.","confidence":"","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006564","count":2},{"id":"GO:0002098","count":2},{"id":"GO:0042420","count":2},{"id":"GO:0042135","count":2}]},{"hash":"939193015733621359","title":"Heat-stress and protein quality control","description":"The cluster centers on heat-related responses (response to heat, thermoception, response to capsazepine) and protein quality control via ubiquitination/ERAD, suggesting a heat-induced stress response linked to protein homeostasis and possibly cell-cycle processes like spindle assembly. Some terms (telomere maintenance, vitamin D response, pinocytosis, NOD signaling) are less tightly connected, but the core theme points to heat stress and protein homeostasis.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051225","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0033280","count":2},{"id":"GO:0009408","count":2},{"id":"GO:0030433","count":2}]},{"hash":"531570451251315422","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0035606","count":1},{"id":"GO:0051402","count":1},{"id":"GO:0042823","count":1},{"id":"GO:0006096","count":1}]},{"hash":"281934073082985413","title":"Cilium-linked signaling and stress-response proteins","description":"The cluster\u2019s top GO terms point to non-motile cilium assembly alongside regulatory and responsive processes: glucocorticoid signaling, interferon response, hydrogen peroxide response, and developmental processes like prostate gland development and male differentiation. This suggests a group of proteins involved in cilium-associated signaling that also modulates hormonal and stress-related pathways, with a broader role in development and immune/oxidative responses.","confidence":"Medium","size":7,"edges":8,"triangles":2,"max_degree":6,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:1903071","count":3},{"id":"GO:2000324","count":3},{"id":"GO:0071357","count":3},{"id":"GO:1905515","count":3},{"id":"GO:0030850","count":3}]},{"hash":"2234949670742941143","title":"Androgen receptor signaling and male reproductive development","description":"Top GO terms are dominated by prostate gland development, male sex differentiation, and steroid hormone receptor complex assembly, with related glucocorticoid signaling. This points to a cohesive module centered on steroid/nuclear receptor signaling guiding male reproductive development. Some additional terms (e.g., non-motile cilium assembly, ureter development) suggest broader developmental roles, but the core theme remains hormone-receptor\u2013mediated development.  ","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030850","count":3},{"id":"GO:0046661","count":3},{"id":"GO:0071357","count":3},{"id":"GO:0006463","count":3},{"id":"GO:1903071","count":2}]},{"hash":"398612752334000704","title":"Stress Response and mRNA Stability Regulation","description":"This cluster centers on cellular responses to stressors (oxidative/harmful stimuli, xenobiotics, peptide hormones) and on post-transcriptional control, notably regulation of mRNA stability, suggesting a compact theme of stress signaling linked to RNA turnover. Some terms are deprecated and the set is heterogeneous, but the core is stress response coupled with RNA stability regulation.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0090502","count":4},{"id":"GO:0080111","count":3},{"id":"GO:0014912","count":3},{"id":"GO:0042493","count":3},{"id":"GO:0070301","count":3}]},{"hash":"1044347587896348189","title":"Endosomal and Vesicle Trafficking","description":"The top GO terms cluster around vesicle movement and membrane trafficking, especially endosomal pathways (endosomal vesicle fusion, endosome-to-melanosome transport, cytoplasm to vacuole targeting by the Cvt pathway, and general protein transmembrane transport). Although a few terms touch on broader processes (mitotic exit, bone resorption, keratinocyte development), the shared theme is vesicle trafficking and endosomal transport, suggesting this as the defining function of the cluster.","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1903542","count":1},{"id":"GO:0071806","count":1},{"id":"GO:0010458","count":1},{"id":"GO:0000747","count":1},{"id":"GO:2000767","count":1}]},{"hash":"1310573443906888913","title":"Ubiquitin-Mediated Protein Degradation and Quality Control","description":"The cluster predominantly features ubiquitin-related processes (ubiquitin-dependent degradation pathways, autoubiquitination, and K63-linked ubiquitination) and chaperone-mediated quality control, suggesting a core function in tagging proteins for turnover and maintaining proteostasis, with a few peripheral stress-response terms.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030579","count":1},{"id":"GO:0008626","count":1},{"id":"GO:0030433","count":1},{"id":"GO:0010200","count":1},{"id":"GO:0051865","count":1}]},{"hash":"938287466643567418","title":"B cell development and adaptive immunity","description":"The top GO terms cluster around B cell homeostasis, V(D)J recombination, and adaptive immune response, indicating this group centers on adaptive immunity and B cell biology. Although there are related terms on ubiquitination and chromatin processes, these often intersect with immune signaling and regulation, supporting a cohesive immune-focused function for the cluster.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001782","count":3},{"id":"GO:0033151","count":3},{"id":"GO:0002250","count":3},{"id":"GO:0009048","count":3},{"id":"GO:0051865","count":3}]},{"hash":"938905378248587906","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0010264","count":1},{"id":"GO:0097171","count":1},{"id":"GO:0044209","count":1},{"id":"GO:0009229","count":1},{"id":"GO:0009228","count":1}]},{"hash":"956149615731099478","title":"Neuronal development and projection extension","description":"Reasoning: The top terms include neuron projection extension and substantia nigra development, pointing to neuronal development and axon growth; other terms (translation, ubiquitination) reflect general cellular regulation but do not override the neuronal theme.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042853","count":2},{"id":"GO:0006783","count":2},{"id":"GO:0006782","count":2},{"id":"GO:0070301","count":2},{"id":"GO:1903833","count":2}]},{"hash":"1093700142912562786","title":"Neuronal signaling and synaptic vesicle exocytosis","description":"The top GO terms point strongly to neural function: regulation of synaptic vesicle exocytosis, neurotransmitter secretion, and brain development, supported by PI-mediated signaling and Rho-related cytoskeletal regulation. While some terms (plant ABA signaling, VEGF pathway) may be annotations outside neurons or represent noise, the dominant signal is neuronal communication and development, guiding a label around synaptic transmission and neural signaling.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":2},{"id":"GO:0032024","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0048015","count":2},{"id":"GO:0007269","count":2}]},{"hash":"326966988997374567","title":"Ubiquitin-dependent proteolysis and proteostasis","description":"The top GO terms cluster around ubiquitin-related degradation and protein quality control, including ubiquitin-dependent SMAD and ERAD pathways, K63-linked ubiquitination, and autoubiquitination, along with chaperone-mediated protein complex assembly. This points to a module centered on ubiquitin signaling and proteostasis, with some stress-related terms appearing as broader context.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030579","count":1},{"id":"GO:0008626","count":1},{"id":"GO:0030433","count":1},{"id":"GO:0010200","count":1},{"id":"GO:0051865","count":1}]},{"hash":"206736681641453993","title":"Unknown","description":"The protein set shows a wide, scattered mix of GO terms\u2014nucleotide biosynthesis (UTP/CTP/GTP), differentiation and development (spermatid differentiation, ventricular system development), cilium movement, chromatin/epigenetic processes, and dosage regulation\u2014without a common dominant function or interaction pattern. With no edges and only singleton term representation, there\u2019s no clear unifying theme to label.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048515","count":1},{"id":"GO:0003351","count":1},{"id":"GO:0006228","count":1},{"id":"GO:0042464","count":1},{"id":"GO:0006241","count":1}]},{"hash":"1636629954180347168","title":"Mitochondrial Transport, Ubiquitination, and Apoptosis","description":"The top GO terms point to mitochondrial transport of metabolites (alpha-ketoglutarate, ATP, pyrimidine nucleotides, ornithine) and protein ubiquitination, with apoptosis seen in hepatocytes and myeloid cells. These collectively suggest a theme of mitochondria-centric metabolism and regulated cell death, where ubiquitination can modulate mitochondrial function and apoptotic pathways. Some terms about cell polarity or dendrite development are less tied to this core theme, so the label focuses on the mitochondrial transport and apoptosis-related aspects. ","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090162","count":2},{"id":"GO:2000171","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0097284","count":2},{"id":"GO:0033028","count":2}]},{"hash":"1214206764833453825","title":"Mitochondrial respiration and aging","description":"The GO terms center on mitochondrial electron transport, proton transmembrane transport, and aerobic respiration, pointing to core energy metabolism. Aging-related terms like lifespan determination and insulin signaling suggest the cluster also touches on lifespan regulation. A few terms (pheromone maturation, symbiont entry, PQQ biosynthesis) are peripheral but do not outweigh the dominant energy- and aging-related themes.","confidence":"Medium","size":7,"edges":7,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071432","count":2},{"id":"GO:0006122","count":2},{"id":"GO:0045861","count":2},{"id":"GO:0008340","count":2},{"id":"GO:0042447","count":2}]},{"hash":"1027090270908929733","title":"Unknown","description":"The GO terms are highly heterogeneous, covering telomere maintenance, endocytic pinocytosis, NOD1 signaling, thermoception, capsazepine response, heat-stress transcription responses, synaptic receptor localization, telomeric chromosome localization, calcium release, and epithelial polarity. With no shared core function and no edges connecting the proteins, there isn\u2019t a single coherent theme to label; thus Unknown is most appropriate. ","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":1},{"id":"GO:0048549","count":1},{"id":"GO:0070427","count":1},{"id":"GO:0050955","count":1},{"id":"GO:1901594","count":1}]},{"hash":"3845182704970473","title":"Unknown","description":"Top GO terms are not listed, so I cannot infer a shared function. The cluster has 7 proteins with moderate connectivity (13 edges, 11 triangles, max degree 6), but without functional terms there is no basis for a specific label.","confidence":"","size":7,"edges":13,"triangles":11,"max_degree":6,"top_function":null,"top_go_terms":[]},{"hash":"934304814676834977","title":"Unknown","description":"The terms span antibiotic response and degradation, nylon catabolism, and various development and metabolic processes, with no single cohesive function linking all proteins. The cluster appears too heterogeneous to assign a specific, representative label.","confidence":"","size":7,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0030655","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0033252","count":1},{"id":"GO:0019876","count":1}]},{"hash":"1803308043978539907","title":"Endodermal Differentiation","description":"The top GO term is endodermal cell differentiation (GO:0035987) with one protein, suggesting a possible theme around endodermal development for this cluster. However, only a single member carries this annotation, so the connection is weak and the label is plausible but not strongly representative.","confidence":"Low","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0035987","count":1}]},{"hash":"903491554814504650","title":"Temperature- and sensory-driven signaling","description":"The top GO terms point to neuronal signaling and sensory functions (thermoception, response to capsazepine, regulation of synaptic plasticity via receptor localization to the synapse) and GPCR/NOD1 signaling, with ancillary terms for SA node activity and cell-cycle-related processes that may reflect annotation noise. Overall, the cluster is best described as signaling centered on sensory/neural and temperature-related processes.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":4},{"id":"GO:0098907","count":4},{"id":"GO:0007205","count":4},{"id":"GO:0032212","count":3},{"id":"GO:0048549","count":3}]},{"hash":"397952186651858911","title":"Cell cycle progression and genome maintenance","description":"The top GO terms cluster around core cell cycle and genome integrity processes: DNA replication, G1/S transition, and double-strand break repair via nonhomologous end joining, plus kinetochore localization, all pointing to replication, chromosome segregation, and genome maintenance during cell division. The calcium/calmodulin\u2013NFAT\u2013calcineurin\u2013glucocorticoid signaling terms suggest regulatory layers that modulate these core processes, including immune-related signaling pathways. Taken together, the proteins likely function in coordinating cell cycle progression with genome stability, with ancillary signaling inputs. ","confidence":"Medium","size":6,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:2000324","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0005513","count":4},{"id":"GO:0001915","count":4},{"id":"GO:0060316","count":4}]},{"hash":"1069664628098618123","title":"Oxylipin and Prostaglandin Biosynthesis","description":"These proteins are enriched for lipid-derived signaling pathways, notably oxylipin biosynthesis and prostaglandin biosynthesis, with supporting evidence from fatty acid omega-oxidation. Stress-related terms (response to ozone, response to immobilization stress) also align with lipid signaling and metabolism, suggesting a cohesive theme around lipid-mediated signaling and fatty-acid metabolism rather than a single enzyme activity. ","confidence":"Medium","size":6,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0010193","count":2},{"id":"GO:0031408","count":2},{"id":"GO:0048565","count":1},{"id":"GO:0035902","count":1},{"id":"GO:0010430","count":1}]},{"hash":"1745369159953380763","title":"Retroviral reverse transcription and genome integration","description":"These proteins cluster around the retroviral life cycle: RNA-templated DNA synthesis (reverse transcription), DNA replication, DNA integration into the host genome, and proviral latency with viral entry into the nucleus. While a couple terms touch on broader host-symbiont interactions, the dominant GO signals strongly reflect retroviral replication, genome integration, and latency steps.","confidence":"High","size":6,"edges":7,"triangles":4,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006278","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0039651","count":3},{"id":"GO:0015074","count":3},{"id":"GO:0075713","count":3}]},{"hash":"407387978382107429","title":"Actin-based cytoskeleton and vesicle trafficking","description":"The top GO terms point to actin-related processes (cytoskeleton organization, actin filament distribution, muscle filament sliding), cell polarity and polarized transport (establishment/maintenance of cell polarity, protein transport to mating projection actin fusion focus), and vesicle trafficking (vesicle docking in exocytosis, vacuole inheritance). Together these imply a cluster centered on actin-driven cytoskeleton dynamics coordinating vesicle delivery and polarity. Some outliers (opsonization, VEGF signaling) may reflect broader annotations but do not override the dominant theme.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000011","count":4},{"id":"GO:0046663","count":2},{"id":"GO:0032796","count":2},{"id":"GO:0071963","count":2},{"id":"GO:1903028","count":2}]},{"hash":"1234376174369705574","title":"Developmental signaling and protein phosphorylation","description":"The top GO terms indicate developmental processes (multicellular organism development, skin development) and regulation of signaling via phosphorylation (positive regulation of GTPase activity, protein serine/threonine kinase activity, autophosphorylation), along with cellular trafficking (ER to Golgi transport) and mRNA transport. This combination suggests a cluster of proteins coordinating development through signaling regulation and trafficking rather than a single enzymatic function.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0043547","count":3},{"id":"GO:0071456","count":3},{"id":"GO:0006888","count":3}]},{"hash":"948731276682315535","title":"GPCR-driven cyclic nucleotide signaling","description":"Reasoning: The GO terms cluster around G protein-coupled receptor signaling and production of cyclic nucleotides, including adenosine receptor and adrenergic receptor pathways with cAMP and cGMP biosynthesis, plus receptor guanylyl cyclase signaling. Additional terms suggest downstream transcription responses and related GTPase regulation, all tying to GPCR-mediated second messenger signaling.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0071880","count":1},{"id":"GO:0070483","count":1},{"id":"GO:0006182","count":1},{"id":"GO:0009785","count":1}]},{"hash":"2101352912048286958","title":"Septin ring assembly and spindle checkpoint in budding yeast","description":"Most GO terms cluster around mitotic spindle checkpoint signaling (assembly and orientation), septin ring formation at the bud neck, and localization to the bud neck in budding yeast, pointing to a coordinated role in septin organization during cytokinesis and spindle regulation. The terms on actin cable regulation and autoubiquitination further reflect regulatory control over this cell-cycle\u2013related module. Therefore, this label captures the core function of the cluster.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031578","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0044810","count":2},{"id":"GO:0090337","count":2},{"id":"GO:0097271","count":2}]},{"hash":"780629255769544944","title":"Unknown","description":"The set includes karyogamy, DNA replication, SRP-dependent cotranslational targeting to membrane, iron-sulfur cluster assembly, iron ion sequestration, and several negative regulatory processes including stress responses. These terms span diverse cellular processes (nuclear fusion, genome maintenance, protein targeting, metal cofactor handling, and stress signaling) with no single dominant theme, so a concise, reliable label is not apparent.","confidence":"","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000742","count":5},{"id":"GO:0090084","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0006616","count":4},{"id":"GO:1900035","count":4}]},{"hash":"308803361316970806","title":"Ribosome biogenesis and cytoplasmic translation","description":"This cluster centers on two closely related processes: cytoplasmic translation and ribosome biogenesis, suggesting proteins involved in protein synthesis machinery. The additional GO term for activation of protein kinase activity hints at regulatory signaling that could modulate translation, but the core theme remains ribosome-associated processes. The small, edge-less network implies a loosely connected set within this functional area.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002181","count":1},{"id":"GO:0032147","count":1},{"id":"GO:0042254","count":1}]},{"hash":"1530255414287803292","title":"Growth signaling and chromatin regulation","description":"The cluster combines growth-related signals (response to growth hormone, positive regulation of epithelial cell proliferation) with chromatin dynamics (chromatin organization, histone H4-K5 acetylation) and genome processes (homologous chromosome segregation, mRNA branch site recognition). The inclusion of peptidyl-serine dephosphorylation adds a signaling layer that could modulate chromatin state and gene expression in response to growth cues, even though the protein connections are sparse (low connectivity). Confidence: Medium","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070262","count":3},{"id":"GO:0000747","count":2},{"id":"GO:0050679","count":2},{"id":"GO:1902510","count":2},{"id":"GO:0001845","count":2}]},{"hash":"555800020576704245","title":"Ribosome Biogenesis and Cell Cycle","description":"The cluster\u2019s strongest GO terms point to ribosome biogenesis and ribosomal large subunit assembly, together with pre-replicative complex assembly involved in nuclear cell cycle DNA replication, suggesting a link between ribosome production and cell cycle regulation. A few terms (thermoception, NOD signaling, etc.) seem unrelated and may reflect noise or multifunctional proteins, but the dominant signal supports ribosome biogenesis coupled with cell cycle processes.","confidence":"Medium","size":6,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0006267","count":1},{"id":"GO:0010197","count":1},{"id":"GO:0000027","count":1}]},{"hash":"1998140772206787081","title":"Unknown","description":"The GO terms in this cluster cover a wide range of processes, including cell morphogenesis and DNA replication, but also autophagy regulation, cardiac muscle differentiation, sodium transport, mitotic spindle organization, and cellular responses to virus. The terms point to several distinct biological themes rather than a single cohesive function, so there isn\u2019t a clear, interpretable common theme to label the cluster with a specific function. Confidence: None","confidence":"","size":6,"edges":10,"triangles":7,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000902","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0046827","count":5},{"id":"GO:0016242","count":4},{"id":"GO:2000727","count":4}]},{"hash":"1171310072168517048","title":"Nuclear transcription regulation and DNA replication","description":"This cluster's top GO terms cluster around two core processes: regulation of RNA polymerase II-driven transcription (preinitiation complex assembly and transcription elongation) and DNA replication, suggesting a nuclear gene-expression/replication module. A few terms relate to fungal cell wall biosynthesis and GDP-mannose metabolism, which are less representative of the core theme and may reflect annotation noise or multifunctionality. Overall, transcription regulation and DNA replication is the dominant theme.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0000902","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0045899","count":2},{"id":"GO:0032968","count":2}]},{"hash":"1290333562254742649","title":"Stress-Responsive RNA Processing and Translation","description":"The terms point to RNA metabolism (tRNA and rRNA processing, transcription-related processes) and translation, with explicit stress-related regulation (cytoplasmic translation initiation under stress and ER stress), suggesting a theme of RNA processing and gene expression control in stress conditions, despite sparse connectivity among members.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0008033","count":1},{"id":"GO:1990611","count":1},{"id":"GO:0097394","count":1},{"id":"GO:0090503","count":1}]},{"hash":"1503317583688455621","title":"Lysosome-related vesicle trafficking and polarity","description":"Most terms point to lysosome- and endosome-related trafficking (lysosomal membrane organization, endosome to melanosome transport, cytoplasm-to-vacuole targeting) and components of the secretory pathway, plus polarized trafficking (apical protein localization, establishment of epithelial cell polarity). The bone resorption term aligns with osteoclast lysosome function. Together these suggest a functional cluster centered on lysosome-related vesicle trafficking and polarized secretion.","confidence":"Medium","size":6,"edges":8,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0031584","count":2},{"id":"GO:0097212","count":2},{"id":"GO:0045453","count":2},{"id":"GO:0032258","count":2},{"id":"GO:0035646","count":2}]},{"hash":"946913078023696453","title":"Angiogenesis and Cell Migration Regulation","description":"The top GO terms are dominated by angiogenesis, cell morphogenesis, negative regulation of cell proliferation, and cell migration, pointing to a cluster tied to vascular development and tissue morphogenesis with coordinated movement and signaling. Other terms like melatonin biosynthesis or chromatin-related processes are present but less representative of the core theme. ","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":3},{"id":"GO:0000902","count":2},{"id":"GO:0008285","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0043065","count":2}]},{"hash":"1053944200638394224","title":"ER protein quality control and degradation","description":"This cluster is strongly driven by ER-associated misfolded protein handling, ubiquitin-related proteolysis, and ATP-dependent proteostasis, pointing to ER stress response and protein turnover as the central theme. Some terms about peroxisomal import and protein complex assembly appear, but the dominant signal is ER quality control and degradation pathways.","confidence":"Medium","size":6,"edges":13,"triangles":12,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0071218","count":4},{"id":"GO:0061166","count":4},{"id":"GO:0046034","count":4},{"id":"GO:0070407","count":4}]},{"hash":"2261696413058113173","title":"RNA processing and ribosome biogenesis","description":"The GO terms point to RNA-level regulation (ncRNA-mediated silencing, splicing regulation) and ribosome biogenesis (rRNA maturation, preribosome assembly, translation initiation complex assembly), indicating a cohesive theme around RNA processing and ribosome assembly despite some obsolete terms.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0000463","count":2},{"id":"GO:1902626","count":2},{"id":"GO:1902625","count":2}]},{"hash":"479599533614318737","title":"Cell Cycle and Chromatin Regulation","description":"The top GO terms point to cell division and genome maintenance, including G1/S transition, embryonic cleavage, and sister chromatid segregation, alongside DNA damage checkpoint control, nucleotide-excision repair, and histone H2A ubiquitination, all of which reflect chromatin-modulated regulation of the cell cycle and genome integrity. Some peripheral terms like axon extension and Rho signaling appear, but the dominant signal centers on cell-cycle control and chromatin dynamics.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0035518","count":3},{"id":"GO:2000001","count":3},{"id":"GO:0051759","count":3},{"id":"GO:0000082","count":3},{"id":"GO:0040016","count":3}]},{"hash":"1573660316285397874","title":"Amine metabolism and redox stress response","description":"These proteins appear linked by redox biology and amine metabolism. Multiple GO terms point to oxidative stress response, oxidant detoxification, and cell redox homeostasis, suggesting roles in managing reactive oxygen species and maintaining redox balance. The presence of methylamine metabolic process and response to amine reinforces an amine-processing angle that could tie into redox-related regulation. A few terms seem tangential (e.g., neural crest migration, obsolete oxidation-reduction process), likely representing annotation noise rather than core function.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0014075","count":2},{"id":"GO:0003147","count":1},{"id":"GO:1903026","count":1},{"id":"GO:0034599","count":1},{"id":"GO:0098869","count":1}]},{"hash":"1848578764371349175","title":"Unknown","description":"The GO terms span both developmental processes (cranial skeleton morphogenesis, cardiac muscle differentiation) and core cellular mechanisms (DNA replication, cell cycle transitions, spindle organization), plus autophagy regulation and stress responses, with no single cohesive theme linking all terms. This mix suggests no clear unifying function for the cluster.","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048701","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0016242","count":2},{"id":"GO:2000727","count":2},{"id":"GO:0010765","count":2}]},{"hash":"2199478930166393487","title":"Epithelial proliferation and differentiation control","description":"The terms cluster around growth, division, and differentiation in epithelial contexts: Hippo signaling, regulation of CDK activity, DNA replication, and keratinocyte differentiation point to epithelial cell growth control and fate decisions. Additional terms like apoptotic processes and cell migration/potential stress responses align with the broader regulatory environment of proliferating epithelial cells, though they are ancillary to the core theme.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0098586","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0033129","count":3},{"id":"GO:0035994","count":3},{"id":"GO:0035329","count":3}]},{"hash":"951905981835855584","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0007049","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0090394","count":2}]},{"hash":"1097195681233203601","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":11,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0030260","count":2},{"id":"GO:0019068","count":2},{"id":"GO:0039651","count":2},{"id":"GO:0015074","count":2},{"id":"GO:0075713","count":2}]},{"hash":"828590873856606184","title":"Bacterial arsenic and metal stress response","description":"The terms strongly point to arsenic- and metal-ion detoxification and response, which is the core signal for the cluster. Peripheral terms like lipopolysaccharide biosynthesis, plasmid partitioning, and cell-cycle regulation are less coherent with this theme, making the overall connection present but not robust. Therefore, the label emphasizes arsenic and metal stress response.","confidence":"Low","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045226","count":1},{"id":"GO:0071722","count":1},{"id":"GO:0009103","count":1},{"id":"GO:0030541","count":1},{"id":"GO:1990507","count":1}]},{"hash":"2209768708410770209","title":"T Cell Regulation and Glucocorticoid Response","description":"The dominant immune-related GO terms indicate modulation of T cell activity, including proliferation, homeostasis, and germinal center formation, along with cellular responses to glucocorticoids and growth factors. While there is a hint of RNA processing (spliceosome) which might reflect shared transcriptional regulation, the immune signaling pattern is the strongest common theme across the cluster.","confidence":"Medium","size":6,"edges":8,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0071385","count":1},{"id":"GO:0045085","count":1},{"id":"GO:0045647","count":1}]},{"hash":"1381785447222273198","title":"Unknown","description":"This cluster has no GO terms to guide labeling and no network connectivity (Edges 0, Triangles 0, Max Degree 0), so there isn\u2019t a shared function evident across the proteins. Without functional anchors, the safe label is Unknown with confidence None.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"407433048216676481","title":"Proteostasis and ubiquitin-proteasome quality control","description":"The cluster\u2019s GO terms cluster around protein quality control and degradation: nuclear proteostasis via the ubiquitin-proteasome system, ubiquitin-dependent ERAD, and misfolded protein transport. While a few terms (e.g., DNA replication, development) seem unrelated and may reflect annotation noise, the dominant theme is proteostasis machinery, justifying this label. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":1},{"id":"GO:0097428","count":1},{"id":"GO:0032781","count":1},{"id":"GO:0001707","count":1},{"id":"GO:0006469","count":1}]},{"hash":"2215487785584320742","title":"Unknown","description":"The top GO terms are very diverse, including DNA replication, apoptosis and death-related processes, development (mesoderm formation, neural patterning), protein quality control (ERAD), iron-sulfur cluster maturation, and general signaling regulation. There is no single dominant biological theme tying these proteins together, and several terms are obsolete, so a concise, meaningful label cannot be assigned.","confidence":"","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":1},{"id":"GO:1905259","count":1},{"id":"GO:0097428","count":1},{"id":"GO:0032781","count":1},{"id":"GO:0001707","count":1}]},{"hash":"1020085659885355961","title":"Unknown","description":"Top GO terms are absent, and with only 4 edges among 6 proteins and no triangles, there is no clear shared function to anchor a label. Without annotations to guide naming, the cluster appears heterogeneous and cannot be confidently characterized.","confidence":"","size":6,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[]},{"hash":"281603196459221426","title":"Ubiquitination and chromatin regulation","description":"The terms are dominated by protein ubiquitination (K48- and K6-linked, autoubiquitination) and epigenetic processes (histone catabolic process; histone H4-K20 methylation; dosage compensation). This suggests a common theme of regulation of protein turnover and chromatin state, with a few outliers that may reflect annotation noise or pleiotropy.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900095","count":1},{"id":"GO:0070936","count":1},{"id":"GO:0033151","count":1},{"id":"GO:0009048","count":1},{"id":"GO:0085020","count":1}]},{"hash":"123028588321538609","title":"Unknown","description":"The terms span cell cycle control, transcription, mitochondrial import and membrane dynamics, lipid metabolism, tRNA and protein modifications, and cofactor biosynthesis, with no dominant shared function among the six proteins. This diversity makes it unclear what unifies the cluster functionally, so a concise, single-label name cannot be reliably assigned.","confidence":"","size":6,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:2000134","count":1},{"id":"GO:0070940","count":1},{"id":"GO:0046902","count":1},{"id":"GO:0010867","count":1},{"id":"GO:1903740","count":1}]},{"hash":"252602103100180351","title":"RNA Pol II Transcription Regulation & Chromatin Modification","description":"This cluster is anchored by GO terms related to RNA polymerase II transcription control, including positive/negative regulation and preinitiation complex assembly, as well as histone acetylation and nucleosome-related processes. Together these point to a common theme of transcription regulation modulated by chromatin state. Some terms (like photomorphogenesis and polyphosphate catabolism) are peripheral, but do not undermine the core link to transcription regulation and chromatin remodeling.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043966","count":1},{"id":"GO:0000436","count":1},{"id":"GO:0061408","count":1},{"id":"GO:0043457","count":1},{"id":"GO:0000122","count":1}]},{"hash":"664683081149511849","title":"Diverse microbial biosynthetic pathways","description":"The top GO terms are all biosynthetic processes across a range of compounds (mycolic acids, antibiotics, melanin, poly-hydroxybutyrate, and steroid-related biosynthesis), indicating the cluster centers on microbial biosynthesis of various metabolites rather than a single specific pathway. Some annotations (e.g., androgen/estrogen biosynthesis) may be broad or incidental, but the unifying theme is diverse biosynthetic activity in microbes.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0071768","count":6},{"id":"GO:0055114","count":6},{"id":"GO:0017000","count":6},{"id":"GO:0042438","count":6},{"id":"GO:0042619","count":6}]},{"hash":"897077552154034980","title":"Unknown","description":"The top GO terms span telomere maintenance, pinocytosis, NOD signaling, thermoception, calcium release, cell cycle, synaptic regulation, telomeric localization, and epithelial polarity, indicating diverse and unrelated functions rather than a single cohesive theme. ","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":3},{"id":"GO:0048549","count":3},{"id":"GO:0070427","count":3},{"id":"GO:0050955","count":3},{"id":"GO:1901594","count":3}]},{"hash":"1274289321775646690","title":"Mitochondrial Transport and Energy Metabolism","description":"The cluster is defined by multiple mitochondrial membrane transport processes (alpha-ketoglutarate, ornithine, ATP, pyrimidine nucleotides) and metabolic shuttling (malate-aspartate), with supporting roles in mitochondrial dynamics and energy regulation (thermogenesis, insulin secretion, and necroptosis control), suggesting a coherent mitochondria-centric transport/metabolism function.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0015742","count":3},{"id":"GO:0000066","count":3},{"id":"GO:1990544","count":3},{"id":"GO:1990519","count":3},{"id":"GO:1990845","count":3}]},{"hash":"320962574673476339","title":"RNA and Protein Methylation","description":"The dominant GO terms center on RNA modification (tRNA wobble uridine modification, tRNA methylation, rRNA modification) and various methylation events on peptides (N-terminal peptidyl-glycine methylation, peptidyl-glutamine methylation), suggesting a cohesive theme of RNA and protein methylation/modification. Some outliers (antibiotic/juvenile hormone biosynthesis, nodulation) are present but likely noise relative to the core methylation signal.","confidence":"High","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035902","count":2},{"id":"GO:0002098","count":2},{"id":"GO:1901052","count":2},{"id":"GO:0000154","count":2},{"id":"GO:0017000","count":2}]},{"hash":"1971429580921613851","title":"Cytoskeleton organization and proteostasis","description":"The top GO terms cluster around tubulin/cytoskeleton assembly (GO:0007021) and cortical microtubule organization (GO:0043622) along with protein folding (GO:0006457) and chaperone-mediated assembly (GO:0051131), plus ubiquitin-proteasome quality control (GO:0071629). These collectively point to cytoskeletal maintenance coupled with protein quality control. A few terms related to viral interactions and interferon regulation appear but do not fit as cohesively with the core theme, so the dominant signal is cytoskeleton plus proteostasis.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007021","count":1},{"id":"GO:0071629","count":1},{"id":"GO:0043622","count":1},{"id":"GO:0006457","count":1},{"id":"GO:0032968","count":1}]},{"hash":"188239537790480730","title":"Neural Calcium Signaling and Schwann Cell Development","description":"The top GO terms cluster around calcium ion detection and calcium-dependent signaling (including postsynaptic calcium concentration and calcineurin-NFAT regulation) together with peripheral nervous system components like Schwann cell development and myelination. This pattern suggests a module focused on calcium-mediated signaling in neural contexts, particularly processes driving Schwann cell maturation and PNS myelination, with some ancillary regulation terms and broader developmental roles. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0005513","count":2},{"id":"GO:0060316","count":2},{"id":"GO:0051531","count":2},{"id":"GO:0001569","count":2},{"id":"GO:0051343","count":2}]},{"hash":"324685193458965485","title":"Unknown","description":"The GO terms shown span a highly diverse set of functions, including telomere maintenance, pinocytosis, NOD1 signaling, thermoception, responses to heat stress, cell cycle, synaptic plasticity regulation, protein localization to telomeric regions, and calcium release. There is no clear, shared biological process or pathway uniting them, and the proteins do not reveal a cohesive theme or interaction pattern within this cluster. Therefore, a single coherent functional label cannot be confidently assigned.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":3},{"id":"GO:0048549","count":3},{"id":"GO:0070427","count":3},{"id":"GO:0050955","count":3},{"id":"GO:1901594","count":3}]},{"hash":"2026006328688821954","title":"Viral DNA replication and proviral integration","description":"The cluster is enriched with GO terms centered on viral genome processing and integration, including RNA-templated DNA biosynthesis, DNA replication, DNA recombination, DNA integration, and establishment of integrated proviral latency, as well as viral entry into the host nucleus. This points to a coherent theme of viral genome maintenance and proviral lifecycle events within the host. ","confidence":"High","size":6,"edges":7,"triangles":2,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006278","count":6},{"id":"GO:0006260","count":6},{"id":"GO:0039651","count":6},{"id":"GO:0015074","count":6},{"id":"GO:0075713","count":6}]},{"hash":"2254293618752036333","title":"Brain development and neuronal signaling","description":"The top GO terms cluster around neural activity (excitatory postsynaptic potential) and brain development (substantia nigra development), with some influence on circadian rhythm and transcriptional regulation, pointing to a neural signaling/development theme. There are additional terms related to cellular transport and xenobiotic response that are less central, which lowers overall specificity but does not negate the neural focus.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0060079","count":2},{"id":"GO:0021762","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0042753","count":1}]},{"hash":"133896320742542302","title":"Retroviral integration and latency","description":"GO terms point to viral genome processing and proviral latency, including DNA replication, DNA integration, DNA recombination, and especially establishment of integrated proviral latency, alongside steps of viral entry and penetration into the host nucleus. This combination strongly suggests retroviral infection pathways culminating in proviral integration and latency.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006278","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0039651","count":3},{"id":"GO:0015074","count":3},{"id":"GO:0075713","count":3}]},{"hash":"874559284418635604","title":"Translation initiation machinery and splicing regulation","description":"This cluster centers on translation initiation (formation of the preinitiation complex, translation reinitiation, eIF4F assembly) with additional signals of mRNA splicing regulation via the spliceosome, suggesting a combined role in RNA processing and translation control.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0031047","count":1},{"id":"GO:0048026","count":1},{"id":"GO:1902625","count":1}]},{"hash":"262088672949446142","title":"Endosome-lysosome trafficking and autophagy regulation","description":"The GO terms cluster around intracellular vesicle trafficking and lysosome/autophagy processes\u2014Golgi-to-endosome and endosome-to-lysosome transport, vesicle docking and exocytosis, lysosomal lumen pH regulation, and autophagosome assembly control\u2014indicating a cohesive vesicle-lysosome/autophagy functional module.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1902902","count":2},{"id":"GO:0035751","count":2},{"id":"GO:0006895","count":2},{"id":"GO:0043524","count":2},{"id":"GO:0006904","count":2}]},{"hash":"83071087361492563","title":"Leucine Metabolism and Fe-S Cluster Assembly","description":"The cluster emphasizes leucine-specific metabolism (biosynthesis and catabolism) alongside iron-sulfur cluster assembly and related metabolic processes (acyl-CoA metabolism, protein maturation), suggesting a cohesive theme around leucine metabolism supported by Fe-S cofactor biology.","confidence":"Medium","size":6,"edges":7,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051604","count":2},{"id":"GO:0006880","count":2},{"id":"GO:0009399","count":2},{"id":"GO:0016226","count":2},{"id":"GO:0009098","count":2}]},{"hash":"1550991875440904496","title":"Unknown","description":"The top terms span epithelial polarity, apoptosis in immune and liver cells, dendrite development regulation, telomere maintenance, pinocytosis, NOD1 signaling, thermoception, and heat-stress responses, with no single dominant function or pathway linking them. The proteins do not form a coherent functional cluster, so a specific label isn\u2019t supported.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090162","count":3},{"id":"GO:0033028","count":3},{"id":"GO:0097284","count":3},{"id":"GO:2000171","count":3},{"id":"GO:0032212","count":2}]},{"hash":"1600113857877592418","title":"Ubiquitin-Dependent Protein Degradation","description":"The cluster\u2019s top GO terms are dominated by ubiquitin-related proteolysis processes (ubiquitin-dependent protein catabolic process, K48-linked ubiquitination, autoubiquitination, ERAD-related terms). This points to a core function in tagging proteins for degradation and turnover, aligning with ubiquitin-proteasome\u2013mediated degradation, even though some terms are obsolete or tangential. ","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:1900095","count":1},{"id":"GO:0042787","count":1},{"id":"GO:0070936","count":1},{"id":"GO:0016558","count":1}]},{"hash":"703823556093443285","title":"Unknown","description":"The top terms cover a highly diverse mix of processes (ER-Golgi vesicle transport, peptidyl-serine dephosphorylation, positive regulation of GTPase activity, glucocorticoid signaling, DNA replication, calcium sensing, T cell regulation, and cell-cycle transitions) with no single cohesive function tying the proteins together. The cluster has no edges or connections, and the ReCIPE re-additions do not reveal a clear shared pathway, so a single interpretable label isn\u2019t supported.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0070262","count":2},{"id":"GO:0043547","count":2},{"id":"GO:2000324","count":1},{"id":"GO:0006260","count":1}]},{"hash":"1436872037017643090","title":"Retroviral DNA integration and proviral latency","description":"The top GO terms point to RNA-templated DNA biosynthesis (reverse transcription), DNA integration into the host genome, and establishment of integrated proviral latency, all key steps in a retroviral lifecycle and provirus formation. Additional terms mention viral entry into the host and nuclear penetration, supporting a viral infection/latency theme. Some symbiont-related terms may reflect host\u2013microbe interaction contexts, but the core signal is retroviral genome integration and latency. High","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006278","count":2},{"id":"GO:0039651","count":2},{"id":"GO:0015074","count":2},{"id":"GO:0075713","count":2},{"id":"GO:0006310","count":2}]},{"hash":"1946798255190687768","title":"RNA processing and translation initiation regulation","description":"The proteins show enrichment for splicing regulation via the spliceosome, eIF4F complex assembly, and nuclear pore organization, indicating a module coordinating RNA processing/export with translation initiation.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006999","count":1},{"id":"GO:0031047","count":1},{"id":"GO:0048026","count":1},{"id":"GO:0060188","count":1},{"id":"GO:1902625","count":1}]},{"hash":"2274532281256731977","title":"Nuclear chromatin remodeling and chromosome maintenance","description":"Most terms cluster around nuclear processes: chromatin organization, histone acetylation, and chromosome segregation, with supporting signals from mRNA processing; a few items (phagolysosome assembly, growth hormone response) may be annotation noise. Overall, ties to chromatin dynamics and genome maintenance.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000747","count":2},{"id":"GO:0050679","count":2},{"id":"GO:1902510","count":2},{"id":"GO:0001845","count":2},{"id":"GO:0031497","count":2}]},{"hash":"477752958619258481","title":"RNA processing and transcription regulation","description":"These proteins are annotated mainly with RNA-related regulatory functions: transcription regulation, spliceosome-mediated mRNA splicing regulation, and ncRNA-mediated gene silencing, with additional links to translation initiation complex assembly. This points to a cohesive RNA processing/regulation theme rather than a single enzymatic activity.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0048026","count":2},{"id":"GO:1902625","count":2},{"id":"GO:0075525","count":2}]},{"hash":"2251284090324459500","title":"Innate immune signaling and cytoskeletal remodeling","description":"This cluster centers on innate immune signals, highlighted by the presence of GO terms for Toll-like receptor 1 signaling and detection of bacterial lipopeptide, alongside actin filament severing which points to cytoskeletal rearrangements often involved in immune responses. While there are also development-related terms (neuron maturation, Wnt signalosome assembly) that suggest broader signaling roles, the most salient and cohesive theme among the terms is innate immune sensing coupled with cytoskeletal dynamics. Confidence: Medium","confidence":"","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0014041","count":2},{"id":"GO:0071287","count":2},{"id":"GO:0034130","count":2},{"id":"GO:0051014","count":2},{"id":"GO:1904887","count":2}]},{"hash":"505582808468908494","title":"Cell growth, division, and vesicle trafficking","description":"The terms cluster around mitotic cell cycle, cell division, and proliferation, with supporting growth signaling via TORC1 and GTPase activity regulation, plus vesicle transport between the ER and Golgi (both directions) and hypoxia-related adaptation. Brain development also aligns with growth and proliferation contexts. This suggests a cohesive theme of growth-driven proliferation coupled with intracellular trafficking, hence the chosen label.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0000747","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0008283","count":2}]},{"hash":"754491140336087138","title":"Amino acid catabolism and redox regulation","description":"Top GO terms cluster around amino acid metabolism (leucine catabolic process, 2-oxoglutarate metabolism, glutamate biosynthesis) and redox/homeostasis (regulation of membrane potential, cell redox homeostasis), with additional signals related to cAMP response and neural development. This points to a theme of metabolic control intertwined with redox signaling and developmental regulation, rather than a single canonical pathway. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042391","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0045454","count":3},{"id":"GO:0071320","count":3},{"id":"GO:0006552","count":3}]},{"hash":"1404017172644749900","title":"Neurogenesis and Gametogenesis with Spindle Machinery","description":"The terms point to broad developmental roles across neural, reproductive, and tissue formation (neurogenesis, oogenesis, spermatid elongation, chaeta development) combined with core cell division and cytoskeletal organization (mitotic spindle orientation, microtubule-centrosome interactions, nuclear pore assembly, transcription). This suggests a cluster centered on developmental processes linked to the cellular machinery that drives division and organization.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":1},{"id":"GO:0051017","count":1},{"id":"GO:0007290","count":1},{"id":"GO:0008039","count":1},{"id":"GO:0022416","count":1}]},{"hash":"939609483597528217","title":"Iron and manganese ion homeostasis","description":"The proteins in this cluster are mainly associated with intracellular handling of iron and manganese ions, including transport and homeostasis, suggesting a shared function in metal ion regulation. A couple of terms (ethylene response, nuclear membrane organization) appear less directly linked, possibly reflecting broader signaling contexts or annotation noise.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071421","count":1},{"id":"GO:0071281","count":1},{"id":"GO:0006880","count":1},{"id":"GO:0030026","count":1},{"id":"GO:0071369","count":1}]},{"hash":"221353019957851400","title":"GPCR-driven cAMP/cGMP signaling","description":"The top GO terms cluster around GPCR signaling pathways (adenosine and adrenergic receptors) and cyclic nucleotide production/signaling (cAMP and cGMP biosynthesis, receptor guanylyl cyclase signaling). Additional terms like blue light signaling and hypoxia detection fit within GPCR-second messenger frameworks that regulate cyclic nucleotides, suggesting a core theme of GPCR-coupled cAMP/cGMP signaling.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071880","count":2},{"id":"GO:0070483","count":2},{"id":"GO:0006182","count":2},{"id":"GO:0009785","count":2},{"id":"GO:0001973","count":2}]},{"hash":"711374947567425336","title":"Proviral integration and viral entry","description":"This cluster centers on DNA replication, recombination, and DNA integration, with terms specific to proviral latency and viral entry into the host nucleus, plus RNA-templated DNA biosynthesis. Additional terms about symbiont entry and host apoptosis modulation, and even negative regulation of siRNA processing, suggest virus-like or proviral activity and host-pathogen interaction, consistent with a cohesive theme of proviral integration and entry mechanisms.","confidence":"High","size":5,"edges":7,"triangles":3,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0006310","count":3},{"id":"GO:0006888","count":2},{"id":"GO:0006278","count":2},{"id":"GO:0039651","count":2}]},{"hash":"761211955833176386","title":"DNA Replication and Cell Cycle Regulation","description":"The cluster is dominated by terms related to DNA replication, cell cycle transitions (G1/S), chromosome maintenance, and kinetochore localization, indicating a core function in DNA replication and cell-cycle control. While there are additional terms touching on calcium signaling and transcriptional regulation, these appear more auxiliary than defining for the group. Therefore, labeling it as DNA Replication and Cell Cycle Regulation best captures the central theme.","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:2000324","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0005513","count":4},{"id":"GO:0001915","count":4},{"id":"GO:0060316","count":4}]},{"hash":"2132327034468041564","title":"Cell Growth and Telomere Maintenance","description":"The dominant signals are cell growth (GO:0016049) and positive regulation of telomere maintenance via telomerase, alongside a link to cell cycle and telomeric chromosome localization. Other terms like pinocytosis, NOD1 signaling, and thermoception appear only once and are less representative. Overall, the cluster seems centered on proliferation and genome maintenance rather than a single, coherent pathway, so \u201cCell Growth and Telomere Maintenance\u201d captures the core theme.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:0032212","count":1},{"id":"GO:0048549","count":1},{"id":"GO:0070427","count":1},{"id":"GO:0050955","count":1}]},{"hash":"1901076823882657627","title":"Adenosine receptor GPCR cAMP/cGMP Signaling","description":"This cluster is dominated by GO terms about GPCR signaling and second messengers: adenosine receptor signaling, adenylate cyclase activation, and receptor guanylyl cyclase pathways, with biosynthesis of cAMP and cGMP. Additional terms reference blue light signaling and hypoxia detection, but the core connection across the proteins is GPCR-mediated control of cyclic nucleotide signaling.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071880","count":2},{"id":"GO:0070483","count":2},{"id":"GO:0006182","count":2},{"id":"GO:0009785","count":2},{"id":"GO:0001973","count":2}]},{"hash":"1234009726528443143","title":"Pro-inflammatory cytokine production","description":"The top GO terms are dominated by positive regulation of interleukin-6 production, TNF production, and overall inflammatory response, indicating a cohesive theme around inflammation and cytokine signaling. A few outlier terms (e.g., telomere maintenance, Cajal body RNA localization) are present but do not override the main inflammatory pattern. Therefore, the cluster most likely represents pro-inflammatory cytokine signaling rather than a single metabolic pathway.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0044053","count":5},{"id":"GO:0050729","count":5},{"id":"GO:2000778","count":5},{"id":"GO:0032212","count":5},{"id":"GO:0002931","count":5}]},{"hash":"666255741723864280","title":"Retroviral DNA integration and proviral latency","description":"The terms cluster around reverse transcription (RNA-templated DNA biosynthesis), DNA integration and proviral latency, DNA recombination, and viral entry into the host nucleus, all characteristic of retroviral life cycles. Some terms reference host\u2013symbiont interactions and apoptosis, reinforcing a host-pathogen theme, while basic translation and phosphorylation terms reflect host machinery involvement. Overall, this cluster represents retroviral genome integration and latency processes.","confidence":"High","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006278","count":2},{"id":"GO:0039651","count":2},{"id":"GO:0015074","count":2},{"id":"GO:0075713","count":2},{"id":"GO:0006310","count":2}]},{"hash":"2127197688259959655","title":"Ribosome Biogenesis and Translation Initiation","description":"The GO terms show a cohesive set around ribosome assembly and translation initiation, including ribosome biogenesis, formation of the translation preinitiation complex, translation reinitiation, maturation of rRNA, and eIF4F complex assembly, indicating a single ribosome/translation\u2013focused module. Some RNA processing terms are present but do not override the dominant translation/ribosome theme.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0000463","count":2},{"id":"GO:0031047","count":2}]},{"hash":"1604251454296897819","title":"Spliceosome-Mediated mRNA Splicing Regulation","description":"The GO terms are dominated by multiple spliceosome-related processes (mRNA splicing via the spliceosome, splice-site recognition, cis splicing) with both positive and negative regulation, plus a regulatory ncRNA silencing angle, pointing to a RNA processing/splicing regulatory cluster rather than other pathways.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":1},{"id":"GO:0048026","count":1},{"id":"GO:1902625","count":1},{"id":"GO:0075525","count":1},{"id":"GO:1905663","count":1}]},{"hash":"957054424639747351","title":"Spliceosome-Mediated mRNA Splicing Regulation","description":"This cluster is dominated by GO terms tied to spliceosome-dependent mRNA splicing, including positive and negative regulation of splicing, splice site recognition, and cis-splicing via the spliceosome, pointing to a core RNA processing/regulatory function rather than other processes.","confidence":"High","size":5,"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:1902625","count":2},{"id":"GO:0075525","count":2},{"id":"GO:1905663","count":2}]},{"hash":"1224885456467417198","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071353","count":2},{"id":"GO:0000350","count":1},{"id":"GO:0000389","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0000387","count":1}]},{"hash":"236854463331489045","title":"Mitotic cell cycle and DNA replication","description":"Dominant GO terms cluster around G1/S transition, DNA replication, and mitotic cell cycle, suggesting this cluster comprises factors involved in cell division and DNA synthesis. While other terms appear, the core theme is cell-cycle progression.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000082","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0016242","count":3},{"id":"GO:2000727","count":3}]},{"hash":"1041968366941599045","title":"Vertebrate Embryonic and Neural Development","description":"The top GO terms cluster around multicellular organism development, forebrain development, skeletal system development, and neural tube closure, indicating a core theme of vertebrate embryogenesis and neural development. Additional terms related to stress and immune responses (cadmium, ER stress\u2013induced apoptosis, defense to Gram-positive bacteria) likely reflect secondary or contextual annotations within this developmental protein set rather than a separate pathway, so the primary signal is developmental. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0001501","count":2}]},{"hash":"2025604958575430375","title":"Xenobiotic metabolism and oxidative stress response","description":"The GO terms point to xenobiotic metabolism together with redox-related processes (oxidation-reduction, nitric oxide biosynthesis, oxidative stress) and signaling interactions (ERK cascade, estradiol response). This pattern suggests a coherent theme around processing foreign compounds and related redox signaling rather than a single narrowly defined function, yielding a concise label that captures the main theme.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006805","count":2},{"id":"GO:0032414","count":1},{"id":"GO:0006809","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0043525","count":1}]},{"hash":"1917529400021755017","title":"Mitotic spindle and kinetochore regulation","description":"This cluster is dominated by GO terms related to mitosis and chromosome segregation, including localization to the kinetochore, centrosome cycle, spindle pole body/mitotic spindle components, and regulation of mitotic processes such as chromatid biorientation and CDK activity. While a single term about postsynaptic density assembly appears, the majority point to spindle assembly and kinetochore/centrosome functions, suggesting the proteins collectively participate in mitotic regulation.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034501","count":2},{"id":"GO:0045736","count":2},{"id":"GO:0010571","count":2},{"id":"GO:0007098","count":2},{"id":"GO:0097107","count":1}]},{"hash":"1598281019879155515","title":"Neural development and transcriptional regulation","description":"The top GO terms point to DNA-templated transcription and neural development processes (forebrain development, neural tube closure) within a broader context of multicellular organism development. This suggests a cluster of proteins involved in transcriptional control during neural development, with some ancillary stress- or defense-related annotations that are secondary. Confidence reflects a clear neural-development signal but some outlier terms reduce certainty to medium.","confidence":"Medium","size":5,"edges":8,"triangles":4,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0007275","count":3},{"id":"GO:0030900","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0071276","count":3}]},{"hash":"1821785000677636190","title":"Ubiquitin-Mediated Endosomal and Autophagic Trafficking","description":"These proteins cluster around ubiquitination processes (including autoubiquitination and K63-linked ubiquitination) and connections to ERAD, aggrephagy, and endosomal transport/fusion, suggesting roles in ubiquitin-dependent quality control and trafficking through the endosomal-lysosomal and autophagy pathways.","confidence":"High","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0048549","count":2},{"id":"GO:0035973","count":2},{"id":"GO:0070534","count":2}]},{"hash":"1646656249198030759","title":"Fungal sterol and sphingolipid biosynthesis","description":"The cluster is dominated by lipid-related GO terms tied to fungal membrane biology: ergosterol (sterol) biosynthesis, sphingolipid metabolism (mannosyl-inositol phosphorylceramide/MIPC), and unsaturated fatty acid biosynthesis. These together suggest a coherent theme of membrane lipid biosynthesis in fungi, with other terms like nitrate assimilation or mitochondrial inheritance appearing as ancillary metabolic contexts. ","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032286","count":5},{"id":"GO:0006675","count":5},{"id":"GO:0006809","count":5},{"id":"GO:0001949","count":5},{"id":"GO:0032443","count":5}]},{"hash":"1719940418467808289","title":"Sensory and Autonomic Regulation","description":"The terms cluster around sensory perception (thermoception, CO2 detection, startle response) and autonomic/physiological control (vasoconstriction, hypoxia response, circadian sleep regulation), with some hints of neural plasticity. Although one plant-related term appears as noise, the overall theme is sensory input integrated with homeostatic and timing-related responses.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042310","count":2},{"id":"GO:0001666","count":2},{"id":"GO:0003031","count":2},{"id":"GO:0001964","count":2},{"id":"GO:0050955","count":2}]},{"hash":"1005492713616941792","title":"Nitric oxide signaling and nutrient response","description":"The GO terms show strong enrichment for nitric oxide biosynthesis (GO:0006809) and nitric oxide\u2013mediated signaling (GO:0007263), indicating a core NO-centered signaling theme. Additional terms point to nutrient and xenobiotic responses (GO:0007584, GO:0042493) and some metabolic/developmental processes (thiamine biosynthesis, Hedgehog-related regulation of smoothened signaling and chondrocyte differentiation). The strongest cohesive thread is NO production/signaling, with secondary links to nutrient stress and metabolism; the Hedgehog and differentiation terms may reflect broader signaling interactions or noise. Therefore, the label captures the central theme with moderate confidence.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045880","count":1},{"id":"GO:0006809","count":1},{"id":"GO:0019475","count":1},{"id":"GO:0014740","count":1},{"id":"GO:0032332","count":1}]},{"hash":"1517053660431380209","title":"Unknown","description":"The GO terms are highly diverse, spanning iron-sulfur cluster biogenesis, plant hormonal signaling (abscisic acid, stomatal movement), multiple catabolic/biosynthetic processes, and even an animal Notch pathway term. There is no clear, cohesive function linking all five proteins, so a single interpretable label cannot be confidently assigned.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018283","count":1},{"id":"GO:0010118","count":1},{"id":"GO:0009688","count":1},{"id":"GO:0044571","count":1},{"id":"GO:0009436","count":1}]},{"hash":"303670365566682894","title":"Retroviral replication and proviral integration","description":"The GO terms cluster around steps of retroviral infection and provirus lifecycle: reverse transcription (RNA-templated DNA biosynthesis), DNA replication and recombination, DNA integration, proviral latency, and viral entry/penetration into the host nucleus. This pattern indicates a retroviral life-cycle module rather than a general cellular process.","confidence":"High","size":5,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006278","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0039651","count":1},{"id":"GO:0015074","count":1},{"id":"GO:0075713","count":1}]},{"hash":"2179037140070644513","title":"Translation and ribosome assembly","description":"The GO terms show a clear enrichment for translation-related processes (cytoplasmic translation, ribosomal small subunit assembly, translation), suggesting the cluster centers on protein synthesis machinery. While other disparate terms appear, the strongest signal is translation, supporting a cohesive function around protein production. ","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001576","count":1},{"id":"GO:0002181","count":1},{"id":"GO:0080028","count":1},{"id":"GO:0000028","count":1},{"id":"GO:0006412","count":1}]},{"hash":"308838858557271497","title":"Nuclear transcription and RNA processing","description":"The terms cluster around nuclear processes: DNA-templated transcription, pre-miRNA processing, miRNA catabolic process, transcription antitermination, and regulation of termination of transcription, plus CRD-mediated mRNA stabilization. In addition, nuclear pore organization and regulation of protein import into the nucleus place these proteins in the nuclear compartment, suggesting a role in coordinating transcription, RNA processing, and nuclear transport. The kidney development term is less central and likely incidental, so the core signal is nuclear RNA metabolism and transcription control.","confidence":"Medium","size":5,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031054","count":2},{"id":"GO:0006351","count":2},{"id":"GO:1902219","count":2},{"id":"GO:0060567","count":2},{"id":"GO:1901724","count":2}]},{"hash":"738044383378906656","title":"Unknown","description":"The top GO terms span plant development (root meristem growth, auxin transport, cytokinin signaling), small GTPase regulation, centrosome/mitotic localization, and even animal-specific processes (lung development) and telomerase assembly, with several obsolete terms. This heterogeneous mix lacks a single coherent biological theme or pathway, making a specific, representative label impossible. ","confidence":"","size":5,"edges":8,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0043947","count":1},{"id":"GO:0010449","count":1},{"id":"GO:1905323","count":1},{"id":"GO:2000299","count":1}]},{"hash":"972306846548893825","title":"Unknown","description":"The GO terms associated with these proteins span a wide range of processes\u2014stress responses ( xenobiotic stimulus, hydrogen peroxide ), regulatory processes ( regulation of mRNA stability, glycogen synthase activity ), signaling ( phosphatidylinositol dephosphorylation ), and cell behavior ( negative regulation of smooth muscle cell migration )\u2014with no clear, dominant shared function. Several terms are obsolete, and there are no interactions (edges/triangles) to suggest a cohesive pathway, so a single precise label cannot be confidently assigned.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080111","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0014912","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0070301","count":2}]},{"hash":"599575278980346938","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":1},{"id":"GO:0042245","count":1},{"id":"GO:0051607","count":1},{"id":"GO:0071037","count":1},{"id":"GO:0071050","count":1}]},{"hash":"2057486556728071499","title":"Nuclear protein quality control","description":"Dominant terms point to proteostasis in the nucleus: nuclear protein quality control by the ubiquitin-proteasome system, misfolded protein transport, and ubiquitin-dependent ERAD. These clearly indicate a core theme of managing damaged/misfolded proteins and their degradation. Other terms such as DNA replication or mesoderm formation may reflect broader roles of these proteins, but the QC-related terms are the strongest signal, supporting the label with high confidence.","confidence":"High","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0097428","count":3},{"id":"GO:0032781","count":3},{"id":"GO:0001707","count":3},{"id":"GO:0006469","count":3}]},{"hash":"1581362026432486161","title":"Unknown","description":"There are no top GO terms and no connections (edges/triangles) to tie these five proteins to a common function, so a specific label cannot be assigned. The appropriate designation is Unknown with confidence None.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"148972012391933649","title":"Protein quality control and degradation","description":"This cluster is dominated by GO terms related to ubiquitin-proteasome\u2013mediated quality control, ER-associated degradation (ERAD), misfolded protein transport, and nuclear protein quality control, indicating a core theme of proteostasis and degradation. A few terms (e.g., DNA replication, mesoderm formation) are less related or older/obsolete annotations, but the strongest signals point to protein quality control pathways. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0006260","count":1},{"id":"GO:0097428","count":1},{"id":"GO:0032781","count":1},{"id":"GO:0001707","count":1}]},{"hash":"1094848125228207589","title":"Unknown","description":"There are no GO terms or connecting edges in this cluster, and the proteins appear isolated, offering no shared functional signal to define a common theme. Without functional annotations, the cluster cannot be confidently labeled.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1420457037992368885","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030260","count":1},{"id":"GO:0019068","count":1},{"id":"GO:0039651","count":1},{"id":"GO:0015074","count":1},{"id":"GO:0075713","count":1}]},{"hash":"1409529002576436246","title":"Unknown","description":"The listed GO terms span disparate biological areas (blood pressure regulation, iron transport, bone resorption, thyroid hormone metabolism, redox processes, integrin biosynthesis, hydrogen peroxide production, and stress responses), with no clear shared pathway or function across the proteins. This makes a cohesive functional label inappropriate, so I assign Unknown.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003081","count":1},{"id":"GO:0098706","count":1},{"id":"GO:0045453","count":1},{"id":"GO:0006590","count":1},{"id":"GO:0055114","count":1}]},{"hash":"595664696354337335","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009258","count":1},{"id":"GO:0033320","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0009103","count":1},{"id":"GO:0071951","count":1}]},{"hash":"1110635827155891221","title":"Ribosome Biogenesis and Translation","description":"The dominant GO terms point to ribosome production and protein synthesis, including translation, large subunit assembly, and large subunit biogenesis, with supporting terms like tRNA modification. Additional terms about protein targeting and stabilization fit with proper assembly and maintenance of translation machinery; a few ubiquitin-related regulatory terms likely reflect quality control rather than a different function. Overall, the cluster centers on ribosome assembly and protein synthesis.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0000027","count":3},{"id":"GO:0006400","count":2},{"id":"GO:0032092","count":1},{"id":"GO:0006605","count":1}]},{"hash":"1746139936387156259","title":"RNA and protein methylation enzymes","description":"Most of the top GO terms describe methylation activities on RNA and proteins (rRNA methylation, tRNA wobble modification, peptidyl-glycine/lysine/glutamine methylation, etc.). This common function links the proteins into a methylation/modification cluster, with only a couple of secondary terms (stress response and biosynthesis) appearing less directly connected.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018013","count":3},{"id":"GO:0031167","count":3},{"id":"GO:0018027","count":3},{"id":"GO:0035902","count":2},{"id":"GO:0002098","count":2}]},{"hash":"2171138338242436664","title":"Regulation of gene expression and apoptosis","description":"Top GO terms show strong emphasis on nuclear transcription (DNA-templated transcription), mRNA processing (splicing, deadenylation-independent decay), and apoptosis (p53-mediated signaling). This suggests a functional cluster tied to gene expression regulation and stress-induced cell death, despite a few less-connected terms like steroid biosynthesis or lipid catabolism that may reflect annotation or multifunctionality. Therefore, a label focusing on gene expression control with apoptotic connection fits best.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0071901","count":2},{"id":"GO:0006694","count":1},{"id":"GO:0072332","count":1},{"id":"GO:0090503","count":1}]},{"hash":"294978707514495097","title":"Unknown","description":"The two GO terms are unrelated (formaldehyde catabolic process vs. pericentric heterochromatin formation), and with only five proteins and no shared functional theme, there isn\u2019t a coherent function tying them together. Therefore, the cluster is best labeled Unknown.","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0046294","count":1},{"id":"GO:0031508","count":1}]},{"hash":"1147804339058965579","title":"Retroviral life cycle and latency","description":"The top GO terms cluster around reverse transcription (RNA-templated DNA biosynthetic process), DNA integration, and proviral latency, together with steps of entry into host cells and viral penetration into the host nucleus. These are hallmark features of retroviruses, including establishment of integrated proviral latency, supported by the reverse-transcription and integration-related terms. While some terms touch on general DNA processing, the concerted theme is clearly retroviral infection, replication, and latency.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006310","count":2},{"id":"GO:0006278","count":1},{"id":"GO:0039651","count":1},{"id":"GO:0015074","count":1},{"id":"GO:0043137","count":1}]},{"hash":"1050500112050005180","title":"RNA modification and protein methylation cluster","description":"This group is dominated by GO terms describing methylation events and RNA modifications (tRNA wobble uridine, rRNA modification, and specific methylations on N-terminal residues and peptide sides). While a few terms reference stress or hormone biosynthesis as outliers, the core signal points to RNA modification and broader methylation processes acting on proteins, making this an RNA/protein methylation-focused cluster.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035902","count":1},{"id":"GO:0002098","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0032259","count":1},{"id":"GO:1901052","count":1}]},{"hash":"1503465182712361569","title":"miRNA processing and transcription regulation","description":"Most of the top GO terms center on RNA processing (pre-miRNA processing, miRNA catabolic process) and transcription regulation (DNA-templated transcription, transcription antitermination, termination regulation) with related mRNA stabilization. These together point to proteins involved in miRNA maturation and regulation of transcription and RNA fate. A couple terms (osmotic-stress\u2013related apoptosis, kidney development) are less directly connected.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031054","count":1},{"id":"GO:0006351","count":1},{"id":"GO:1902219","count":1},{"id":"GO:0060567","count":1},{"id":"GO:1901724","count":1}]},{"hash":"220191421514430143","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034396","count":1},{"id":"GO:0034724","count":1},{"id":"GO:0050821","count":1},{"id":"GO:0006508","count":1},{"id":"GO:0030574","count":1}]},{"hash":"778957936530813623","title":"Glycine cleavage and one-carbon metabolism","description":"Enriched terms center on glycine decarboxylation via the glycine cleavage system and tetrahydrofolate metabolism, with linked methylation and amino-acid catabolic processes, pointing to a one-carbon metabolism theme. Some RNA modification terms may reflect folate-dependent modifications; overall, the cluster ties glycine/GCS activity to THF-driven one-carbon cycling.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":2},{"id":"GO:0032259","count":2},{"id":"GO:0019464","count":2},{"id":"GO:0006579","count":2},{"id":"GO:0046653","count":2}]},{"hash":"1815946603664896086","title":"Unknown","description":"The top GO terms span highly diverse processes\u2014telomere maintenance, endocytosis/pinocytosis, innate immune signaling (NOD1), temperature sensation and heat-stress responses, transcriptional regulation, cell cycle, chromosomal telomere localization, synaptic plasticity, and calcium signaling\u2014offering no single cohesive function to bind the cluster. Confidence: None","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":1},{"id":"GO:0048549","count":1},{"id":"GO:0070427","count":1},{"id":"GO:0050955","count":1},{"id":"GO:1901594","count":1}]},{"hash":"2049440921915957275","title":"RNA Pol II Transcriptional Repression","description":"This cluster centers on transcriptional control by RNA polymerase II, with top GO terms including DNA-templated transcription and negative regulation of transcription by RNA Pol II, as well as regulator-region binding and related transcriptional control. A few terms touch ER stress and redox detox, which may reflect stress-responsive transcriptional regulation, but the dominant theme is Pol II\u2013mediated transcriptional repression.","confidence":"High","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0000122","count":1},{"id":"GO:1903206","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0080058","count":1}]},{"hash":"344134493696905307","title":"Unknown","description":"The top GO terms are scattered across metabolism (glycolysis, pyruvate biosynthesis, amino acid and mandelate catabolic processes) and non-metabolic roles (cell wall organization, skeletal muscle regeneration, vacuole fusion regulation, apoptosis regulation). This broad mix lacks a single cohesive function for the cluster, suggesting no clear unifying theme.","confidence":"","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":2},{"id":"GO:0009405","count":2},{"id":"GO:0042866","count":2},{"id":"GO:0009063","count":1},{"id":"GO:1903298","count":1}]},{"hash":"1804645897808505189","title":"Thermoception, Pain, and Calcium Signaling","description":"The top GO terms cluster around temperature/thermoception (cold response, capsazepine response) and pain, with calcium ion import as a core signaling event, and related physiological readouts (vasopressin secretion, SA node action potential regulation, endothelial changes). This suggests a unifying theme of temperature- and pain-related signaling interconnected with calcium dynamics, despite the cluster\u2019s small size.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050955","count":2},{"id":"GO:1901594","count":2},{"id":"GO:0098907","count":2},{"id":"GO:1903444","count":2},{"id":"GO:0098703","count":2}]},{"hash":"333570631040460371","title":"Unknown","description":"The GO terms are highly diverse, spanning digestive tract and reproductive gland development, muscle differentiation, various lipid metabolism and prostaglandin processes, and epigenetic methylation/demethylation, with no clear common function or pathway tying the proteins together. There are no edges or triangles to support a cohesive cluster function, so a single cohesive label cannot be inferred.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048565","count":1},{"id":"GO:0035902","count":1},{"id":"GO:0010430","count":1},{"id":"GO:0008585","count":1},{"id":"GO:0001516","count":1}]},{"hash":"2176181238827394393","title":"Mitochondrial Import and Membrane Regulation","description":"The prominent GO terms point to mitochondrial processes, especially protein import into the mitochondrial matrix and regulation of mitochondrial membrane permeability, suggesting a mitochondria-focused cluster. While other terms involve lipid metabolism and tRNA modification, the strongest shared function across the cluster centers on mitochondrial transport and membrane dynamics.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:2000134","count":1},{"id":"GO:0070940","count":1},{"id":"GO:0046902","count":1},{"id":"GO:0010867","count":1}]},{"hash":"550980838008859965","title":"Calcium-Driven Muscle Contraction and Signaling","description":"The cluster centers on calcium signaling and muscle contraction\u2014diaphragm and cardiac muscle contraction, detection of calcium ion, phosphatidylinositol-mediated signaling, and Ryanodine receptor\u2013related calcium release\u2014all pointing to Ca2+-dependent muscle activity and cardiovascular regulation. Some terms like digestion, kidney development, and bioluminescence are less connected and may reflect broader or secondary roles, but the dominant theme is calcium-enabled muscle function and associated signaling. ","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0002086","count":3},{"id":"GO:0007586","count":3},{"id":"GO:0060048","count":3},{"id":"GO:0048015","count":2},{"id":"GO:0045944","count":2}]},{"hash":"2287612549963493969","title":"Unknown","description":"There are no Top Terms provided to tie the five proteins to a common function, so a meaningful label cannot be inferred from GO terms alone; the cluster cannot be confidently characterized beyond Unknown.","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[]},{"hash":"459018645950432490","title":"Retroviral Infection and Genome Integration","description":"The cluster is dominated by terms tied to the retroviral life cycle: RNA-templated DNA biosynthesis, DNA replication, DNA integration, and establishment of proviral latency, along with signals of viral entry into the host nucleus. Supporting terms reference host\u2013virus interactions (apoptosis modulation and RNAi regulation) that accompany infection. Together these indicate a core function centered on retroviral infection, genome integration, and latency.","confidence":"High","size":5,"edges":7,"triangles":3,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006278","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0039651","count":4},{"id":"GO:0015074","count":4},{"id":"GO:0075713","count":4}]},{"hash":"345873314130862143","title":"Viral entry, replication, and proviral latency","description":"The terms converge on viral infection biology: entry into the host, nucleus penetration, genome replication and integration, and establishment of proviral latency, with accompanying host-response modulation (apoptosis activation and RNAi interference). This supports a cohesive theme of viral genome maintenance and host manipulation.","confidence":"High","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":3},{"id":"GO:0006278","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0039651","count":2},{"id":"GO:0015074","count":2}]},{"hash":"496805127738687744","title":"Unknown","description":"The GO terms are highly diverse (lipid biosynthesis, cuticle pigmentation, neurotransmitter loading and synthesis, cell differentiation, methanofuran biosynthesis, growth factor response, serotonin production, aging), with no single shared function connecting the proteins, so no clear cluster theme can be assigned.","confidence":"","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042759","count":1},{"id":"GO:1902321","count":1},{"id":"GO:0048085","count":1},{"id":"GO:0015842","count":1},{"id":"GO:0042136","count":1}]},{"hash":"1330367363678901009","title":"Unknown","description":"The top GO terms are a mix of protein sumoylation and various unrelated metabolic processes (amino acid biosynthesis, nucleotide metabolism, and catabolic pathways) with no clear shared function or connectivity among the five proteins, suggesting heterogeneous annotations rather than a coherent cluster.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":2},{"id":"GO:0009090","count":1},{"id":"GO:0009086","count":1},{"id":"GO:0009435","count":1},{"id":"GO:0055114","count":1}]},{"hash":"954317659757670552","title":"Carbohydrate Metabolism and Osmotic Stress Response","description":"This cluster centers on carbohydrate metabolism (glucose and sucrose) and osmotic stress responses (water deprivation and mannitol) with supporting hints from mycothiol biosynthesis and membrane-related processes, suggesting a link between energy metabolism and osmoregulatory adaptation. Some GO terms are obsolete, but the core signals point to metabolic activity tied to osmotic stress. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008654","count":1},{"id":"GO:0009414","count":1},{"id":"GO:0006490","count":1},{"id":"GO:0097502","count":1},{"id":"GO:0010555","count":1}]},{"hash":"252133207361489478","title":"Mitotic regulation and GTPase signaling","description":"Based on the most frequent GO terms, the proteins are enriched for mitotic processes (mitotic cell cycle, cell division, positive regulation of cytokinesis) and regulation of GTPase activity, which together point to control of cell-cycle progression and cytoskeletal/trafficking dynamics. Additional terms for mRNA transport and vacuole fusion suggest involvement in intracellular transport and organelle dynamics that accompany cell division. A few terms related to neural differentiation appear but are less representative of the cluster's core function.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0051028","count":3},{"id":"GO:0000278","count":3},{"id":"GO:1904948","count":2}]},{"hash":"2117100951784397017","title":"Unknown","description":"The top GO terms include telomere maintenance, pinocytosis, NOD1 signaling, thermoception, response to capsazepine, heat-stress transcription, cell cycle, synaptic receptor localization, telomeric chromosome localization, and calcium release, with no single cohesive function linking them. This diversity suggests no unifying theme for a specific cluster function, so the label Unknown is appropriate.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":3},{"id":"GO:0048549","count":3},{"id":"GO:0070427","count":3},{"id":"GO:0050955","count":3},{"id":"GO:1901594","count":3}]},{"hash":"39353572749450218","title":"ER protein folding and oxidative stress response","description":"The top GO terms point to endoplasmic reticulum\u2013associated protein folding, redox homeostasis, and protein repair, suggesting a module focused on protein quality control under oxidative stress; some viral process and transcription-related terms are present but less central to the core function.","confidence":"Medium","size":5,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0034975","count":3},{"id":"GO:0045454","count":3},{"id":"GO:0016032","count":3},{"id":"GO:0030091","count":2},{"id":"GO:0006662","count":2}]},{"hash":"1027352767047597618","title":"Unknown","description":"No GO terms or connections present to define a common function; the cluster lacks identifiable thematic content, so a specific label cannot be assigned.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"935146111421128218","title":"Unknown","description":"There is no clear shared function among these proteins; the top GO terms span sensory perception (auditory differentiation, thermoception, startle), vascular/respiratory responses (vasoconstriction, hypoxia, CO2 detection), and development (genitalia, lung epithelium) plus autophagosome maturation, offering no single unifying theme.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042491","count":1},{"id":"GO:0042310","count":1},{"id":"GO:0001666","count":1},{"id":"GO:0003031","count":1},{"id":"GO:0001964","count":1}]},{"hash":"1635782079662448974","title":"Fungal carbohydrate metabolism and biofilm formation","description":"The terms point to catabolic processing of fungal cell wall and storage polysaccharides (beta-glucan, mannan, xylan, cellulose) and related carbohydrate metabolism, along with strong biofilm formation signals in single-species contexts, indicating a cluster of proteins involved in fungal carbohydrate utilization and biofilm development.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904462","count":2},{"id":"GO:0070879","count":2},{"id":"GO:0044407","count":2},{"id":"GO:0046355","count":2},{"id":"GO:0045493","count":2}]},{"hash":"1691791804861138638","title":"Diverse membrane transporters for nutrients and metabolites","description":"The GO terms cluster around membrane transport across various substrates (amino acids, vitamins, sugars, lipids, ions) and include both export and translocation activities, indicating a group of transporter proteins with broad specificity rather than a single, specific substrate function.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090374","count":1},{"id":"GO:0030253","count":1},{"id":"GO:0015803","count":1},{"id":"GO:0015734","count":1},{"id":"GO:0035461","count":1}]},{"hash":"1001654691325230077","title":"DNA replication and mitotic regulation","description":"This cluster centers on nuclear processes related to genome maintenance and cell division, as indicated by DNA replication, DNA repair (NHEJ), G1/S transition, and kinetochore localization terms. The presence of kinetochore localization and maintenance of trinucleotide repeats supports roles in chromosome maintenance and mitosis. A few terms touch on calcium- and NFAT-mediated signaling, which may reflect broader regulatory context rather than core function. Overall, the proteins seem linked to DNA replication/repair and cell cycle control.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:2000324","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0005513","count":4},{"id":"GO:0001915","count":4},{"id":"GO:0060316","count":4}]},{"hash":"1774763878702498035","title":"Unknown","description":"The GO terms include muscle/cardiac regulation, dendritic spine morphogenesis, cell cycle and autophagy control, and even virus response, with no single dominant function across all members. Because there is no coherent shared theme linking the terms, a specific, informative label cannot be confidently assigned.","confidence":"","size":4,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0014850","count":2},{"id":"GO:0060997","count":2},{"id":"GO:0060044","count":2},{"id":"GO:0031647","count":2},{"id":"GO:0016242","count":1}]},{"hash":"1048467492916551824","title":"GPCR and cGMP Signaling","description":"The GO terms center on GPCR-mediated signaling (adenosine and adrenergic receptors) with downstream cyclic nucleotide production, including cGMP biosynthesis and receptor guanylyl cyclase signaling, suggesting a core GPCR-to-cGMP signaling module. Sensory cues like blue light and hypoxia detection fit within this signaling framework, reinforcing the notion of extracellular signal detection feeding into GPCR/cGMP pathways.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071880","count":1},{"id":"GO:0070483","count":1},{"id":"GO:0006182","count":1},{"id":"GO:0009785","count":1},{"id":"GO:0001973","count":1}]},{"hash":"1606807296429214010","title":"Endosomal and vacuolar trafficking","description":"I named this cluster Endosomal and vacuolar trafficking because the top GO terms cluster around intracellular transport pathways: cytoplasm-to-vacuole targeting via the Cvt pathway, endosome-to-melanosome transport, plasma membrane-to-endosome transport, and positive regulation of the secretory pathway. These collectively indicate vesicle trafficking through endosomal and vacuolar/secretory routes, rather than a single enzymatic function.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032258","count":3},{"id":"GO:0045453","count":2},{"id":"GO:0035646","count":2},{"id":"GO:0071287","count":2},{"id":"GO:0043525","count":2}]},{"hash":"1668964061182647174","title":"Actin-driven cell polarity and morphogenesis","description":"The GO terms cluster around actin cytoskeleton dynamics (actin filament bundle distribution, muscle filament sliding), cell polarity establishment/maintenance (dorsal closure, uropod organization), and morphogenetic processes, plus vesicle trafficking relevant to polarized movement. This suggests a coherent theme of actin-dependent polarity and morphogenesis, with some signaling regulation hints from tyrosine dephosphorylation. ","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035335","count":2},{"id":"GO:0046663","count":1},{"id":"GO:0032796","count":1},{"id":"GO:0071963","count":1},{"id":"GO:1903028","count":1}]},{"hash":"2129826805151226431","title":"Unknown","description":"This cluster has no GO terms or interaction signals (Edges 0, Triangles 0, Max Degree 0) and no shared functional annotations to tie the proteins together. Without a detectable theme, the correct label is Unknown and there is no confidence to assign.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1045025256486717307","title":"Spliceosome-Dependent mRNA Splicing Regulation","description":"Based on the GO terms, the proteins are primarily connected with spliceosome-mediated mRNA processing, including both positive and negative regulation of splicing, splice-site recognition, and general mRNA splicing. There is also a note of regulatory ncRNA-mediated gene silencing, indicating RNA-level regulatory roles. Together, these terms point to a cluster centered on RNA processing and regulation via the spliceosome (with a possible incidental link to translation initiation components).","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":1},{"id":"GO:0048026","count":1},{"id":"GO:1902625","count":1},{"id":"GO:0075525","count":1},{"id":"GO:1905663","count":1}]},{"hash":"1737943934223926255","title":"RNA processing and Pol II transcription regulation","description":"The top GO terms are centered on RNA processing and transcription control by RNA polymerase II, notably mRNA splicing via the spliceosome and termination/positive regulation of Pol II transcription. These indicate a nuclear cluster of proteins involved in RNA maturation and transcription regulation, with some secondary involvement in related DNA metabolic processes. ","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0006369","count":3},{"id":"GO:0045944","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0001666","count":2}]},{"hash":"505255822422164574","title":"Unknown","description":"GO terms span mating-related signaling (pheromone response, karyogamy) and general processes (DNA replication, SRP-dependent membrane targeting) plus miscellaneous stress and obsolete annotations, with no single cohesive function tying all members, so a specific, representative label cannot be assigned.","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019236","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0090084","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0006616","count":2}]},{"hash":"579778410360051288","title":"Unknown","description":"This cluster has no edges and no shared GO terms, so there is no clear functional theme to group the proteins; with only identifiers and no annotated terms, Unknown is the appropriate label.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1625692352095535507","title":"Spliceosome-Mediated mRNA Splicing Regulation","description":"The terms are dominated by regulation of mRNA splicing via the spliceosome, including positive/negative regulation of splicing, spliceosome-mediated mRNA processing, and splice site recognition, indicating a cohesive theme around mRNA splicing control. A few translation-related terms are present but secondary to the splicing focus.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":1},{"id":"GO:0048026","count":1},{"id":"GO:1902625","count":1},{"id":"GO:0075525","count":1},{"id":"GO:1905663","count":1}]},{"hash":"34740608072317037","title":"Ribosome biogenesis and translation regulation","description":"The top GO terms point to ribosome assembly and function (ribosome biogenesis, translation, tRNA charging, rRNA modification) and regulation of translation fidelity and initiation; these together suggest a cluster tied to ribosome-related protein synthesis and its control, despite a few transcription/stress terms that may reflect broader cellular roles.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0006353","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0045947","count":1},{"id":"GO:0034605","count":1}]},{"hash":"360257143837168359","title":"Ribosome Biogenesis and Translation","description":"The top GO terms are dominated by translation and ribosome biogenesis (including ribosomal small subunit biogenesis), which together point to a cluster of proteins involved in protein synthesis machinery. Other terms (TOR signaling, cell cycle, apoptosis, development) are present but appear ancillary to the dominant ribosome/translation signature, suggesting these proteins mainly participate in ribosome biogenesis and protein production.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0002309","count":1},{"id":"GO:0022605","count":1},{"id":"GO:0042274","count":1}]},{"hash":"436567973066571074","title":"Regulatory Signaling and Sensory Processes","description":"The top GO terms indicate regulatory roles across diverse processes, including transcription regulation, GPCR-driven signaling, sensory perception (thermoception, capsazepine response), and cell shape regulation. While these terms span different biological areas (cardiac signaling, immune signaling, cytoskeletal changes), the common thread is regulation rather than a single enzyme activity, suggesting these proteins act as regulators of signaling and sensory-related processes rather than a unified, specific function.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045944","count":2},{"id":"GO:0098907","count":2},{"id":"GO:0008360","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0007626","count":1}]},{"hash":"1521879418179630159","title":"Cerebellar neuronal development","description":"The top GO terms include Bergmann glial cell differentiation, cerebellar cortex formation, dendritic spine morphogenesis, and regulation of axon regeneration, all aspects of neural development and cerebellar maturation. While there are a few immune signaling and cell-cycle terms, the strongest cohesive theme is cerebellar neuron development and morphogenesis, so this label reflects the dominant function of the cluster.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0050852","count":4},{"id":"GO:0060020","count":4},{"id":"GO:0014850","count":4},{"id":"GO:0008286","count":4},{"id":"GO:0060997","count":4}]},{"hash":"291654547368171715","title":"Unknown","description":"The top GO terms cover very different processes (autophagy regulation, cardiac differentiation, sodium transport, mitotic G1/S transition, meiotic spindle organization/checkpoint signaling, cellular response to virus, p53-mediated signaling, and receptor serine/threonine kinase signaling). There is no single shared function or pathway tying the four proteins together, and the network has no edges or triangles, so there is no coherent cluster label beyond Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016242","count":1},{"id":"GO:2000727","count":1},{"id":"GO:0010765","count":1},{"id":"GO:0000082","count":1},{"id":"GO:0000212","count":1}]},{"hash":"2248954064518368393","title":"Isoprenoid Biosynthesis","description":"Top GO terms reveal a consistent theme of terpenoid/isoprenoid production, including cholesterol biosynthesis and multiple steps producing geranyl, farnesyl, geranylgeranyl diphosphates, monoterpenes, and quinones. This points to a shared function in isoprenoid/terpenoid biosynthesis among the cluster\u2019s proteins. Some terms like DNA integration/transposition and protein transport appear unrelated or generic, likely reflecting annotation noise or multifunctionality, but they do not override the main biosynthetic signal.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006695","count":1},{"id":"GO:0033384","count":1},{"id":"GO:0015031","count":1},{"id":"GO:0051290","count":1},{"id":"GO:1901663","count":1}]},{"hash":"1885801413442274205","title":"Ubiquitin-proteasome system and mitophagy regulation","description":"This cluster is dominated by ubiquitin-related processes: deubiquitination, ubiquitin-dependent proteasomal degradation, and autoubiquitination, along with mitophagy and regulation of autophagosome maturation. While there are a few additional terms (ribosomal assembly, rRNA maturation, ER-stress-related signaling), the core theme is protein turnover and quality control via ubiquitin-proteasome pathways and mitophagy.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":4},{"id":"GO:1903071","count":3},{"id":"GO:0045944","count":3},{"id":"GO:0000423","count":3},{"id":"GO:0000028","count":3}]},{"hash":"1545140373297658818","title":"Cell division and vesicle docking","description":"The terms point to mitotic processes (spindle organization, regulation of asymmetric cell division) and membrane trafficking (vesicle docking/exocytosis, vacuole inheritance), suggesting a cluster tied to cellular division coupled with intracellular transport. Peripheral terms like VEGF signaling and reproductive development appear less central but don\u2019t override the core theme. Therefore, the label focuses on mitosis-related organization with vesicle dynamics, assigned a Medium confidence.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007051","count":1},{"id":"GO:1903480","count":1},{"id":"GO:1900748","count":1},{"id":"GO:0006904","count":1},{"id":"GO:0045769","count":1}]},{"hash":"1084472415125294275","title":"P-body and stress granule dynamics in antiviral signaling","description":"These terms cluster around RNA metabolism and storage: deadenylation-independent decapping, translational repression, P-body and stress granule assembly, with antiviral signaling connections (RIG-I pathway and type I interferon responses). The core theme is mRNA decay and stress granule\u2013mediated antiviral responses, with glucocorticoid response and IL-2 regulation appearing as peripheral immune-related terms.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031087","count":1},{"id":"GO:0045947","count":1},{"id":"GO:0039529","count":1},{"id":"GO:0033962","count":1},{"id":"GO:0034063","count":1}]},{"hash":"2099440339223434509","title":"RNA processing and transcription regulation","description":"The listed GO terms cluster around RNA biogenesis and processing (pre-miRNA processing, miRNA catabolic process, transcription antitermination) and transcription-related activities (DNA-templated transcription, CRD-mediated mRNA stabilization, transcription regulation). This suggests a coherent theme of post-transcriptional RNA handling and transcription control, with a few peripheral terms related to stress signaling and development.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031054","count":1},{"id":"GO:0006351","count":1},{"id":"GO:1902219","count":1},{"id":"GO:0060567","count":1},{"id":"GO:1901724","count":1}]},{"hash":"2214593195296561809","title":"Unknown","description":"There are no GO terms provided to identify a shared function; the Top Terms section is empty and the small, sparsely connected network (2 edges, max degree 2, 0 triangles) offers no clear functional theme. The note about ReCIPE re-added proteins suggests mixed provenance rather than a single biological process.","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[]},{"hash":"2138318652412725421","title":"RNA processing and transcription regulation","description":"The top GO terms cluster around RNA biology\u2014pre-miRNA processing, miRNA catabolic process, transcription-related processes (DNA-templated transcription, transcription antitermination, termination control), and related RNA stability/processing; a couple terms appear peripheral (apoptosis, kidney development), which lowers but does not negate the overall RNA-centric theme.","confidence":"Medium","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0031054","count":1},{"id":"GO:0006351","count":1},{"id":"GO:1902219","count":1},{"id":"GO:0060567","count":1},{"id":"GO:1901724","count":1}]},{"hash":"2205584087108455070","title":"Muscle development and sarcomere organization","description":"The terms are dominated by muscle-related processes, notably sarcomere organization and cardiac muscle cell proliferation, with mesoderm formation indicating broader developmental context. Other terms are peripheral, making the core theme muscle structure and development.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007612","count":2},{"id":"GO:0060038","count":1},{"id":"GO:0051447","count":1},{"id":"GO:0046827","count":1},{"id":"GO:0045214","count":1}]},{"hash":"69811272614852583","title":"Ubiquitination and chromatin regulation","description":"Most top GO terms cluster around protein ubiquitination (K48- and K6-linked) and autoubiquitination, plus histone catabolic processes, suggesting a theme of ubiquitin-mediated regulation of chromatin dynamics and nuclear processes. Some terms (V(D)J recombination, dosage compensation, viral material transport) are peripheral but can relate to nuclear regulation contexts; overall the set points to ubiquitination controlling chromatin-associated functions.","confidence":"Medium","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1900095","count":3},{"id":"GO:0070936","count":3},{"id":"GO:0033151","count":3},{"id":"GO:0009048","count":3},{"id":"GO:0085020","count":3}]},{"hash":"199578647529520676","title":"Unknown","description":"There are no GO terms reported for this cluster, and with only 4 proteins and a single edge (no triangles), there is insufficient functional signal to infer a shared theme. As a result, a specific, representative label cannot be assigned.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[]},{"hash":"847591236121478459","title":"Proteostasis and protein quality control","description":"This cluster is driven by terms tied to protein maturation, misfolded protein handling, and degradation via the ubiquitin-proteasome system (e.g., nuclear protein quality control by the ubiquitin-proteasome system, misfolded protein transport, and ubiquitin-dependent ERAD). These points suggest the proteins collectively participate in maintaining protein homeostasis. Some other terms (DNA replication, mesoderm formation) appear less connected and may reflect annotation noise given the small cluster size. Overall, the proteostasis theme best explains the shared functions.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0097428","count":4},{"id":"GO:0032781","count":4},{"id":"GO:0001707","count":4},{"id":"GO:0006469","count":4}]},{"hash":"14658475203856937","title":"Membrane Transport and Secretion","description":"GO terms show diverse membrane transport activities (amino acids, vitamins, bile acids, taurine, cadmium) and secretion/docking processes (type I secretion, exocytosis), suggesting a cohesive role in transport and secretion across membranes.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0090374","count":1},{"id":"GO:0030253","count":1},{"id":"GO:0015803","count":1},{"id":"GO:0032782","count":1}]},{"hash":"1960140600484789270","title":"Unknown","description":"The GO terms span immune signaling (IL-2 production, TLR3 pathway), metabolism (SREBP signaling, lipid localization), protein quality control (ubiquitin-dependent ERAD), and development/excretion, with no single dominant function connecting the proteins, so a coherent label cannot be justified.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032623","count":1},{"id":"GO:0045861","count":1},{"id":"GO:0034141","count":1},{"id":"GO:1990046","count":1},{"id":"GO:0030433","count":1}]},{"hash":"1657292959546478852","title":"RNA-based gene expression regulation","description":"The GO terms cluster around RNA-level control of gene expression, including transcription regulation, ncRNA-mediated silencing, miRNA turnover, and RNA processing/translation initiation, suggesting a theme of RNA-centric regulation of transcription, splicing, and translation.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":1},{"id":"GO:0060567","count":1},{"id":"GO:0031047","count":1},{"id":"GO:0048026","count":1},{"id":"GO:1902625","count":1}]},{"hash":"656026162097557926","title":"Unknown","description":"The top terms cover very different processes (neuronal development and memory, hypoxia response, metamorphosis, T cell and hemocyte development, heart development, xenobiotic response) with no clear common function, and the cluster has no edges or connectivity, suggesting it does not represent a cohesive pathway.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007611","count":1},{"id":"GO:0001666","count":1},{"id":"GO:0007552","count":1},{"id":"GO:0043029","count":1},{"id":"GO:0007507","count":1}]},{"hash":"1471699592761881446","title":"Vesicle trafficking and lysosome function","description":"In this cluster, the strongest cohesion comes from GO terms related to intracellular vesicle transport and lysosome-associated processes, such as endosome to melanosome transport, cytoplasm to vacuole targeting, and lysosomal membrane organization, all of which point to vesicle trafficking and lysosome dynamics. The presence of small GTPase\u2013mediated signal transduction further supports a trafficking-control role. Some bone-related terms could reflect osteoclast lysosome involvement; other terms appear peripheral but do not override the central trafficking theme.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007264","count":2},{"id":"GO:0043931","count":2},{"id":"GO:0040040","count":2},{"id":"GO:0031584","count":1},{"id":"GO:0097212","count":1}]},{"hash":"2287479107134485288","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0044805","count":2},{"id":"GO:0032258","count":2},{"id":"GO:0006501","count":2},{"id":"GO:0000422","count":2},{"id":"GO:0034727","count":2}]},{"hash":"1756514517874593251","title":"ERAD- and Mitochondrial Autophagy Quality Control","description":"The top GO terms cluster around ER-associated degradation (ERAD) via ubiquitin, mitophagy, and regulation of autophagosome maturation, plus mitochondrial fusion, all signaling a shared role in organelle quality control and proteostasis through ubiquitin-proteasome and autophagy pathways. Ribosomal subunit assembly and rRNA maturation appear more secondary, but the dominant theme is ER/mitochondrial quality control via autophagy. ","confidence":"High","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1903071","count":3},{"id":"GO:0000423","count":3},{"id":"GO:0000028","count":3},{"id":"GO:1902236","count":3},{"id":"GO:0002109","count":3}]},{"hash":"1642441093212816664","title":"Wnt-driven development and differentiation","description":"The top GO terms are dominated by regulation of the canonical Wnt pathway, mesoderm morphogenesis, and intestinal epithelial differentiation, pointing to roles in developmental signaling and lineage specification. There are also broader terms for transcription regulation and ubiquitination, suggesting auxiliary control of gene expression in these processes. Overall, the cluster appears enriched for developmental signaling and tissue differentiation programs centered on Wnt signaling.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090263","count":3},{"id":"GO:0019089","count":2},{"id":"GO:0045944","count":2},{"id":"GO:0035519","count":2},{"id":"GO:0001666","count":2}]},{"hash":"895004244716597707","title":"Unknown","description":"The GO terms are diverse and only loosely related, spanning metabolism (riboflavin biosynthesis; carnitine and fatty acid beta-oxidation) and cellular structures/processes (actin bundle assembly; regulation of endocytosis; cell polarity; platelet aggregation) as well as chromatin-related processes. There isn\u2019t a single dominant function tying all four proteins together, making a coherent, specific label difficult. Therefore, I\u2019m assigning Unknown.","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009231","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0009437","count":1},{"id":"GO:0033539","count":1},{"id":"GO:0051017","count":1}]},{"hash":"1765531231340501647","title":"Biosynthesis and RNA Modification Enzymes","description":"The top GO terms include several biosynthetic processes (cobalamin biosynthesis, mycolic acid biosynthesis, antibiotic biosynthesis) alongside RNA-related modification processes (tRNA wobble uridine modification, rRNA modification, methylation). This points to a cluster of proteins involved in producing biomolecules and adding chemical modifications, especially to RNA and related substrates, rather than a single, narrow function. Some transcription- or stress-related terms may be annotation noise, but the core theme is biosynthesis plus RNA modification.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":2},{"id":"GO:0006351","count":1},{"id":"GO:0035902","count":1},{"id":"GO:0002098","count":1},{"id":"GO:0000122","count":1}]},{"hash":"1528977258844958077","title":"RNA Processing and Transcription Regulation","description":"This cluster centers on RNA biogenesis and transcription control, with terms such as pre-miRNA processing, miRNA catabolic process, DNA-templated transcription, transcription termination regulation, and transcription antitermination, plus ribosomal small subunit biogenesis. Together these suggest a shared role in RNA metabolism and regulation of gene expression at transcriptional and post-transcriptional levels. A few terms (kidney development, osmotic-stress\u2013related apoptosis) are less directly connected and may reflect broader multifunctionality, but the dominant pattern supports RNA processing and transcription control.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031054","count":1},{"id":"GO:0006351","count":1},{"id":"GO:1902219","count":1},{"id":"GO:0060567","count":1},{"id":"GO:1901724","count":1}]},{"hash":"784761589983742852","title":"Unknown","description":"With only a single GO term (negative regulation of fibroblast apoptotic process), four proteins, and noConnecting edges or shared broader terms, there isn\u2019t a clear, cohesive theme tying the cluster together. The lone term is very specific and sparsely represented, so a confident functional label cannot be assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000270","count":1}]},{"hash":"2107676250729392858","title":"Zinc Ion Homeostasis and Transport","description":"The GO terms point to intracellular and transmembrane zinc ion handling, including homeostasis, detoxification, and response, with some related metal ion terms (cadmium, cobalt, iron). This suggests a cohesive module centered on zinc regulation and transport.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006877","count":1},{"id":"GO:0010043","count":1},{"id":"GO:0010312","count":1},{"id":"GO:0006882","count":1},{"id":"GO:0006876","count":1}]},{"hash":"2172183348542211677","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034628","count":1},{"id":"GO:1990966","count":1},{"id":"GO:0097171","count":1},{"id":"GO:0046444","count":1},{"id":"GO:0019350","count":1}]},{"hash":"455429028857501212","title":"Cilium assembly and motility regulation","description":"Predominant signals are cilium-related: regulation of cilium beat frequency in ciliary motility and non-motile cilium assembly. Other nearby terms touch on organ development (ureter, prostate gland) and generic regulatory processes, which may reflect broader roles for ciliary signaling in development, while some terms are unrelated. Overall, the cluster centers on ciliary structure and function.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0003085","count":1},{"id":"GO:1903071","count":1},{"id":"GO:0060296","count":1},{"id":"GO:2000324","count":1},{"id":"GO:0071357","count":1}]},{"hash":"2182717336440293363","title":"Neuronal mRNA regulation and splicing","description":"The cluster is driven by post-transcriptional RNA control terms\u2014mRNA binding, mRNA stability in stress, spliceosome-regulated splicing, and miRNA-mediated silencing\u2014with two brain-related terms (pallium forebrain proliferation and regulation of neuronal action potential), suggesting a brain-focused module of RNA processing and gene regulation.","confidence":"Medium","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090503","count":2},{"id":"GO:1902416","count":1},{"id":"GO:0010738","count":1},{"id":"GO:0022013","count":1},{"id":"GO:2000627","count":1}]},{"hash":"289146759867646016","title":"Ciliary Hedgehog signaling and vesicle trafficking in neural development","description":"The top GO terms strongly point to primary cilium\u2013mediated Hedgehog signaling (Smoothened pathway) and neural development, with supporting evidence of ciliary localization and vesicle trafficking processes (Golgi/COPII, lysosomal membranes, and synaptic vesicle budding). This suggests a coherent cluster of proteins involved in ciliary signaling that coordinates neural development with intracellular trafficking and organogenesis, including kidney development as a related ciliary pathway. ","confidence":"High","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":4},{"id":"GO:0007224","count":3},{"id":"GO:0031584","count":3},{"id":"GO:0070142","count":3},{"id":"GO:0097212","count":3}]},{"hash":"2144979632075251195","title":"Actin Cytoskeleton Remodeling and Filament Assembly","description":"The top GO terms cluster around actin cytoskeleton processes\u2014actin filament bundle assembly, Arp2/3 complex\u2013mediated nucleation, and thin filament assembly\u2014with related roles in endocytosis regulation and muscle fiber adaptation, indicating a cohesive theme of actin-driven cytoskeletal remodeling.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051017","count":4},{"id":"GO:0071963","count":4},{"id":"GO:0043981","count":4},{"id":"GO:0030100","count":4},{"id":"GO:0070527","count":4}]},{"hash":"758659771534842100","title":"Unknown","description":"The top terms span vesicle transport, cytoskeleton dynamics, mitotic processes, translation regulation, pollen tube growth, and signaling, with no single cohesive function tying the proteins together, so a generic Unknown label is most appropriate.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006891","count":1},{"id":"GO:0009860","count":1},{"id":"GO:0032258","count":1},{"id":"GO:1905792","count":1},{"id":"GO:0031122","count":1}]},{"hash":"583298186976076850","title":"Unknown","description":"The GO terms are a mix of bacterial cell wall metabolism (peptidoglycan turnover/biosynthesis, cell wall organization) and unrelated eukaryotic processes (cell cycle/division, telomere maintenance, pinocytosis, NOD signaling), with no clear shared function across all proteins. The lack of edges and cohesive theme suggests no single representative function emerges.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0009254","count":1},{"id":"GO:0008360","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0071555","count":1}]},{"hash":"1889469901395076005","title":"Unknown","description":"The listed GO terms span diverse processes, including chromatin organization and histone modification, chromosome segregation, RNA splicing, phagolysosome assembly, growth hormone response, GTPase signaling, and epithelial proliferation. With no clear shared function tying them together and no observed edges among the proteins, there is no coherent theme to name a specific cluster beyond Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000747","count":1},{"id":"GO:0050679","count":1},{"id":"GO:1902510","count":1},{"id":"GO:0001845","count":1},{"id":"GO:0031497","count":1}]},{"hash":"1749208160018340450","title":"Post-transcriptional gene regulation","description":"This cluster is driven by terms related to RNA-level control of gene expression, including regulatory ncRNA-mediated gene silencing, positive regulation of mRNA splicing via the spliceosome, negative regulation of mRNA decay, and eukaryotic translation initiation factor 4F complex assembly. While a few terms touch on signaling or development that may reflect broader cellular contexts, the dominant signals point to post-transcriptional regulation of transcripts.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045314","count":1},{"id":"GO:0031047","count":1},{"id":"GO:0048026","count":1},{"id":"GO:1902625","count":1},{"id":"GO:0075525","count":1}]},{"hash":"2261468497174211980","title":"Proteostasis and ubiquitin-proteasome regulation","description":"The cluster features terms centered on protein quality control, including nuclear protein quality control by the ubiquitin-proteasome system, misfolded protein transport, and ubiquitin-dependent ERAD pathways. These collectively point to proteostasis and regulated protein turnover as the core theme, while some other terms appear as noise or historical annotations. ","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":1},{"id":"GO:0097428","count":1},{"id":"GO:0032781","count":1},{"id":"GO:0001707","count":1},{"id":"GO:0006469","count":1}]},{"hash":"142596019494873848","title":"Pyridoxine and amino acid metabolism","description":"The cluster's GO terms are mainly pyridoxine biosynthesis and amino acid metabolism (alanine catabolism, serine biosynthesis, methionine cycle), indicating vitamin B6\u2013related metabolic functions. A few terms reference stress and circadian processes, but they appear less central to the cluster's core function.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008615","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0042853","count":2},{"id":"GO:0006564","count":2},{"id":"GO:0002439","count":1}]},{"hash":"239338990412200077","title":"Plant hormone biosynthesis and secondary metabolism","description":"The GO terms cluster around plant hormone pathways (gibberellin and auxin biosynthesis/catabolism) and secondary metabolite production (proanthocyanidin biosynthesis), with related processes like fruit ripening and hormone catabolic activity. Even though there are no edges, the terms point to a cohesive theme of plant growth regulation and metabolism, supporting this label.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042426","count":2},{"id":"GO:0010023","count":1},{"id":"GO:1902835","count":1},{"id":"GO:0042318","count":1},{"id":"GO:0046244","count":1}]},{"hash":"1902732895544530514","title":"Male Reproductive Development and Cell Cycle","description":"This cluster is driven by terms linking cell division and the cell cycle with male reproductive development (prostate gland development, male sex differentiation) and steroid hormone receptor complex assembly, suggesting involvement in hormone-regulated proliferation in male tissues. While some stress and RNA/protein modification terms appear, the dominant theme appears to be male reproductive development intertwined with cell-cycle processes.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0030850","count":2},{"id":"GO:0046661","count":2},{"id":"GO:0006463","count":2},{"id":"GO:0007049","count":2}]},{"hash":"556387078425862134","title":"Unknown","description":"The set of GO terms spans chromatin regulation (histone demethylation, rDNA heterochromatin), general growth and developmental processes (growth rate regulation, stem cell maintenance, mammary gland growth, brain morphogenesis), and plant-specific photoperiodism/flowering terms, plus a spermatid elongation term. The terms are heterogeneous across species and contexts, with no single coherent function tying them all together, so a specific, representative label cannot be meaningfully assigned.","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070544","count":2},{"id":"GO:0040010","count":2},{"id":"GO:0048577","count":2},{"id":"GO:0007290","count":2},{"id":"GO:0048579","count":2}]},{"hash":"1947440632306148893","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0035606","count":3},{"id":"GO:0009089","count":3},{"id":"GO:0051402","count":3},{"id":"GO:0042823","count":3},{"id":"GO:0006096","count":3}]},{"hash":"1812735887246871284","title":"Unknown","description":"Top GO terms span diverse biological areas (nitric oxide biosynthesis, CNS myelin maintenance, fatty acid and sterol metabolism, nitrate assimilation, fungal sphingolipid metabolism, sebaceous gland differentiation, mitochondrial inheritance). There isn't a clear shared function or pathway linking these terms for this small cluster, so a specific functional label cannot be confidently assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006809","count":3},{"id":"GO:0032286","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0006636","count":3},{"id":"GO:0042128","count":3}]},{"hash":"728005697099451611","title":"Mitosis: centromere assembly & spindle dynamics","description":"The highest-frequency GO terms point to mitotic processes (microtubule severing, CENP-A\u2013containing chromatin assembly, and cell division), indicating a cluster centered on chromosome segregation and spindle function. While vesicle transport and lysosome-related terms appear, they are secondary to the dominant mitotic signals.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051013","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0051260","count":2}]},{"hash":"1861876024955966577","title":"Unknown","description":"The terms span development in multiple organs and broad metabolic/epigenetic processes without a unifying function, so a single representative label is not evident.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048565","count":1},{"id":"GO:0035902","count":1},{"id":"GO:0010430","count":1},{"id":"GO:0008585","count":1},{"id":"GO:0001516","count":1}]},{"hash":"1086401019850086767","title":"Unknown","description":"There is no GO term data or functional signal provided for this cluster (Top Terms is empty; no edges or connections). Without a common function to anchor a label, the safest choice is Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"610943111319101728","title":"Vesicle trafficking and lysosome-related transport","description":"This cluster\u2019s GO terms cluster around lysosomal membrane organization, endosome-to-melanosome transport, Cvt pathway targeting to vacuoles, apical protein localization, and establishment of epithelial polarity, all of which point to a shared theme of vesicle trafficking, membrane sorting, and lysosome/endosome\u2013mediated transport. While there are a few outliers (bone resorption, neuronal apoptosis, manganese response), the dominant signal is trafficking and membrane organization in secretory and polarized contexts.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031584","count":1},{"id":"GO:0097212","count":1},{"id":"GO:0045453","count":1},{"id":"GO:0032258","count":1},{"id":"GO:0035646","count":1}]},{"hash":"1884787361519223164","title":"Oxygen-sensing prolyl hydroxylation","description":"The cluster is characterized by a strong signal for peptidyl-proline hydroxylation to hydroxyproline and intracellular oxygen homeostasis, which together align with the prolyl hydroxylase\u2013mediated oxygen-sensing pathway that modulates protein function via proline hydroxylation under different oxygen levels. The negative regulation of post-translational modification also fits into regulatory layers of PTMs in response to oxygen availability.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018401","count":1},{"id":"GO:1901874","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0032364","count":1}]},{"hash":"1361470064857665301","title":"Diverse metabolite biosynthesis","description":"The top GO terms cover a range of biosynthetic processes for different compound classes (mycolic acid, antibiotics, melanin, PHB, steroids, cofactors, etc.) with no single shared pathway. This suggests the cluster reflects broad biosynthetic capabilities rather than one specific function, hence the label Diverse metabolite biosynthesis.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0071768","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0006706","count":3},{"id":"GO:0042438","count":3}]},{"hash":"350443107741396592","title":"Unknown","description":"The GO terms span a broad mix of metabolic processes, with several catabolic pathways for sugars (glycolysis, lactose/tagatose-6-phosphate) and nucleotide/sugar catabolism, plus some lysine biosynthesis. There isn\u2019t a single cohesive function or pathway uniting these terms, so a concise, representative label isn\u2019t clear.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019877","count":1},{"id":"GO:0009089","count":1},{"id":"GO:0046386","count":1},{"id":"GO:0009073","count":1},{"id":"GO:0006096","count":1}]},{"hash":"1430819805698592805","title":"Unknown","description":"The annotations span transcription antitermination, proteolysis, and box C/D snoRNP assembly, representing distinct processes (transcription regulation, protein degradation, RNA processing) with no unifying function or interaction apparent in this cluster, so a single coherent label cannot be assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031564","count":1},{"id":"GO:0006508","count":1},{"id":"GO:0000492","count":1}]},{"hash":"1378311194820451601","title":"Ubiquitin-Driven Mitosis and Chromatin Regulation","description":"The terms cluster around protein ubiquitination (K29- and K48-linked), exit from mitosis and spindle dynamics, and chromatin organization, suggesting a core theme of ubiquitin-mediated regulation of mitosis and chromatin state. Some terms (peroxisome import, C-type lectin signaling, neuron survival) appear peripheral, likely due to multifunctional proteins or annotation noise, but the dominant signal supports the chosen name.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0035519","count":4},{"id":"GO:0010458","count":4},{"id":"GO:0070936","count":4},{"id":"GO:0000022","count":4},{"id":"GO:0002223","count":4}]},{"hash":"2235114534966374199","title":"Unknown","description":"The Top Terms are a broad mix of metabolic processes (methionine cycle, triglyceride metabolism, L-alanine catabolic, pyridoxine biosynthesis) and stress/immune related responses (inflammatory response, hypoxia, circadian cycle), with several terms marked obsolete. The sparse connectivity (one edge, no triangles) suggests there is no coherent, single function uniting these proteins, so a meaningful label cannot be determined.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002439","count":1},{"id":"GO:0033353","count":1},{"id":"GO:0001666","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0006641","count":1}]},{"hash":"438548878698650991","title":"Unknown","description":"The terms span immune signaling, development, ubiquitination, peroxisome import, viral suppression, and dosage compensation, with no single coherent function tying the four proteins together. Because of this heterogeneity, a confident, representative label cannot be assigned beyond Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900095","count":1},{"id":"GO:1903883","count":1},{"id":"GO:0048536","count":1},{"id":"GO:0070936","count":1},{"id":"GO:1902187","count":1}]},{"hash":"2076607035544786954","title":"Unknown","description":"The terms span sensory (thermoception, capsazepine response), immune signaling (NOD1), neural plasticity, calcium signaling, telomere maintenance, and vitamin D response, with no single cohesive function linking all four proteins. ","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033280","count":4},{"id":"GO:0032212","count":3},{"id":"GO:0048549","count":3},{"id":"GO:0070427","count":3},{"id":"GO:0050955","count":3}]},{"hash":"886390689674325744","title":"Mitochondrial Transport and Energy Metabolism","description":"The GO terms are dominated by mitochondrial membrane transport and energy-related processes (alpha-ketoglutarate, ornithine, ATP, and nucleotide import; malate-aspartate shuttle; adaptive thermogenesis; magnesium export; membrane fission), suggesting the proteins function together in mitochondrial metabolite transport and energy handling.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015742","count":2},{"id":"GO:0000066","count":2},{"id":"GO:1990544","count":2},{"id":"GO:1990519","count":2},{"id":"GO:1990845","count":2}]},{"hash":"1924856475573703283","title":"Unknown","description":"The GO terms span multiple developmental processes (midbrain morphogenesis, male gonad and spermatid development, osteoblast differentiation) and broad regulatory activities (transcription regulation, chromatin/heterochromatin formation), with no single clear function tying all proteins together, so no coherent label can be assigned.","confidence":"","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1904693","count":1},{"id":"GO:1904815","count":1},{"id":"GO:0008584","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0030543","count":1}]},{"hash":"355929779942360112","title":"Endosomal trafficking and vesicle transport","description":"The GO terms clustered around endosomal processes (endosome organization, endosome-to-melanosome transport, Cvt pathway targeting) and vesicle-related functions (lipid tube assembly, protein transmembrane transport, exosomal secretion), suggesting a core role in endomembrane trafficking and vesicle transport. Some terms (bone resorption, mitosis exit) are peripheral annotations or reflect multi-functional proteins, but the dominant theme is vesicular trafficking. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903542","count":1},{"id":"GO:0060988","count":1},{"id":"GO:0071806","count":1},{"id":"GO:0000747","count":1},{"id":"GO:0010458","count":1}]},{"hash":"1073791822560933129","title":"Calcium signaling regulation","description":"This cluster centers on calcium dynamics, with multiple GO terms about detecting Ca2+, regulating calcium channels (ryanodine and voltage-gated channels), and calcium-dependent signaling cascades (calcineurin-NFAT). It also includes a PI-mediated signaling term that links membrane signaling to Ca2+ signaling. While a couple terms touch on vascular morphogenesis and complement, the dominant theme is regulation of calcium signaling pathways.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048015","count":2},{"id":"GO:0005513","count":2},{"id":"GO:0060316","count":2},{"id":"GO:0008218","count":2},{"id":"GO:0090281","count":2}]},{"hash":"2267436715548114990","title":"Unknown","description":"No shared function signals (no GO terms, no edges among the proteins), so there is no clear theme tying the four proteins together; without terms or interactions, a confident label cannot be assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"494839304113585749","title":"Two-component phosphorelay signaling","description":"The top GO term is GO:0000160, phosphorelay signal transduction system, which corresponds to two-component signaling via phosphorylation. With four proteins and several interactions, the cluster likely represents a small phosphorelay signaling module typical of bacterial signaling systems.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000160","count":1}]},{"hash":"1467810713697927976","title":"GPCR-mediated cAMP/cGMP signaling","description":"The cluster centers on GPCR signaling and production of cyclic nucleotides, with multiple GO terms for adenosine receptor signaling, adenylate cyclase and guanylyl cyclase pathways, and cAMP/cGMP biosynthesis. Related terms include blue light signaling and hypoxia detection, which commonly funnel through GPCR-second messenger cascades. There are also broader terms like regulation of transcription and oocyte maturation, which may be less central in this small cluster. Overall, the dominant theme is receptor-driven second-messenger signaling via cAMP/cGMP.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071880","count":1},{"id":"GO:0070483","count":1},{"id":"GO:0006182","count":1},{"id":"GO:0009785","count":1},{"id":"GO:0001973","count":1}]},{"hash":"1807820000157799679","title":"Actin-based cell polarity and morphogenesis","description":"Top GO terms point to actin cytoskeleton organization (actin filament bundle distribution, vesicle docking in exocytosis, actin fusion focus) and to cell polarity/morphogenesis (establishment/maintenance of cell polarity, dorsal closure). Some terms are peripheral (opsonization, VEGF signaling, fourth ventricle development) but can relate to cytoskeletal remodeling during development and signaling. Overall, the common theme is actin-driven polarity and morphogenetic cell movements.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046663","count":1},{"id":"GO:0032796","count":1},{"id":"GO:0071963","count":1},{"id":"GO:1903028","count":1},{"id":"GO:1900748","count":1}]},{"hash":"1233782261366943577","title":"Unknown","description":"There are only four proteins with no edges, no triangles, and no top GO terms to indicate a shared function. Without a common term or interaction signal, a meaningful thematic label cannot be assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"901091949729911640","title":"Neural Vesicle Trafficking and Development","description":"Top GO terms indicate a focus on intracellular vesicle trafficking (melanosome transport; ER-to-Golgi transport; Golgi-to-plasma membrane transport; lysosomal membrane organization) alongside neural development (hippocampus and substantia nigra development) and synaptic activity (excitatory postsynaptic potential). This combination suggests a cluster of proteins involved in vesicle trafficking within neural contexts, affecting both brain development and synaptic function.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032402","count":2},{"id":"GO:0021766","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0060079","count":2},{"id":"GO:0021762","count":2}]},{"hash":"1295137824507701141","title":"Unknown","description":"There are no shared GO terms or interactions among the four proteins, so there is no clear common function to assign a label; label as Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1946359324131019456","title":"Unknown","description":"There is no GO signal or network connection to tie these four proteins to a common function (no top terms, no edges/triangles). Without a shared term, the cluster cannot be meaningfully named; thus Unknown with no confidence.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"475463027616766430","title":"Neural and muscle signaling","description":"This cluster\u2019s top GO terms point to signal transduction and development, including receptor guanylyl cyclase signaling, cAMP biosynthesis, and regulation of Rho signaling, along with neural and muscle development terms (substantia nigra and skeletal muscle fiber development) and synaptic transmission. Although there are no observed edges, the shared emphasis on signaling and development suggests proteins involved in neural/muscle communication and maturation. A broader hypoxia and cytokine-response presence is noted but does not override the central theme of signaling in neural and muscle contexts.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007168","count":2},{"id":"GO:0007268","count":2},{"id":"GO:0006470","count":2},{"id":"GO:0048741","count":2},{"id":"GO:0021762","count":2}]},{"hash":"356114969940805187","title":"GPCR-driven cyclic nucleotide signaling","description":"The top GO terms cluster around G protein-coupled receptor signaling and production of cyclic nucleotides (cAMP and cGMP) via adenylate and guanylyl cyclases, including adrenergic/adenosine receptor pathways. Additional terms (blue light signaling, hypoxia detection) fit within broader GPCR-related signaling contexts, supporting a GPCR-mediated second-messenger signaling theme for this cluster.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0071880","count":1},{"id":"GO:0070483","count":1},{"id":"GO:0006182","count":1},{"id":"GO:0009785","count":1}]},{"hash":"2119122749427685284","title":"GPCR and Guanylyl Cyclase Signaling","description":"The top GO terms cluster around G protein-coupled receptor pathways, including receptor guanylyl cyclase signaling and adenosine/adrenergic receptor signaling, with downstream cGMP and cAMP production. Phototransduction-related terms (blue light signaling) and hypoxia detection further support GPCR-mediated signaling roles. Negative regulation of calcium signaling and macroautophagy also fits within GPCR-driven regulatory networks. Overall, the proteins appear to function in GPCR-driven cyclic nucleotide signaling.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016242","count":2},{"id":"GO:0050849","count":2},{"id":"GO:0071880","count":1},{"id":"GO:0070483","count":1},{"id":"GO:0006182","count":1}]},{"hash":"399832967471348455","title":"RNA processing and transcription regulation","description":"The cluster is dominated by RNA metabolism terms: miRNA catabolic process, pre-miRNA processing, transcription-related terms (DNA-templated transcription, transcription antitermination, negative regulation of termination of transcription) and CRD-mediated mRNA stabilization, suggesting a cohesive role in RNA processing and transcription control. Some peripheral terms relate to apoptosis or development and viral processes, but the core signal points to RNA maturation and transcription regulation.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010587","count":3},{"id":"GO:0031054","count":2},{"id":"GO:0006351","count":2},{"id":"GO:1902219","count":2},{"id":"GO:0060567","count":2}]},{"hash":"2209036460745214986","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030260","count":2},{"id":"GO:0019068","count":2},{"id":"GO:0075713","count":2},{"id":"GO:0019076","count":2},{"id":"GO:1902416","count":1}]},{"hash":"859480825686977695","title":"Pro-inflammatory Cytokine Regulation","description":"This cluster is driven by GO terms related to positive regulation of inflammatory responses and cytokine production (e.g., IL-6 and TNF), suggesting a shared role in promoting inflammatory signaling. Some terms (translocation into host cytoplasm, telomere maintenance, Cajal body RNA localization) appear as outliers and do not define the core theme.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0044053","count":3},{"id":"GO:0050729","count":3},{"id":"GO:2000778","count":3},{"id":"GO:0032212","count":3},{"id":"GO:0002931","count":3}]},{"hash":"1708104225088900233","title":"ER Proteostasis and Misfolded Protein Degradation","description":"This cluster is driven by terms related to cellular response to misfolded proteins, ER-associated degradation of misfolded proteins, and regulation of ubiquitin-specific protease activity, indicating a focus on protein quality control and proteostasis in the endoplasmic reticulum. The presence of DNA replication terms appears unrelated to the core theme and likely represents annotation noise. ","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071218","count":2},{"id":"GO:0061166","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0046034","count":2},{"id":"GO:0070407","count":2}]},{"hash":"368020049416603635","title":"RNA modification and ribosome biogenesis","description":"These proteins center on RNA modification (tRNA wobble uridine modification; tRNA modification; rRNA pseudouridine synthesis) and ribosome-related processes (ribosome disassembly), with transcription and growth regulation as secondary signals. ","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0040008","count":1},{"id":"GO:0002098","count":1},{"id":"GO:0031118","count":1},{"id":"GO:1901052","count":1}]},{"hash":"2066921086742005469","title":"RNA processing and splicing machinery","description":"This cluster is dominated by GO terms related to RNA biogenesis and processing, including tRNA processing, maturation of SSU-rRNA, mRNA splicing via the spliceosome, spliceosomal complex assembly, and histone mRNA metabolism, with additional links to DNA-templated transcription. While some stress-response terms appear, the core signal centers on RNA maturation and splicing functions, justifying a focused label on RNA processing and splicing machinery.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":1},{"id":"GO:0009737","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0000245","count":1},{"id":"GO:0009414","count":1}]},{"hash":"1648259573256604524","title":"Mitotic spindle assembly and chromosome segregation","description":"The top GO terms are dominated by processes related to microtubule-driven mitosis, including spindle assembly, chromosome segregation, minus-end directed microtubule sliding, kinetochore attachment, and cytokinesis-related events. There is an outlier term about Purkinje cell layer organization, but the prevailing theme ties to spindle dynamics and chromosome handling during cell division, justifying this label.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000743","count":2},{"id":"GO:1990942","count":2},{"id":"GO:0021693","count":2},{"id":"GO:0000022","count":2},{"id":"GO:0051296","count":2}]},{"hash":"2260074674443244700","title":"Protein Tyrosine Phosphatase\u2013Mediated Immune Signaling","description":"These proteins show enrichment for immune-related terms (negative regulation of humoral immune response, positive regulation of CD8+ T cell proliferation, TLR3 signaling) and for tyrosine phosphatase\u2013driven signaling (peptidyl-tyrosine dephosphorylation, receptor protein tyrosine phosphatase signaling). This points to a coherent function centered on phosphatase-controlled modulation of immune signaling and related pathways (e.g., PI3K/AKT). Peripheral terms like platelet formation or kinetochore localization may reflect broader roles but do not outweigh the immune/phosphatase theme.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008285","count":1},{"id":"GO:0002924","count":1},{"id":"GO:0035335","count":1},{"id":"GO:0010633","count":1},{"id":"GO:0051898","count":1}]},{"hash":"2079185587793861766","title":"Neural development and cytoskeletal organization","description":"This cluster centers on neuron development and myelin-related processes, with intermediate filament organization and regulatory phosphatase activities, suggesting a common theme of neural differentiation coupled with cytoskeletal remodeling.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046856","count":2},{"id":"GO:0048666","count":1},{"id":"GO:0045109","count":1},{"id":"GO:0048633","count":1},{"id":"GO:0035335","count":1}]},{"hash":"1262119648452316052","title":"Cardiac calcium signaling and blood pressure regulation","description":"The top GO terms center on heart function, including regulation of SA node action potential and systemic arterial blood pressure, supported by calcium signaling and phosphatidylinositol/GPCR pathways. While there are additional terms pointing to transcriptional regulation and other processes, the strongest, most coherent theme across the cluster is cardiovascular calcium signaling and blood pressure control. Confidence: Medium","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098907","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0043388","count":2},{"id":"GO:0048015","count":1},{"id":"GO:0045944","count":1}]},{"hash":"238009006791017939","title":"Unknown","description":"The listed GO terms span neuronal development, immune signaling, cytoskeletal dynamics, metal response, ubiquitination, organ size regulation, and bacterial detection, with no clear shared function or pathway linking them. The cluster has no edges and only three proteins, making it impossible to assign a cohesive, specific function. ","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014041","count":1},{"id":"GO:0071287","count":1},{"id":"GO:0034130","count":1},{"id":"GO:0051014","count":1},{"id":"GO:1904887","count":1}]},{"hash":"772539361464020826","title":"Neurotransmitter transport and glycinergic signaling","description":"This cluster is dominated by GO terms related to transmembrane transport of neurotransmitters (protons, sodium, glycine, taurine) and neurotransmitter uptake/secretion, especially glycinergic, dopaminergic, and serotonergic signaling, with a note on glial involvement. The common theme is transporter- or regulation-related roles in synaptic transmission rather than a single metabolic pathway.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015992","count":2},{"id":"GO:0035725","count":2},{"id":"GO:0061537","count":1},{"id":"GO:0042420","count":1},{"id":"GO:0051610","count":1}]},{"hash":"683083850033061035","title":"Unknown","description":"There are no GO terms or interactions linking these proteins (Edges: 0, Triangles: 0, Max Degree: 0) and no shared functional signal to derive a meaningful label from; without terms to guide a theme, the cluster cannot be named beyond Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"79743673737627793","title":"Unknown","description":"Insufficient data to define a shared function: there are no top GO terms and the cluster has no edges or connections, so the proteins cannot be linked to a common biological process or function. Therefore, the label is Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"582296926644410261","title":"Transmembrane Solute and Ion Transporters","description":"The top GO terms indicate diverse transmembrane transport activities for a range of substrates (sodium ions, phosphate, sugars, sialic acid, vitamins, xenobiotics) and even neurotransmitter loading into vesicles, all pointing to membrane transporter proteins. This cohesive theme suggests a cluster of transporters handling solute movement across membranes, despite substrate diversity. ","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006796","count":1},{"id":"GO:0042891","count":1},{"id":"GO:0006855","count":1},{"id":"GO:0035725","count":1},{"id":"GO:0015739","count":1}]},{"hash":"314167500644872688","title":"mRNA splicing regulation","description":"These proteins cluster around spliceosome-mediated mRNA processing, with multiple terms for cis splicing, splice site recognition, and both positive and negative regulation of mRNA splicing, indicating a core role in spliceosome-driven RNA processing. Some ncRNA-mediated silencing is listed but the dominant signal is mRNA splicing regulation.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":1},{"id":"GO:0048026","count":1},{"id":"GO:1902625","count":1},{"id":"GO:0075525","count":1},{"id":"GO:1905663","count":1}]},{"hash":"1138691808516349044","title":"RNA processing and translation","description":"The top GO terms include rRNA base methylation and phenylalanyl-tRNA aminoacylation, both linked to ribosome function and protein synthesis. A cytokinin biosynthetic process term appears but seems unrelated to the others; with only three proteins and no edges, the strongest shared theme is RNA modification and translation rather than hormone biosynthesis.","confidence":"Low","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009691","count":1},{"id":"GO:0070475","count":1},{"id":"GO:0006432","count":1}]},{"hash":"1342521838578653046","title":"Unknown","description":"The Top Terms span immune signaling (NF-kappaB sequestration, NOD1 pathway), telomere biology (telomere maintenance via telomerase, chromosome telomere localization), endocytosis/trafficking (pinocytosis, receptor localization to synapse), and sensory/temperature responses (thermoception, response to capsazepine), with no clear unifying function across the proteins. This broad, disparate mix makes it hard to assign a coherent, specific cluster label.","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007253","count":2},{"id":"GO:0032212","count":1},{"id":"GO:0048549","count":1},{"id":"GO:0070427","count":1},{"id":"GO:0050955","count":1}]},{"hash":"2123615990959543507","title":"Unknown","description":"These GO terms span UV protection, RNA processing, dosage compensation, hypoxia response, transcription initiation/clearance, DNA repair, embryonic development, intracellular DNA clearance, and translation regulation, with no single cohesive theme. The lack of edges/triangles also suggests weak functional linkage, so a specific, meaningful label cannot be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009650","count":1},{"id":"GO:0000294","count":1},{"id":"GO:0009048","count":1},{"id":"GO:0001666","count":1},{"id":"GO:0001111","count":1}]},{"hash":"741462615172528439","title":"Unknown","description":"The GO terms are highly diverse and include valine biosynthesis, DNA-templated transcription, immune-related MHC biosynthesis, chromatin/epigenetic processes, ER stress-induced apoptosis, and several obsolete terms. With only three proteins and no clear, shared functional theme, there isn\u2019t a coherent function to name the cluster beyond Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009099","count":2},{"id":"GO:0009097","count":2},{"id":"GO:0006351","count":1},{"id":"GO:0045348","count":1},{"id":"GO:1905549","count":1}]},{"hash":"2015137773778856471","title":"Unknown","description":"There is no GO term enrichment or interaction evidence to indicate a common function; edges and triangles are zero, and top terms are empty, so a shared biological role cannot be inferred from the cluster data.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"733484827501557197","title":"Mitochondrial metabolism and innate immune signaling","description":"The top GO terms point to mitochondria-driven energy and protein handling (mitochondrial protein processing; proton motive force\u2013driven ATP synthesis; stress-induced mitochondrial fusion) alongside immune-related processes (interleukin-2 production; positive regulation of TLR3 signaling). Lipid localization and SREBP signaling extend the theme to membrane/lipid metabolism that interfaces with mitochondrial function. Taken together, the proteins appear to cluster around mitochondrial energy metabolism with coordinated innate immune signaling and lipid/membrane dynamics.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032623","count":1},{"id":"GO:0034982","count":1},{"id":"GO:0042776","count":1},{"id":"GO:0045861","count":1},{"id":"GO:0034141","count":1}]},{"hash":"1354878977474095379","title":"Calcium signaling and NFAT pathway regulation","description":"Predominant theme is calcium signaling and its regulation, especially PI-mediated signaling, calcium ion detection, and control of the calcineurin-NFAT pathway, with accompanying negative regulation of kinase activity. Minor terms hint at broader cellular context (kidney development and cytoskeleton).","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048015","count":2},{"id":"GO:0005513","count":2},{"id":"GO:0072221","count":2},{"id":"GO:0060316","count":2},{"id":"GO:0008218","count":2}]},{"hash":"374754697036972282","title":"Unknown","description":"The listed GO terms span plant hormone response, various aspects of development, DNA replication/repair, signaling, and immune recombination with no clear common function linking the proteins; there are no edges among the proteins, so no cohesive cluster function emerges. Therefore no specific label can be assigned beyond Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009737","count":1},{"id":"GO:1990506","count":1},{"id":"GO:0048536","count":1},{"id":"GO:0008069","count":1},{"id":"GO:1904762","count":1}]},{"hash":"1721746352429204439","title":"DNA-templated Transcription Regulation","description":"The top GO terms are strongly centered on DNA-templated transcription and negative regulation of transcription by RNA polymerase II, pointing to transcription control as the core function of this cluster. The inclusion of DNA replication suggests involvement in broader nuclear processes tied to transcription. Some other terms are obsolete or peripheral, but the main signal supports a transcription-regulatory role.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0006260","count":1},{"id":"GO:0097428","count":1},{"id":"GO:0032781","count":1}]},{"hash":"1021363238373808461","title":"RNA methylation and RNA modification","description":"The GO terms show clear signals for tRNA wobble uridine modification, tRNA methylation, rRNA modification, and various forms of methylation, pointing to a shared function in RNA modification/methylation. Other terms appear incidental and not central to the cluster, so RNA methylation best represents the cluster's theme.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035902","count":1},{"id":"GO:0002098","count":1},{"id":"GO:0071768","count":1},{"id":"GO:0032259","count":1},{"id":"GO:1901052","count":1}]},{"hash":"441023919161771132","title":"Vacuolar ion transport and acidification","description":"The top GO terms cluster around vacuolar processes (vacuole organization, protein targeting to vacuole, vacuolar acidification) and membrane ion/ proton transport (proton transmembrane transport, sodium ion transport, proton motive force-driven ATP synthesis), pointing to proteins involved in vacuolar pH maintenance and ion homeostasis.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015991","count":3},{"id":"GO:0006878","count":3},{"id":"GO:0006626","count":3},{"id":"GO:0007035","count":3},{"id":"GO:0007033","count":3}]},{"hash":"1782529813540951673","title":"Viral entry, replication, and host response","description":"The terms center on viral processes: fusion of the viral membrane with the host cell, virion assembly, and the viral life cycle, with RNA-templated DNA synthesis indicating replication steps. The inclusion of leukocyte migration points to host immune response, and protein folding/secretion hints at cellular stress during infection. Together, they suggest a cluster of proteins involved in viral infection and host interaction.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010849","count":1},{"id":"GO:2000276","count":1},{"id":"GO:0019064","count":1},{"id":"GO:0050900","count":1},{"id":"GO:0019058","count":1}]},{"hash":"20312913405117763","title":"Microtubule Dynamics and Cytoskeletal Organization","description":"GO terms point to centriole cohesion, cytoplasmic microtubule organization, microtubule polymerization regulation, and vesicle transport along microtubules, suggesting a common theme of cytoskeletal dynamics and microtubule-based trafficking. A few terms (immune lineage commitment, necroptotic complex assembly) appear peripheral to this core signal but do not override the main pattern.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000743","count":1},{"id":"GO:0043369","count":1},{"id":"GO:0010457","count":1},{"id":"GO:0048491","count":1},{"id":"GO:1990108","count":1}]},{"hash":"2202172357259531336","title":"Notch-Glycosylation in development","description":"Top terms center on Notch signaling and protein O-linked glycosylation (fucose, mannose), suggesting regulation of Notch receptor activity. The links to EMT and mesoderm formation point to broader developmental signaling roles, while larval cuticle development indicates an insect developmental context where Notch and glycosylation modulate morphogenesis. Together, these terms support a theme of Notch-dependent glycosylation in development.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008363","count":1},{"id":"GO:0097370","count":1},{"id":"GO:0035269","count":1},{"id":"GO:0010717","count":1},{"id":"GO:0001707","count":1}]},{"hash":"2129015654516934967","title":"RNA Processing and Ribosome Biogenesis","description":"The cluster centers on RNA-related processes: tRNA wobble uridine modification, tRNA methylation, rRNA modification, and mRNA capping, plus export of the ribosomal small subunit from the nucleus, pointing to RNA maturation and ribosome assembly. Some terms like histone methylation, nodulation, and antibiotic biosynthesis are less directly connected, but the dominant signal is RNA processing and ribosome biogenesis.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002098","count":2},{"id":"GO:0000154","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0009877","count":2},{"id":"GO:0030488","count":2}]},{"hash":"1108403639912683808","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006530","count":1},{"id":"GO:0006450","count":1},{"id":"GO:0000453","count":1},{"id":"GO:0002938","count":1},{"id":"GO:0006189","count":1}]},{"hash":"1536826606697555824","title":"Unknown","description":"The listed GO terms span distinct areas: fatty acid metabolism, ectoine biosynthesis/catabolism, a fungal secondary metabolite (verruculogen) biosynthetic process, glycosylation, and cell growth. With no single dominant function linking all terms, a cohesive, precise label for this small cluster isn\u2019t supported.","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001561","count":1},{"id":"GO:0097089","count":1},{"id":"GO:1902181","count":1},{"id":"GO:0042400","count":1},{"id":"GO:0019491","count":1}]},{"hash":"796840271767435485","title":"Central metabolism and xenobiotic response","description":"Dominant signals are TCA cycle and glyoxylate cycle terms, pointing to central carbon metabolism, with an additional xenobiotic response term implying metabolic adaptation to toxins. Several DNA-related terms are low-frequency and less cohesive with the main theme, so the core pattern reflects metabolism plus stress response rather than a single unified function.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":2},{"id":"GO:0006099","count":2},{"id":"GO:0006097","count":2},{"id":"GO:0090656","count":1},{"id":"GO:0051106","count":1}]},{"hash":"1789560955563034778","title":"Retroviral integration and latency","description":"Top GO terms cluster around retroviral replication and host genome interaction: RNA-templated DNA biosynthetic process (reverse transcription), DNA replication and recombination, DNA integration, and establishment of integrated proviral latency, plus viral penetration into the host nucleus. Some terms mention symbiont entry and host apoptosis activation, which can accompany viral infection and manipulation of host cells, as well as RNA silencing regulation by a viral or symbiont partner. Altogether, these annotations point to proteins involved in proviral infection and latency maintenance rather than general cellular metabolism.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006278","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0039651","count":1},{"id":"GO:0015074","count":1},{"id":"GO:0075713","count":1}]},{"hash":"2169352625644683382","title":"Mitochondrial Protein Import and Lipid Biosynthesis","description":"This cluster is best named \u2018Mitochondrial Protein Import and Lipid Biosynthesis\u2019 because the most represented terms describe mitochondrial protein transport into the matrix and regulation of membrane permeability, together with lipid/isoprenoid biosynthesis (cholesterol, triglycerides, geranyl diphosphate). While a few terms are obsolete, the core theme centers on mitochondrial function and associated lipid metabolism.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000134","count":1},{"id":"GO:0070940","count":1},{"id":"GO:0046902","count":1},{"id":"GO:0010867","count":1},{"id":"GO:1903740","count":1}]},{"hash":"433342893499758325","title":"Unknown","description":"The top GO terms are scattered across heat response, development (stamen/mesoderm), chlorophyll biosynthesis, protein degradation, and other unrelated processes, with no single cohesive function linking the proteins. The lack of interactions and presence of organism-specific terms suggest annotation noise rather than a shared pathway, so a reliable label cannot be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":2},{"id":"GO:0048455","count":1},{"id":"GO:0015995","count":1},{"id":"GO:0006511","count":1},{"id":"GO:0090502","count":1}]},{"hash":"128102164836983411","title":"Golgi Trafficking to PM and Endosomes","description":"The GO terms are dominated by Golgi-related localization and transport: from Golgi to the plasma membrane and from Golgi to endosomes, indicating a cluster of proteins involved in Golgi-associated trafficking, despite a few unrelated terms that may be noise.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000042","count":1},{"id":"GO:0043001","count":1},{"id":"GO:0006895","count":1},{"id":"GO:0006885","count":1},{"id":"GO:0045454","count":1}]},{"hash":"1253933422557055125","title":"Diverse Metabolic Pathways","description":"The GO terms show a broad mix of metabolic activities\u2014from amino acid and vitamin biosynthesis to various catabolic processes and core energy metabolism (electron transport chain). There isn\u2019t a single cohesive pathway linking all terms, so a high-level label like \u201cDiverse Metabolic Pathways\u201d best captures the cluster\u2019s broad metabolic nature while remaining specific enough to be useful.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034077","count":1},{"id":"GO:0019310","count":1},{"id":"GO:0009436","count":1},{"id":"GO:0009234","count":1},{"id":"GO:0009099","count":1}]},{"hash":"663366048431304498","title":"TNF-NF-kappaB/JNK Signaling Regulators","description":"The dominant GO terms point to TNF-mediated signaling, NF-kappaB activation (including I-kappaB phosphorylation), and regulation of the JNK cascade, suggesting proteins involved in inflammatory signaling pathways. Some terms about peroxisomal import and histone modification appear as possible noise or outdated annotations, but the core theme remains TNF/NF-kappaB/JNK signaling regulation.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016558","count":2},{"id":"GO:0036205","count":2},{"id":"GO:0033209","count":2},{"id":"GO:1903721","count":2},{"id":"GO:1903265","count":2}]},{"hash":"1386320143028717274","title":"Unknown","description":"The three proteins show a highly diverse set of GO terms (interferon response, cilium assembly, prostate/hormonal development, glucocorticoid signaling, male differentiation, hydrogen peroxide response, protein oligomerization) with no clear shared biological process or interaction to bind them into a coherent function. Several terms are obsolete, and there are no edges to suggest a related cluster, so a singular, meaningful label cannot be inferred.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903071","count":1},{"id":"GO:2000324","count":1},{"id":"GO:0071357","count":1},{"id":"GO:1905515","count":1},{"id":"GO:0030850","count":1}]},{"hash":"1512143886677545769","title":"Unknown","description":"These proteins show a broad and inconsistent set of GO terms, spanning ion transport, metabolism, signaling, development, and cell cycle regulation, with no single dominant function or cohesive pathway linking them. The cluster also has no observed edges, making it difficult to assign a representative, specific function label.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006813","count":2},{"id":"GO:0045722","count":1},{"id":"GO:0006177","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0032147","count":1}]},{"hash":"1345925138040109895","title":"RNA processing and ribonucleotide excision repair","description":"These terms point to RNA metabolism (RNA catabolic process) and a ribonucleotide excision repair pathway, suggesting the proteins participate in RNA turnover and in removing ribonucleotides from DNA. The obsolete endonuclease term adds noise but does not overturn the common theme.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1990516","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0006401","count":2}]},{"hash":"1718869706803866630","title":"Vesicle trafficking with apoptotic signaling","description":"The GO terms point to vesicle fusion and trafficking across ER, Golgi, and lysosomes, plus anterograde synaptic vesicle transport, alongside apoptosis-related processes (extrinsic signaling and mitochondrial outer membrane permeabilization). This suggests a group of proteins linked to membrane trafficking and, in parallel, apoptotic signaling pathways.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016320","count":1},{"id":"GO:0048280","count":1},{"id":"GO:0048279","count":1},{"id":"GO:0032418","count":1},{"id":"GO:0048490","count":1}]}]